Talk:Developmental Signals - Homