Difference between revisions of "Talk:Developmental Signals - Homeobox"

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'''Search All Databases''' [http://www.ncbi.nlm.nih.gov/sites/gquery?itool=toolbar&cmd=search&term=hox hox]
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PMID 20485555 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010600
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==2019==
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{{#pmid:31346080}}
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Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16430-16435. doi: 10.1073/pnas.1816024116. Epub 2019 Jul 25.
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Hox genes limit germ cell formation in the short germ insect Gryllus bimaculatus.
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Barnett AA1, Nakamura T1, Extavour CG2,3.
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Author information
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1
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Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138.
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2
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Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; extavour@oeb.harvard.edu.
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3
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Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138.
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Abstract
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Hox genes are conserved transcription factor-encoding genes that specify the identity of body regions in bilaterally symmetrical animals. In the cricket Gryllus bimaculatus, a member of the hemimetabolous insect group Orthoptera, the induction of a subset of mesodermal cells to form the primordial germ cells (PGCs) is restricted to the second through the fourth abdominal segments (A2 to A4). In numerous insect species, the Hox genes Sex-combs reduced (Scr), Antennapedia (Antp), Ultrabithorax (Ubx), and abdominal-A (abd-A) jointly regulate the identities of middle and posterior body segments, suggesting that these genes may restrict PGC formation to specific abdominal segments in G. bimaculatus Here we show that reducing transcript levels of some or all of these Hox genes results in supernumerary and/or ectopic PGCs, either individually or in segment-specific combinations, suggesting that the role of these Hox genes is to limit PGC development with respect to their number, segmental location, or both. These data provide evidence of a role for this ancient group of genes in PGC development.
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KEYWORDS:
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Gryllus bimaculatus; Hox; evo-devo; germ cells; insect
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PMID: 31346080 PMCID: PMC6697791 [Available on 2020-01-25] DOI: 10.1073/pnas.1816024116
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===Evolutionary selection and morphological integration in the vertebral column of modern humans===
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Am J Phys Anthropol. 2019 Nov 1. doi: 10.1002/ajpa.23950. [Epub ahead of print]
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Arlegi M1,2, Veschambre-Couture C2, Gómez-Olivencia A1,3,4.
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Author information
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1
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Departamento de Estratigrafía y Paleontología, Facultad de Ciencia y Tecnología, Universidad del País Vasco-Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Spain.
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2
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Université de Bordeaux, PACEA UMR 5199, Pessac, France.
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3
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IKERBASQUE. Basque Foundation for Science, Bizkaia, Spain.
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4
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Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain.
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Abstract
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OBJECTIVES:
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The main objective is to quantify integration, modularity, and response to selection in the presacral vertebral column of modern humans.
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MATERIALS AND METHODS:
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Seventeen linear variables on each presacral vertebra were collected in 108 modern humans producing a total of ~39,000 measurements. Then, we studied patterns and magnitudes of integration at regional, vertebral, and intra-vertebral levels. Additionally, we calculated the ability of vertebrae to respond to selection by quantifying differences in evolvability, flexibility, and constraint throughout the spine.
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RESULTS:
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The results indicate that caudal vertebrae are more evolvable than those located more cranially in the presacral vertebral column, following an increasing pattern of evolvability from the cervical to the lumbar region. Additionally, the atlas and fifth lumbar vertebra show the lowest values of integration, while central thoracic vertebrae display the highest magnitudes of integration.
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DISCUSSION:
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These results could be related to three main factors: body plan organization expressed by the Hox genes, the strong developmental constraints that determine the number of mammalian vertebrae, and, finally, the functional requirements of an adaptation to bipedal locomotion in the human lineage.
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© 2019 Wiley Periodicals, Inc.
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KEYWORDS:
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adaptation; constraints; evolvability; flexibility; modularity
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PMID: 31675109 DOI: 10.1002/ajpa.23950
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===Hox13 is essential for formation of a sensory organ at the terminal end of the sperm duct in Ciona===
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Dev Biol. 2019 Nov 1. pii: S0012-1606(19)30270-2. doi: 10.1016/j.ydbio.2019.10.028. [Epub ahead of print]
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Tajima Y1, Hozumi A1, Yoshida K1, Treen N1, Sakuma T2, Yamamoto T2, Sasakura Y3.
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Author information
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1
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Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan.
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2
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Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan.
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3
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Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan. Electronic address: sasakura@shimoda.tsukuba.ac.jp.
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Abstract
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Species-specific traits are thought to have been acquired by natural selection. Transcription factors play central roles in the evolution of species-specific traits. Hox genes encode a set of conserved transcription factors essential for establishing the anterior-posterior body axis of animals. Changes in the expression or function of Hox genes can lead to the diversification of animal-body plans. The tunicate ascidian Ciona intestinalis Type A has an orange-colored structure at the sperm duct terminus. This orange-pigmented organ (OPO) is the characteristic that can distinguish this ascidian from other closely related species. The OPO is formed by the accumulation of orange-pigmented cells (OPCs) that are present throughout the adult body. We show that Hox13 is essential for formation of the OPO. Hox13 is expressed in the epithelium of the sperm duct and neurons surrounding the terminal openings for sperm ejection, while OPCs themselves do not express this gene. OPCs are mobile cells that can move through the body vasculature by pseudopodia, suggesting that the OPO is formed by the accumulation of OPCs guided by Hox13-positive cells. Another ascidian species, Ciona savignyi, does not have an OPO. Like Hox13 of C. intestinalis, Hox13 of C. savignyi is expressed at the terminus of its sperm duct; however, its expression domain is limited to the circular area around the openings. The genetic changes responsible for the acquisition or loss of OPO are likely to occur in the expression pattern of Hox13.
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Copyright © 2019. Published by Elsevier Inc.
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KEYWORDS:
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Ciona; Evolution; Hox; Species-specific trait; Sperm duct
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PMID: 31682808 DOI: 10.1016/j.ydbio.2019.10.028
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===Analysis of a limb-specific regulatory element in the promoter of the link protein gene===
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Biochem Biophys Res Commun. 2019 Oct 22;518(4):672-677. doi: 10.1016/j.bbrc.2019.08.104. Epub 2019 Aug 27.
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Rhodes CS1, Matsunobu T2, Yamada Y3.
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Author information
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1
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Molecular Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA. Electronic address: Rhodes@dir.nidcr.nih.gov.
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2
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Department of Orthopaedic Surgery, Kyushu Rosai Hospital, 1-1 Sonekitamachi, Kokuraminami-ku, Kitakyushu, Fukuoka, 800-0296, Japan.
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3
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Molecular Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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Abstract
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Link protein is encoded by the Hapln1 gene and is a prototypical protein found in the cartilage matrix. It acts as an important component of the endochondral skeleton during early development. To study its transcriptional regulation, promoter fragments derived from the link protein gene were coupled to the β-galactosidase reporter and used to study in vivo transgene expression in mice. In day 15.5 mouse embryos, a link promoter fragment spanning -1020 to +40 nucleotides demonstrated highly specific β-galactosidase staining of skeletal structures, including the appendicular and axial cartilaginous tissues. Two shorter promoter fragments, spanning -690 to +40 and -315 to +40 nucleotides, demonstrated limb- and genitalia-specific expression resembling that of homeodomain-regulated tissues. Bioinformatic analysis revealed a highly conserved, Hox-like binding site (HLBS) at approximately -220 bp of the promoter, shared by both constructs, which contained the Hox-core consensus sequence TAATTA. Electromobility shift assays demonstrated binding of Hox-B4 recombinant protein to the HLBS, which was eliminated with nucleotide substitutions within the core-binding element. Co-transfection analysis of the HLBS demonstrated a 22-fold transcriptional activation by HoxA9 expression, which was ablated with a substitution within the core HLBS element. Together these findings establish promoter regions within the link protein gene that are important for in vivo expression and identify the potential role of homeodomain-containing proteins in controlling cartilage and limb gene expression.
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Published by Elsevier Inc.
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KEYWORDS:
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Cartilage; Hox proteins; Limb; Link protein; Promoter; Transcriptional regulation
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PMID: 31470976 DOI: 10.1016/j.bbrc.2019.08.104
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===A genome-wide assessment of the ancestral neural crest gene regulatory network===
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Nat Commun. 2019 Oct 16;10(1):4689. doi: 10.1038/s41467-019-12687-4.
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Hockman D1,2, Chong-Morrison V1,3, Green SA4, Gavriouchkina D1,5, Candido-Ferreira I1, Ling ITC1, Williams RM1, Amemiya CT6, Smith JJ7, Bronner ME4, Sauka-Spengler T8.
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Author information
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1
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Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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2
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Division of Cell Biology, Department of Human Biology, Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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3
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Division of Biosciences, Faculty of Life Sciences, University College London, London, UK.
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4
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Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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5
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Okinawa Institute of Science and Technology, Molecular Genetics Unit, Onna, Japan.
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6
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Molecular Cell Biology, School of Natural Sciences, University of California, Merced, CA, USA.
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7
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Department of Biology, University of Kentucky, Lexington, KY, USA.
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8
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Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK. tatjana.sauka-spengler@imm.ox.ac.uk.
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Abstract
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The neural crest (NC) is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional and epigenomic profiles of NC cells in the sea lamprey, in order to gain insight into the ancestral state of the NC gene regulatory network (GRN). Transcriptome analyses identify clusters of co-regulated genes during NC specification and migration that show high conservation across vertebrates but also identify transcription factors (TFs) and cell-adhesion molecules not previously implicated in NC migration. ATAC-seq analysis uncovers an ensemble of cis-regulatory elements, including enhancers of Tfap2B, SoxE1 and Hox-α2 validated in the embryo. Cross-species deployment of lamprey elements identifies the deep conservation of lamprey SoxE1 enhancer activity, mediating homologous expression in jawed vertebrates. Our data provide insight into the core GRN elements conserved to the base of the vertebrates and expose others that are unique to lampreys.
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PMID: 31619682 PMCID: PMC6795873 DOI: 10.1038/s41467-019-12687-4
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==2018==
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===Hox genes in the pharyngeal region: how Hoxa3 controls early embryonic development of the pharyngeal organs===
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Int J Dev Biol. 2018;62(11-12):775-783. doi: 10.1387/ijdb.180284jg.
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Gordon J1.
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Abstract
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The pharyngeal organs, namely the thyroid, thymus, parathyroids, and ultimobranchial bodies, derive from the pharyngeal endoderm during embryonic development. The pharyngeal region is a segmented structure comprised of a series of reiterated structures: the pharyngeal arches on the exterior surface, the pharyngeal pouches on the interior, and a mesenchymal core. It is well known that Hox genes control spatial identity along the anterior-posterior axis of the developing vertebrate embryo, and nowhere is this is more evident than in the pharyngeal region. Each of the distinct segmented regions has a unique pattern of Hox expression, which conveys crucial positional information to the cells and tissues within it. In the context of pharyngeal organ development, molecular data suggest that HOXA3 is responsible for specifying organ identity within the third pharyngeal pouch, and in its absence, thymus and parathyroid organogenesis fails to proceed normally. Recent studies comprising a series of Hoxa3 mutations identified specific spatial and temporal roles for HOXA3 in pharyngeal organ development, including both cell-autonomous and non-autonomous functions, revealing a system that is more complex than originally thought. Here, we will review the current understanding of the role of Hox genes in the early embryonic development of the pharyngeal organs in the mouse, with a particular focus on the function of HOXA3 in thymus and parathyroid organogenesis.
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PMID: 30604847 DOI: 10.1387/ijdb.180284jg
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==2017==
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===Classification and nomenclature of all human homeobox genes===
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BMC Biol. 2007 Oct 26;5:47.
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Holland PW1, Booth HA, Bruford EA.
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Author information
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1
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Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK. peter.holland@zoo.ox.ac.uk.
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Abstract
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BACKGROUND:
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The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described.
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RESULTS:
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We have identified all homeobox genes and pseudogenes in the euchromatic regions of the human genome, finding many unannotated, incorrectly annotated, unnamed, misnamed or misclassified genes and pseudogenes. We describe 300 human homeobox loci, which we divide into 235 probable functional genes and 65 probable pseudogenes. These totals include 3 genes with partial homeoboxes and 13 pseudogenes that lack homeoboxes but are clearly derived from homeobox genes. These figures exclude the repetitive DUX1 to DUX5 homeobox sequences of which we identified 35 probable pseudogenes, with many more expected in heterochromatic regions. Nomenclature is established for approximately 40 formerly unnamed loci, reflecting their evolutionary relationships to other loci in human and other species, and nomenclature revisions are proposed for around 30 other loci. We use a classification that recognizes 11 homeobox gene 'classes' subdivided into 102 homeobox gene 'families'.
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CONCLUSION:
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We have conducted a comprehensive survey of homeobox genes and pseudogenes in the human genome, described many new loci, and revised the classification and nomenclature of homeobox genes. The classification scheme may be widely applicable to homeobox genes in other animal genomes and will facilitate comparative genomics of this important gene superclass.
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{{PMID}}17963489] PMCID: PMC2211742 DOI: 10.1186/1741-7007-5-47
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{|
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! Class
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! Subclass
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! Number of gene families
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! Number of genes
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! Number of pseudogenes
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|-
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| ANTP
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| HOXL
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| 14
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| 52
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| 0
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|-
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|
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| NKL
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| 23
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| 48
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| 19
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|-
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| PRD
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| PAX
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| 3
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| 7
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| 0
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|-
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|
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| PAXL
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| 28
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| 43
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| 24
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|-
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| LIM
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|  
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| 6
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| 12
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| 0
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|-
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| POU
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| 7
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| 16
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| 8
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|-
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| HNF
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|  
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| 2
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| 3
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| 0
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|-
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| SINE
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| 3
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| 6
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| 0
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|-
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| TALE
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|  
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| 6
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| 20
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| 10
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|-
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| CUT
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|  
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| 3
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| 7
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| 3g
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|-
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| PROS
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|  
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| 1
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| 2
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| 0
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|-
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| ZF
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|
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| 5
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| 14
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| 1h
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|-
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| CERS
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|  
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| 1
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| 5
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| 10
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|-
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! Totals
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|
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| 102
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| 235
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| 65
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|}
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{{Hox family table}}
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{{Hox family collapsetable}}
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==2016==
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===Diversity of human and mouse homeobox gene expression in development and adult tissues===
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BMC Dev Biol. 2016 Nov 3;16(1):40.
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Dunwell TL1, Holland PW2.
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* 20 human homeobox genes with widespread expression, primarily from the TALE, CERS and ZF classes.
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* Human - 8-cell and morula -  12 eutherian-specific homeobox genes not detectable outside of reproductive tissues or the embryo.
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** RHOXF2, RHOXF2B, CPHX1, CPHX2, DPRX, LEUTX, TPRX1, TPRX2, ARGFX, NANOGNB, DUXA, DUXB
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* Mouse - four phases of homeobox gene expression - oocyte to zygote; 2-cell; 4-cell to blastocyst; early to mid post-implantation. The most dramatic shifts in homeobox gene expression are between 2-cell and 4-cell, and between blastocyst and post-implantation. Within this group there is a gradual shift in expression between e8.5 and e9.5 dominated by new expression of HOXL ANTP class genes.
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Abstract
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BACKGROUND:
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Homeobox genes encode a diverse set of transcription factors implicated in a vast range of biological processes including, but not limited to, embryonic cell fate specification and patterning. Although numerous studies report expression of particular sets of homeobox genes, a systematic analysis of the tissue specificity of homeobox genes is lacking.
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RESULTS:
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Here we analyse publicly-available transcriptome data from human and mouse developmental stages, and adult human tissues, to identify groups of homeobox genes with similar expression patterns. We calculate expression profiles for 242 human and 278 mouse homeobox loci across a combination of 59 human and 12 mouse adult tissues, early and late developmental stages. This revealed 20 human homeobox genes with widespread expression, primarily from the TALE, CERS and ZF classes. Most homeobox genes, however, have greater tissue-specificity, allowing us to compile homeobox gene expression lists for neural tissues, immune tissues, reproductive and developmental samples, and for numerous organ systems. In mouse development, we propose four distinct phases of homeobox gene expression: oocyte to zygote; 2-cell; 4-cell to blastocyst; early to mid post-implantation. The final phase change is marked by expression of ANTP class genes. We also use these data to compare expression specificity between evolutionarily-based gene classes, revealing that ANTP, PRD, LIM and POU homeobox gene classes have highest tissue specificity while HNF, TALE, CUT and CERS are most widely expressed.
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CONCLUSIONS:
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The homeobox genes comprise a large superclass and their expression patterns are correspondingly diverse, although in a broad sense related to an evolutionarily-based classification. The ubiquitous expression of some genes suggests roles in general cellular processes; in contrast, most human homeobox genes have greater tissue specificity and we compile useful homeobox datasets for particular tissues, organs and developmental stages. The identification of a set of eutherian-specific homeobox genes peaking from human 8-cell to morula stages suggests co-option of new genes to new developmental roles in evolution.
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KEYWORDS:
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Embryo; Homeodomain; Organs; Transcription factor
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PMID: 27809766 PMCID: PMC5094009 DOI: 10.1186/s12861-016-0140-y
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https://bmcdevbiol.biomedcentral.com/articles/10.1186/s12861-016-0140-y
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===A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation===
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Nat Genet. 2016 Feb 1. doi: 10.1038/ng.3497. [Epub ahead of print]
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Acemel RD1, Tena JJ1, Irastorza-Azcarate I1, Marlétaz F2, Gómez-Marín C1, de la Calle-Mustienes E1, Bertrand S3, Diaz SG1, Aldea D3, Aury JM4, Mangenot S4, Holland PW2, Devos DP1, Maeso I1, Escrivá H3, Gómez-Skarmeta JL1.
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Abstract
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The HoxA and HoxD gene clusters of jawed vertebrates are organized into bipartite three-dimensional chromatin structures that separate long-range regulatory inputs coming from the anterior and posterior Hox-neighboring regions. This architecture is instrumental in allowing vertebrate Hox genes to pattern disparate parts of the body, including limbs. Almost nothing is known about how these three-dimensional topologies originated. Here we perform extensive 4C-seq profiling of the Hox cluster in embryos of amphioxus, an invertebrate chordate. We find that, in contrast to the architecture in vertebrates, the amphioxus Hox cluster is organized into a single chromatin interaction domain that includes long-range contacts mostly from the anterior side, bringing distant cis-regulatory elements into contact with Hox genes. We infer that the vertebrate Hox bipartite regulatory system is an evolutionary novelty generated by combining ancient long-range regulatory contacts from DNA in the anterior Hox neighborhood with new regulatory inputs from the posterior side.
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PMID 26829752
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==2015==
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===The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis===
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PLoS One. 2015 May 29;10(5):e0126947. doi: 10.1371/journal.pone.0126947.
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Hench J1, Henriksson J1, Abou-Zied AM1, Lüppert M1, Dethlefsen J1, Mukherjee K1, Tong YG1, Tang L1, Gangishetti U2, Baillie DL3, Bürglin TR1.
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Abstract
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Homeobox genes play crucial roles for the development of multicellular eukaryotes. We have generated a revised list of all homeobox genes for Caenorhabditis elegans and provide a nomenclature for the previously unnamed ones. We show that, out of 103 homeobox genes, 70 are co-orthologous to human homeobox genes. 14 are highly divergent, lacking an obvious ortholog even in other Caenorhabditis species. One of these homeobox genes encodes 12 homeodomains, while three other highly divergent homeobox genes encode a novel type of double homeodomain, termed HOCHOB. To understand how transcription factors regulate cell fate during development, precise spatio-temporal expression data need to be obtained. Using a new imaging framework that we developed, Endrov, we have generated spatio-temporal expression profiles during embryogenesis of over 60 homeobox genes, as well as a number of other developmental control genes using GFP reporters. We used dynamic feedback during recording to automatically adjust the camera exposure time in order to increase the dynamic range beyond the limitations of the camera. We have applied the new framework to examine homeobox gene expression patterns and provide an analysis of these patterns. The methods we developed to analyze and quantify expression data are not only suitable for C. elegans, but can be applied to other model systems or even to tissue culture systems.
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PMID 26024448
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126947
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===The Intersection of the Extrinsic Hedgehog and WNT/Wingless Signals with the Intrinsic Hox Code Underpins Branching Pattern and Tube Shape Diversity in the Drosophila Airways===
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PLoS Genet. 2015 Jan 23;11(1):e1004929. doi: 10.1371/journal.pgen.1004929. eCollection 2015.
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Matsuda R1, Hosono C1, Saigo K2, Samakovlis C3.
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Abstract
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The tubular networks of the Drosophila respiratory system and our vasculature show distinct branching patterns and tube shapes in different body regions. These local variations are crucial for organ function and organismal fitness. Organotypic patterns and tube geometries in branched networks are typically controlled by variations of extrinsic signaling but the impact of intrinsic factors on branch patterns and shapes is not well explored. Here, we show that the intersection of extrinsic hedgehog(hh) and WNT/wingless (wg) signaling with the tube-intrinsic Hox code of distinct segments specifies the tube pattern and shape of the Drosophila airways. In the cephalic part of the airways, hh signaling induces expression of the transcription factor (TF) knirps (kni) in the anterior dorsal trunk (DTa1). kni represses the expression of another TF spalt major (salm), making DTa1 a narrow and long tube. In DTa branches of more posterior metameres, Bithorax Complex (BX-C) Hox genes autonomously divert hh signaling from inducing kni, thereby allowing DTa branches to develop as salm-dependent thick and short tubes. Moreover, the differential expression of BX-C genes is partly responsible for the anterior-to-posterior gradual increase of the DT tube diameter through regulating the expression level of Salm, a transcriptional target of WNT/wg signaling. Thus, our results highlight how tube intrinsic differential competence can diversify tube morphology without changing availabilities of extrinsic factors.
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PMID 25615601
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http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004929
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==2014==
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===A Hox regulatory network of hindbrain segmentation is conserved to the base of vertebrates===
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Nature. 2014 Oct 23;514(7523):490-3. doi: 10.1038/nature13723. Epub 2014 Sep 14.
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Parker HJ1, Bronner ME2, Krumlauf R3.
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Abstract
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 +
A defining feature governing head patterning of jawed vertebrates is a highly conserved gene regulatory network that integrates hindbrain segmentation with segmentally restricted domains of Hox gene expression. Although non-vertebrate chordates display nested domains of axial Hox expression, they lack hindbrain segmentation. The sea lamprey, a jawless fish, can provide unique insights into vertebrate origins owing to its phylogenetic position at the base of the vertebrate tree. It has been suggested that lamprey may represent an intermediate state where nested Hox expression has not been coupled to the process of hindbrain segmentation. However, little is known about the regulatory network underlying Hox expression in lamprey or its relationship to hindbrain segmentation. Here, using a novel tool that allows cross-species comparisons of regulatory elements between jawed and jawless vertebrates, we report deep conservation of both upstream regulators and segmental activity of enhancer elements across these distant species. Regulatory regions from diverse gnathostomes drive segmental reporter expression in the lamprey hindbrain and require the same transcriptional inputs (for example, Kreisler (also known as Mafba), Krox20 (also known as Egr2a)) in both lamprey and zebrafish. We find that lamprey hox genes display dynamic segmentally restricted domains of expression; we also isolated a conserved exonic hox2 enhancer from lamprey that drives segmental expression in rhombomeres 2 and 4. Our results show that coupling of Hox gene expression to segmentation of the hindbrain is an ancient trait with origin at the base of vertebrates that probably led to the formation of rhombomeric compartments with an underlying Hox code.
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PMID 25219855
  
'''Search All Databases''' [http://www.ncbi.nlm.nih.gov/sites/gquery?itool=toolbar&cmd=search&term=hox hox]
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===Hoxb1b controls oriented cell division, cell shape and microtubule dynamics in neural tube morphogenesis===
 +
 
 +
Development. 2014 Feb;141(3):639-49. doi: 10.1242/dev.098731.
 +
 
 +
Zigman M1, Laumann-Lipp N, Titus T, Postlethwait J, Moens CB.
 +
Author information
 +
 
 +
Abstract
 +
 
 +
Hox genes are classically ascribed to function in patterning the anterior-posterior axis of bilaterian animals; however, their role in directing molecular mechanisms underlying morphogenesis at the cellular level remains largely unstudied. We unveil a non-classical role for the zebrafish hoxb1b gene, which shares ancestral functions with mammalian Hoxa1, in controlling progenitor cell shape and oriented cell division during zebrafish anterior hindbrain neural tube morphogenesis. This is likely distinct from its role in cell fate acquisition and segment boundary formation. We show that, without affecting major components of apico-basal or planar cell polarity, Hoxb1b regulates mitotic spindle rotation during the oriented neural keel symmetric mitoses that are required for normal neural tube lumen formation in the zebrafish. This function correlates with a non-cell-autonomous requirement for Hoxb1b in regulating microtubule plus-end dynamics in progenitor cells in interphase. We propose that Hox genes can influence global tissue morphogenesis by control of microtubule dynamics in individual cells in vivo.
 +
KEYWORDS:
 +
Cell polarity, Hoxa1, Hoxb1b, In vivo tissue morphogenesis, Neural tube formation, Oriented cell division, Zebrafish
 +
 
 +
PMID 24449840
 +
 
 +
==2011==
  
UNSW Embryology - [http://embryology.med.unsw.edu.au/MolDev/MolDev.htm Molecular Notes] | [http://embryology.med.unsw.edu.au/Notes/skmus.htm Musculoskeletal Notes]
+
===Evolution of anterior Hox regulatory elements among chordates===
 +
BMC Evol Biol. 2011 Nov 15;11:330.
  
 +
Natale A, Sims C, Chiusano ML, Amoroso A, D'Aniello E, Fucci L, Krumlauf R, Branno M, Locascio A.
 +
Source
 +
Laboratory of Cellular and Developmental Biology, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.
 +
Abstract
 +
BACKGROUND:
 +
The Hox family of transcription factors has a fundamental role in segmentation pathways and axial patterning of embryonic development and their clustered organization is linked with the regulatory mechanisms governing their coordinated expression along embryonic axes. Among chordates, of particular interest are the Hox paralogous genes in groups 1-4 since their expression is coupled to the control of regional identity in the anterior nervous system, where the highest structural diversity is observed.
 +
RESULTS:
 +
To investigate the degree of conservation in cis-regulatory components that form the basis of Hox expression in the anterior nervous system, we have used assays for transcriptional activity in ascidians and vertebrates to compare and contrast regulatory potential. We identified four regulatory sequences located near the CiHox1, CiHox2 and CiHox4 genes of the ascidian Ciona intestinalis which direct neural specific domains of expression. Using functional assays in Ciona and vertebrate embryos in combination with sequence analyses of enhancer fragments located in similar positions adjacent to Hox paralogy group genes, we compared the activity of these four Ciona cis-elements with a series of neural specific enhancers from the amphioxus Hox1-3 genes and from mouse Hox paralogous groups 1-4.
 +
CONCLUSIONS:
 +
This analysis revealed that Kreisler and Krox20 dependent enhancers critical in segmental regulation of the hindbrain appear to be specific for the vertebrate lineage. In contrast, neural enhancers that function as Hox response elements through the action of Hox/Pbx binding motifs have been conserved during chordate evolution. The functional assays reveal that these Hox response cis-elements are recognized by the regulatory components of different and extant species. Together, our results indicate that during chordate evolution, cis-elements dependent upon Hox/Pbx regulatory complexes, are responsible for key aspects of segmental Hox expression in neural tissue and appeared with urochordates after cephalochordate divergence.
  
PMID 20485555 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010600
+
PMID 22085760
  
  

Latest revision as of 09:10, 20 November 2019

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Cite this page: Hill, M.A. (2019, December 15) Embryology Developmental Signals - Homeobox. Retrieved from https://embryology.med.unsw.edu.au/embryology/index.php/Talk:Developmental_Signals_-_Homeobox

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PMID 20485555 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010600


2019

Barnett AA, Nakamura T & Extavour CG. (2019). Hox genes limit germ cell formation in the short germ insect Gryllus bimaculatus. Proc. Natl. Acad. Sci. U.S.A. , 116, 16430-16435. PMID: 31346080 DOI.

Proc Natl Acad Sci U S A. 2019 Aug 13;116(33):16430-16435. doi: 10.1073/pnas.1816024116. Epub 2019 Jul 25. Hox genes limit germ cell formation in the short germ insect Gryllus bimaculatus. Barnett AA1, Nakamura T1, Extavour CG2,3. Author information 1 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138. 2 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; extavour@oeb.harvard.edu. 3 Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138. Abstract Hox genes are conserved transcription factor-encoding genes that specify the identity of body regions in bilaterally symmetrical animals. In the cricket Gryllus bimaculatus, a member of the hemimetabolous insect group Orthoptera, the induction of a subset of mesodermal cells to form the primordial germ cells (PGCs) is restricted to the second through the fourth abdominal segments (A2 to A4). In numerous insect species, the Hox genes Sex-combs reduced (Scr), Antennapedia (Antp), Ultrabithorax (Ubx), and abdominal-A (abd-A) jointly regulate the identities of middle and posterior body segments, suggesting that these genes may restrict PGC formation to specific abdominal segments in G. bimaculatus Here we show that reducing transcript levels of some or all of these Hox genes results in supernumerary and/or ectopic PGCs, either individually or in segment-specific combinations, suggesting that the role of these Hox genes is to limit PGC development with respect to their number, segmental location, or both. These data provide evidence of a role for this ancient group of genes in PGC development. KEYWORDS: Gryllus bimaculatus; Hox; evo-devo; germ cells; insect PMID: 31346080 PMCID: PMC6697791 [Available on 2020-01-25] DOI: 10.1073/pnas.1816024116


Evolutionary selection and morphological integration in the vertebral column of modern humans

Am J Phys Anthropol. 2019 Nov 1. doi: 10.1002/ajpa.23950. [Epub ahead of print]

Arlegi M1,2, Veschambre-Couture C2, Gómez-Olivencia A1,3,4. Author information 1 Departamento de Estratigrafía y Paleontología, Facultad de Ciencia y Tecnología, Universidad del País Vasco-Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Spain. 2 Université de Bordeaux, PACEA UMR 5199, Pessac, France. 3 IKERBASQUE. Basque Foundation for Science, Bizkaia, Spain. 4 Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain. Abstract OBJECTIVES: The main objective is to quantify integration, modularity, and response to selection in the presacral vertebral column of modern humans. MATERIALS AND METHODS: Seventeen linear variables on each presacral vertebra were collected in 108 modern humans producing a total of ~39,000 measurements. Then, we studied patterns and magnitudes of integration at regional, vertebral, and intra-vertebral levels. Additionally, we calculated the ability of vertebrae to respond to selection by quantifying differences in evolvability, flexibility, and constraint throughout the spine. RESULTS: The results indicate that caudal vertebrae are more evolvable than those located more cranially in the presacral vertebral column, following an increasing pattern of evolvability from the cervical to the lumbar region. Additionally, the atlas and fifth lumbar vertebra show the lowest values of integration, while central thoracic vertebrae display the highest magnitudes of integration. DISCUSSION: These results could be related to three main factors: body plan organization expressed by the Hox genes, the strong developmental constraints that determine the number of mammalian vertebrae, and, finally, the functional requirements of an adaptation to bipedal locomotion in the human lineage. © 2019 Wiley Periodicals, Inc. KEYWORDS: adaptation; constraints; evolvability; flexibility; modularity PMID: 31675109 DOI: 10.1002/ajpa.23950


Hox13 is essential for formation of a sensory organ at the terminal end of the sperm duct in Ciona

Dev Biol. 2019 Nov 1. pii: S0012-1606(19)30270-2. doi: 10.1016/j.ydbio.2019.10.028. [Epub ahead of print]

Tajima Y1, Hozumi A1, Yoshida K1, Treen N1, Sakuma T2, Yamamoto T2, Sasakura Y3. Author information 1 Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan. 2 Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan. 3 Shimoda Marine Research Center, University of Tsukuba, Shimoda, Shizuoka, 415-0025, Japan. Electronic address: sasakura@shimoda.tsukuba.ac.jp. Abstract Species-specific traits are thought to have been acquired by natural selection. Transcription factors play central roles in the evolution of species-specific traits. Hox genes encode a set of conserved transcription factors essential for establishing the anterior-posterior body axis of animals. Changes in the expression or function of Hox genes can lead to the diversification of animal-body plans. The tunicate ascidian Ciona intestinalis Type A has an orange-colored structure at the sperm duct terminus. This orange-pigmented organ (OPO) is the characteristic that can distinguish this ascidian from other closely related species. The OPO is formed by the accumulation of orange-pigmented cells (OPCs) that are present throughout the adult body. We show that Hox13 is essential for formation of the OPO. Hox13 is expressed in the epithelium of the sperm duct and neurons surrounding the terminal openings for sperm ejection, while OPCs themselves do not express this gene. OPCs are mobile cells that can move through the body vasculature by pseudopodia, suggesting that the OPO is formed by the accumulation of OPCs guided by Hox13-positive cells. Another ascidian species, Ciona savignyi, does not have an OPO. Like Hox13 of C. intestinalis, Hox13 of C. savignyi is expressed at the terminus of its sperm duct; however, its expression domain is limited to the circular area around the openings. The genetic changes responsible for the acquisition or loss of OPO are likely to occur in the expression pattern of Hox13. Copyright © 2019. Published by Elsevier Inc. KEYWORDS: Ciona; Evolution; Hox; Species-specific trait; Sperm duct PMID: 31682808 DOI: 10.1016/j.ydbio.2019.10.028


Analysis of a limb-specific regulatory element in the promoter of the link protein gene

Biochem Biophys Res Commun. 2019 Oct 22;518(4):672-677. doi: 10.1016/j.bbrc.2019.08.104. Epub 2019 Aug 27.

Rhodes CS1, Matsunobu T2, Yamada Y3. Author information 1 Molecular Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA. Electronic address: Rhodes@dir.nidcr.nih.gov. 2 Department of Orthopaedic Surgery, Kyushu Rosai Hospital, 1-1 Sonekitamachi, Kokuraminami-ku, Kitakyushu, Fukuoka, 800-0296, Japan. 3 Molecular Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA. Abstract Link protein is encoded by the Hapln1 gene and is a prototypical protein found in the cartilage matrix. It acts as an important component of the endochondral skeleton during early development. To study its transcriptional regulation, promoter fragments derived from the link protein gene were coupled to the β-galactosidase reporter and used to study in vivo transgene expression in mice. In day 15.5 mouse embryos, a link promoter fragment spanning -1020 to +40 nucleotides demonstrated highly specific β-galactosidase staining of skeletal structures, including the appendicular and axial cartilaginous tissues. Two shorter promoter fragments, spanning -690 to +40 and -315 to +40 nucleotides, demonstrated limb- and genitalia-specific expression resembling that of homeodomain-regulated tissues. Bioinformatic analysis revealed a highly conserved, Hox-like binding site (HLBS) at approximately -220 bp of the promoter, shared by both constructs, which contained the Hox-core consensus sequence TAATTA. Electromobility shift assays demonstrated binding of Hox-B4 recombinant protein to the HLBS, which was eliminated with nucleotide substitutions within the core-binding element. Co-transfection analysis of the HLBS demonstrated a 22-fold transcriptional activation by HoxA9 expression, which was ablated with a substitution within the core HLBS element. Together these findings establish promoter regions within the link protein gene that are important for in vivo expression and identify the potential role of homeodomain-containing proteins in controlling cartilage and limb gene expression. Published by Elsevier Inc. KEYWORDS: Cartilage; Hox proteins; Limb; Link protein; Promoter; Transcriptional regulation PMID: 31470976 DOI: 10.1016/j.bbrc.2019.08.104

A genome-wide assessment of the ancestral neural crest gene regulatory network

Nat Commun. 2019 Oct 16;10(1):4689. doi: 10.1038/s41467-019-12687-4.

Hockman D1,2, Chong-Morrison V1,3, Green SA4, Gavriouchkina D1,5, Candido-Ferreira I1, Ling ITC1, Williams RM1, Amemiya CT6, Smith JJ7, Bronner ME4, Sauka-Spengler T8. Author information 1 Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK. 2 Division of Cell Biology, Department of Human Biology, Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. 3 Division of Biosciences, Faculty of Life Sciences, University College London, London, UK. 4 Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. 5 Okinawa Institute of Science and Technology, Molecular Genetics Unit, Onna, Japan. 6 Molecular Cell Biology, School of Natural Sciences, University of California, Merced, CA, USA. 7 Department of Biology, University of Kentucky, Lexington, KY, USA. 8 Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK. tatjana.sauka-spengler@imm.ox.ac.uk. Abstract The neural crest (NC) is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional and epigenomic profiles of NC cells in the sea lamprey, in order to gain insight into the ancestral state of the NC gene regulatory network (GRN). Transcriptome analyses identify clusters of co-regulated genes during NC specification and migration that show high conservation across vertebrates but also identify transcription factors (TFs) and cell-adhesion molecules not previously implicated in NC migration. ATAC-seq analysis uncovers an ensemble of cis-regulatory elements, including enhancers of Tfap2B, SoxE1 and Hox-α2 validated in the embryo. Cross-species deployment of lamprey elements identifies the deep conservation of lamprey SoxE1 enhancer activity, mediating homologous expression in jawed vertebrates. Our data provide insight into the core GRN elements conserved to the base of the vertebrates and expose others that are unique to lampreys. PMID: 31619682 PMCID: PMC6795873 DOI: 10.1038/s41467-019-12687-4


2018

Hox genes in the pharyngeal region: how Hoxa3 controls early embryonic development of the pharyngeal organs

Int J Dev Biol. 2018;62(11-12):775-783. doi: 10.1387/ijdb.180284jg.

Gordon J1.

Abstract The pharyngeal organs, namely the thyroid, thymus, parathyroids, and ultimobranchial bodies, derive from the pharyngeal endoderm during embryonic development. The pharyngeal region is a segmented structure comprised of a series of reiterated structures: the pharyngeal arches on the exterior surface, the pharyngeal pouches on the interior, and a mesenchymal core. It is well known that Hox genes control spatial identity along the anterior-posterior axis of the developing vertebrate embryo, and nowhere is this is more evident than in the pharyngeal region. Each of the distinct segmented regions has a unique pattern of Hox expression, which conveys crucial positional information to the cells and tissues within it. In the context of pharyngeal organ development, molecular data suggest that HOXA3 is responsible for specifying organ identity within the third pharyngeal pouch, and in its absence, thymus and parathyroid organogenesis fails to proceed normally. Recent studies comprising a series of Hoxa3 mutations identified specific spatial and temporal roles for HOXA3 in pharyngeal organ development, including both cell-autonomous and non-autonomous functions, revealing a system that is more complex than originally thought. Here, we will review the current understanding of the role of Hox genes in the early embryonic development of the pharyngeal organs in the mouse, with a particular focus on the function of HOXA3 in thymus and parathyroid organogenesis.

PMID: 30604847 DOI: 10.1387/ijdb.180284jg

2017

Classification and nomenclature of all human homeobox genes

BMC Biol. 2007 Oct 26;5:47.

Holland PW1, Booth HA, Bruford EA. Author information 1 Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK. peter.holland@zoo.ox.ac.uk. Abstract BACKGROUND: The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described. RESULTS: We have identified all homeobox genes and pseudogenes in the euchromatic regions of the human genome, finding many unannotated, incorrectly annotated, unnamed, misnamed or misclassified genes and pseudogenes. We describe 300 human homeobox loci, which we divide into 235 probable functional genes and 65 probable pseudogenes. These totals include 3 genes with partial homeoboxes and 13 pseudogenes that lack homeoboxes but are clearly derived from homeobox genes. These figures exclude the repetitive DUX1 to DUX5 homeobox sequences of which we identified 35 probable pseudogenes, with many more expected in heterochromatic regions. Nomenclature is established for approximately 40 formerly unnamed loci, reflecting their evolutionary relationships to other loci in human and other species, and nomenclature revisions are proposed for around 30 other loci. We use a classification that recognizes 11 homeobox gene 'classes' subdivided into 102 homeobox gene 'families'. CONCLUSION: We have conducted a comprehensive survey of homeobox genes and pseudogenes in the human genome, described many new loci, and revised the classification and nomenclature of homeobox genes. The classification scheme may be widely applicable to homeobox genes in other animal genomes and will facilitate comparative genomics of this important gene superclass. [1] PMCID: PMC2211742 DOI: 10.1186/1741-7007-5-47


Class Subclass Number of gene families Number of genes Number of pseudogenes
ANTP HOXL 14 52 0
NKL 23 48 19
PRD PAX 3 7 0
PAXL 28 43 24
LIM   6 12 0
POU   7 16 8
HNF   2 3 0
SINE 3 6 0
TALE   6 20 10
CUT   3 7 3g
PROS   1 2 0
ZF 5 14 1h
CERS   1 5 10
Totals 102 235 65
Table - Human Homeobox Family
Class Subclass Number of gene families Number of genes Number of pseudogenes
ANTP HOXL 14 52 0
NKL 23 48 19
PRD PAX 3 7 0
PAXL 28 43 24
LIM   6 12 0
POU   7 16 8
HNF   2 3 0
SINE 3 6 0
TALE   6 20 10
CUT   3 7 3
PROS   1 2 0
ZF 5 14 1h
CERS   1 5 10
Totals 102 235 65
     Classification data from[1] does not include table supplementary information.

Links: Hox | Hox family | Bmp Family | Fgf Family | Hedgehog Family | Sox Family | Tbx Family


Human Hox Family  
Table - Human Homeobox Family
Class Subclass Number of gene families Number of genes Number of pseudogenes
ANTP HOXL 14 52 0
NKL 23 48 19
PRD PAX 3 7 0
PAXL 28 43 24
LIM   6 12 0
POU   7 16 8
HNF   2 3 0
SINE 3 6 0
TALE   6 20 10
CUT   3 7 3
PROS   1 2 0
ZF 5 14 1h
CERS   1 5 10
Totals 102 235 65
     Classification data from[1] does not include table supplementary information.

Links: Hox | Hox family | Bmp Family | Fgf Family | Hedgehog Family | Sox Family | Tbx Family

2016

Diversity of human and mouse homeobox gene expression in development and adult tissues

BMC Dev Biol. 2016 Nov 3;16(1):40.

Dunwell TL1, Holland PW2.

  • 20 human homeobox genes with widespread expression, primarily from the TALE, CERS and ZF classes.
  • Human - 8-cell and morula - 12 eutherian-specific homeobox genes not detectable outside of reproductive tissues or the embryo.
    • RHOXF2, RHOXF2B, CPHX1, CPHX2, DPRX, LEUTX, TPRX1, TPRX2, ARGFX, NANOGNB, DUXA, DUXB
  • Mouse - four phases of homeobox gene expression - oocyte to zygote; 2-cell; 4-cell to blastocyst; early to mid post-implantation. The most dramatic shifts in homeobox gene expression are between 2-cell and 4-cell, and between blastocyst and post-implantation. Within this group there is a gradual shift in expression between e8.5 and e9.5 dominated by new expression of HOXL ANTP class genes.

Abstract

BACKGROUND: Homeobox genes encode a diverse set of transcription factors implicated in a vast range of biological processes including, but not limited to, embryonic cell fate specification and patterning. Although numerous studies report expression of particular sets of homeobox genes, a systematic analysis of the tissue specificity of homeobox genes is lacking. RESULTS: Here we analyse publicly-available transcriptome data from human and mouse developmental stages, and adult human tissues, to identify groups of homeobox genes with similar expression patterns. We calculate expression profiles for 242 human and 278 mouse homeobox loci across a combination of 59 human and 12 mouse adult tissues, early and late developmental stages. This revealed 20 human homeobox genes with widespread expression, primarily from the TALE, CERS and ZF classes. Most homeobox genes, however, have greater tissue-specificity, allowing us to compile homeobox gene expression lists for neural tissues, immune tissues, reproductive and developmental samples, and for numerous organ systems. In mouse development, we propose four distinct phases of homeobox gene expression: oocyte to zygote; 2-cell; 4-cell to blastocyst; early to mid post-implantation. The final phase change is marked by expression of ANTP class genes. We also use these data to compare expression specificity between evolutionarily-based gene classes, revealing that ANTP, PRD, LIM and POU homeobox gene classes have highest tissue specificity while HNF, TALE, CUT and CERS are most widely expressed. CONCLUSIONS: The homeobox genes comprise a large superclass and their expression patterns are correspondingly diverse, although in a broad sense related to an evolutionarily-based classification. The ubiquitous expression of some genes suggests roles in general cellular processes; in contrast, most human homeobox genes have greater tissue specificity and we compile useful homeobox datasets for particular tissues, organs and developmental stages. The identification of a set of eutherian-specific homeobox genes peaking from human 8-cell to morula stages suggests co-option of new genes to new developmental roles in evolution. KEYWORDS: Embryo; Homeodomain; Organs; Transcription factor PMID: 27809766 PMCID: PMC5094009 DOI: 10.1186/s12861-016-0140-y

https://bmcdevbiol.biomedcentral.com/articles/10.1186/s12861-016-0140-y

A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation

Nat Genet. 2016 Feb 1. doi: 10.1038/ng.3497. [Epub ahead of print]

Acemel RD1, Tena JJ1, Irastorza-Azcarate I1, Marlétaz F2, Gómez-Marín C1, de la Calle-Mustienes E1, Bertrand S3, Diaz SG1, Aldea D3, Aury JM4, Mangenot S4, Holland PW2, Devos DP1, Maeso I1, Escrivá H3, Gómez-Skarmeta JL1.

Abstract

The HoxA and HoxD gene clusters of jawed vertebrates are organized into bipartite three-dimensional chromatin structures that separate long-range regulatory inputs coming from the anterior and posterior Hox-neighboring regions. This architecture is instrumental in allowing vertebrate Hox genes to pattern disparate parts of the body, including limbs. Almost nothing is known about how these three-dimensional topologies originated. Here we perform extensive 4C-seq profiling of the Hox cluster in embryos of amphioxus, an invertebrate chordate. We find that, in contrast to the architecture in vertebrates, the amphioxus Hox cluster is organized into a single chromatin interaction domain that includes long-range contacts mostly from the anterior side, bringing distant cis-regulatory elements into contact with Hox genes. We infer that the vertebrate Hox bipartite regulatory system is an evolutionary novelty generated by combining ancient long-range regulatory contacts from DNA in the anterior Hox neighborhood with new regulatory inputs from the posterior side. PMID 26829752

2015

The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis

PLoS One. 2015 May 29;10(5):e0126947. doi: 10.1371/journal.pone.0126947.

Hench J1, Henriksson J1, Abou-Zied AM1, Lüppert M1, Dethlefsen J1, Mukherjee K1, Tong YG1, Tang L1, Gangishetti U2, Baillie DL3, Bürglin TR1.

Abstract

Homeobox genes play crucial roles for the development of multicellular eukaryotes. We have generated a revised list of all homeobox genes for Caenorhabditis elegans and provide a nomenclature for the previously unnamed ones. We show that, out of 103 homeobox genes, 70 are co-orthologous to human homeobox genes. 14 are highly divergent, lacking an obvious ortholog even in other Caenorhabditis species. One of these homeobox genes encodes 12 homeodomains, while three other highly divergent homeobox genes encode a novel type of double homeodomain, termed HOCHOB. To understand how transcription factors regulate cell fate during development, precise spatio-temporal expression data need to be obtained. Using a new imaging framework that we developed, Endrov, we have generated spatio-temporal expression profiles during embryogenesis of over 60 homeobox genes, as well as a number of other developmental control genes using GFP reporters. We used dynamic feedback during recording to automatically adjust the camera exposure time in order to increase the dynamic range beyond the limitations of the camera. We have applied the new framework to examine homeobox gene expression patterns and provide an analysis of these patterns. The methods we developed to analyze and quantify expression data are not only suitable for C. elegans, but can be applied to other model systems or even to tissue culture systems.

PMID 26024448

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126947

The Intersection of the Extrinsic Hedgehog and WNT/Wingless Signals with the Intrinsic Hox Code Underpins Branching Pattern and Tube Shape Diversity in the Drosophila Airways

PLoS Genet. 2015 Jan 23;11(1):e1004929. doi: 10.1371/journal.pgen.1004929. eCollection 2015.

Matsuda R1, Hosono C1, Saigo K2, Samakovlis C3.

Abstract

The tubular networks of the Drosophila respiratory system and our vasculature show distinct branching patterns and tube shapes in different body regions. These local variations are crucial for organ function and organismal fitness. Organotypic patterns and tube geometries in branched networks are typically controlled by variations of extrinsic signaling but the impact of intrinsic factors on branch patterns and shapes is not well explored. Here, we show that the intersection of extrinsic hedgehog(hh) and WNT/wingless (wg) signaling with the tube-intrinsic Hox code of distinct segments specifies the tube pattern and shape of the Drosophila airways. In the cephalic part of the airways, hh signaling induces expression of the transcription factor (TF) knirps (kni) in the anterior dorsal trunk (DTa1). kni represses the expression of another TF spalt major (salm), making DTa1 a narrow and long tube. In DTa branches of more posterior metameres, Bithorax Complex (BX-C) Hox genes autonomously divert hh signaling from inducing kni, thereby allowing DTa branches to develop as salm-dependent thick and short tubes. Moreover, the differential expression of BX-C genes is partly responsible for the anterior-to-posterior gradual increase of the DT tube diameter through regulating the expression level of Salm, a transcriptional target of WNT/wg signaling. Thus, our results highlight how tube intrinsic differential competence can diversify tube morphology without changing availabilities of extrinsic factors.

PMID 25615601

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004929

2014

A Hox regulatory network of hindbrain segmentation is conserved to the base of vertebrates

Nature. 2014 Oct 23;514(7523):490-3. doi: 10.1038/nature13723. Epub 2014 Sep 14.

Parker HJ1, Bronner ME2, Krumlauf R3.

Abstract

A defining feature governing head patterning of jawed vertebrates is a highly conserved gene regulatory network that integrates hindbrain segmentation with segmentally restricted domains of Hox gene expression. Although non-vertebrate chordates display nested domains of axial Hox expression, they lack hindbrain segmentation. The sea lamprey, a jawless fish, can provide unique insights into vertebrate origins owing to its phylogenetic position at the base of the vertebrate tree. It has been suggested that lamprey may represent an intermediate state where nested Hox expression has not been coupled to the process of hindbrain segmentation. However, little is known about the regulatory network underlying Hox expression in lamprey or its relationship to hindbrain segmentation. Here, using a novel tool that allows cross-species comparisons of regulatory elements between jawed and jawless vertebrates, we report deep conservation of both upstream regulators and segmental activity of enhancer elements across these distant species. Regulatory regions from diverse gnathostomes drive segmental reporter expression in the lamprey hindbrain and require the same transcriptional inputs (for example, Kreisler (also known as Mafba), Krox20 (also known as Egr2a)) in both lamprey and zebrafish. We find that lamprey hox genes display dynamic segmentally restricted domains of expression; we also isolated a conserved exonic hox2 enhancer from lamprey that drives segmental expression in rhombomeres 2 and 4. Our results show that coupling of Hox gene expression to segmentation of the hindbrain is an ancient trait with origin at the base of vertebrates that probably led to the formation of rhombomeric compartments with an underlying Hox code. PMID 25219855

Hoxb1b controls oriented cell division, cell shape and microtubule dynamics in neural tube morphogenesis

Development. 2014 Feb;141(3):639-49. doi: 10.1242/dev.098731.

Zigman M1, Laumann-Lipp N, Titus T, Postlethwait J, Moens CB. Author information

Abstract

Hox genes are classically ascribed to function in patterning the anterior-posterior axis of bilaterian animals; however, their role in directing molecular mechanisms underlying morphogenesis at the cellular level remains largely unstudied. We unveil a non-classical role for the zebrafish hoxb1b gene, which shares ancestral functions with mammalian Hoxa1, in controlling progenitor cell shape and oriented cell division during zebrafish anterior hindbrain neural tube morphogenesis. This is likely distinct from its role in cell fate acquisition and segment boundary formation. We show that, without affecting major components of apico-basal or planar cell polarity, Hoxb1b regulates mitotic spindle rotation during the oriented neural keel symmetric mitoses that are required for normal neural tube lumen formation in the zebrafish. This function correlates with a non-cell-autonomous requirement for Hoxb1b in regulating microtubule plus-end dynamics in progenitor cells in interphase. We propose that Hox genes can influence global tissue morphogenesis by control of microtubule dynamics in individual cells in vivo. KEYWORDS: Cell polarity, Hoxa1, Hoxb1b, In vivo tissue morphogenesis, Neural tube formation, Oriented cell division, Zebrafish

PMID 24449840

2011

Evolution of anterior Hox regulatory elements among chordates

BMC Evol Biol. 2011 Nov 15;11:330.

Natale A, Sims C, Chiusano ML, Amoroso A, D'Aniello E, Fucci L, Krumlauf R, Branno M, Locascio A. Source Laboratory of Cellular and Developmental Biology, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy. Abstract BACKGROUND: The Hox family of transcription factors has a fundamental role in segmentation pathways and axial patterning of embryonic development and their clustered organization is linked with the regulatory mechanisms governing their coordinated expression along embryonic axes. Among chordates, of particular interest are the Hox paralogous genes in groups 1-4 since their expression is coupled to the control of regional identity in the anterior nervous system, where the highest structural diversity is observed. RESULTS: To investigate the degree of conservation in cis-regulatory components that form the basis of Hox expression in the anterior nervous system, we have used assays for transcriptional activity in ascidians and vertebrates to compare and contrast regulatory potential. We identified four regulatory sequences located near the CiHox1, CiHox2 and CiHox4 genes of the ascidian Ciona intestinalis which direct neural specific domains of expression. Using functional assays in Ciona and vertebrate embryos in combination with sequence analyses of enhancer fragments located in similar positions adjacent to Hox paralogy group genes, we compared the activity of these four Ciona cis-elements with a series of neural specific enhancers from the amphioxus Hox1-3 genes and from mouse Hox paralogous groups 1-4. CONCLUSIONS: This analysis revealed that Kreisler and Krox20 dependent enhancers critical in segmental regulation of the hindbrain appear to be specific for the vertebrate lineage. In contrast, neural enhancers that function as Hox response elements through the action of Hox/Pbx binding motifs have been conserved during chordate evolution. The functional assays reveal that these Hox response cis-elements are recognized by the regulatory components of different and extant species. Together, our results indicate that during chordate evolution, cis-elements dependent upon Hox/Pbx regulatory complexes, are responsible for key aspects of segmental Hox expression in neural tissue and appeared with urochordates after cephalochordate divergence.

PMID 22085760


2009

Hedgehog signaling is dispensable for adult murine hematopoietic stem cell function and hematopoiesis

Cell Stem Cell. 2009 Jun 5;4(6):559-67.

Hofmann I, Stover EH, Cullen DE, Mao J, Morgan KJ, Lee BH, Kharas MG, Miller PG, Cornejo MG, Okabe R, Armstrong SA, Ghilardi N, Gould S, de Sauvage FJ, McMahon AP, Gilliland DG. Source Division of Hematology, Department of Medicine, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA.

Abstract

We report the unexpected finding that loss of Hh signaling through conditional deletion of Smoothened (Smo) in the adult hematopoietic compartment has no apparent effect on adult hematopoiesis, including peripheral blood count, number or cell-cycle status of stem or progenitor cells, hematopoietic colony-forming potential, long-term repopulating activity in competitive repopulation assays, or stress response to serial 5-fluorouracil treatment. Furthermore, pharmacologic inhibition of Hh signaling with a potent and selective small molecule antagonist has no substantive effect on hematopoiesis in the mouse. In addition, Hh signaling is not required for the development of MLL-AF9-mediated acute myeloid leukemia (AML). Taken together, these data demonstrate that Hh signaling is dispensable for normal hematopoietic development and hematopoietic stem cell function, indicating that targeting of Hh signaling in solid tumors is not likely to result in hematopoietic toxicity. Furthermore, the Hh pathway may not be a compelling target in certain hematopoietic malignancies.

Comment in Cell Stem Cell. 2009 Jun 5;4(6):470-1.

PMID 19497284

2006

Hox transcription factors and their elusive mammalian gene targets

Heredity. 2006 Aug;97(2):88-96. Epub 2006 May 24.

Svingen T, Tonissen KF. Source Cell Biology Group, Eskitis Institute for Cell and Molecular Therapies and School of Biomolecular and Biomedical Science, Griffith University, Nathan, Queensland 4111, Australia.

Abstract

The Hox family of homeodomain transcription factors regulate numerous pathways during developmental and normal cellular processes. All Hox proteins recognise similar sequences in vitro yet display functional diversity in an in vivo environment. This review focuses on the transcriptional and functional specificity elicited by Hox proteins, giving an overview of homeodomain-DNA interactions and the gain of binding specificity through cooperative binding with cofactors. Furthermore, currently identified mammalian Hox target genes are presented, of which the most striking feature is that very few direct Hox targets have been identified. The direct targets participate in an array of cellular functions including organogenesis and cellular differentiation, cell adhesion and migration and cell cycle and apoptotic pathways. A further assessment of identified mammalian promoter targets and the contribution of bases outside the canonical recognition motif is given, highlighting roles they may play in either trans-activation or repression by Hox proteins.

PMID 16721389

The list contains likely Hox gene targets and the Hox protein responsible for the trans-regulatory effect. The (+/-) symbols represent either a positive or negative regulatory effect on the target gene and (?) symbol indicates an unknown effect. Also, note that although there is some experimental evidence to suggest all are likely direct gene targets, not all have been exclusively verified of being so through in vivo experiments. The corresponding reference(s) for each gene target is also shown.

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Hox protein

+/-

Target

Species

Reference

Hoxa2-Six2Mouse

Kutejova et al (2005)

Hoxa5+p53Mouse

Raman et al (2000a)

HOXA5  Human 
HOXA5+Progesterone receptorHuman

Raman et al (2000b)

HOXA5+PleiotrophinHuman

Chen et al (2005)

HOXA5+IGFBP-1Human

Foucher et al (2002); Gao et al (2002)

HOXA10    
HOXB4    
Hoxa9-OsteopontinMouse

Shi et al (1999, 2001)

Hoxc8    
HOXA9+EphB4Human

Bruhl et al (2004)

HOXA10+p21Human

Bromleigh and Freedman (2000)

HOXA10+ beta 3-IntegrinHuman

Daftary et al (2002)

HOXA10-EMX2Human

Troy et al (2003)

Hoxa10+IGFBP-1Baboon

Kim et al (2003)

Hoxa13, Hoxd13+EphA7Mouse

Salsi and Zappavigna (2006)

HOXB1+COL5A2Human

Penkov et al (2000)

Hoxb3+TTF-1Rat

Guazzi et al (1994)

Hoxb5+SPI3Mouse

Safaei (1997)

Hoxb5+Flk1Mouse

Wu et al (2003)

HOXB7+BFGFHuman

Carè et al (1996)

Hoxb8-N-CAMMouse

Jones et al (1992)

Hoxb9+N-CAMMouse

Jones et al (1992)

Hoxc8?mgl-1Mouse

Tomotsune et al (1993)

Hoxc13-KeratinsMouse

Tkatchenko et al (2001)

Hoxd10, b6, b7, b9, c8+ReninMouse

Pan et al (2004)

2005

Developmental regulation of the Hox genes during axial morphogenesis in the mouse

Development. 2005 Jul;132(13):2931-42.

Deschamps J, van Nes J. Source Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands. jacqueli@niob.knaw.nl

Abstract

The Hox genes confer positional information to the axial and paraxial tissues as they emerge gradually from the posterior aspect of the vertebrate embryo. Hox genes are sequentially activated in time and space, in a way that reflects their organisation into clusters in the genome. Although this co-linearity of expression of the Hox genes has been conserved during evolution, it is a phenomenon that is still not understood at the molecular level. This review aims to bring together recent findings that have advanced our understanding of the regulation of the Hox genes during mouse embryonic development. In particular, we highlight the integration of these transducers of anteroposterior positional information into the genetic network that drives tissue generation and patterning during axial elongation.

PMID 15944185

  1. 1.0 1.1 Holland PW, Booth HA & Bruford EA. (2007). Classification and nomenclature of all human homeobox genes. BMC Biol. , 5, 47. PMID: 17963489 DOI.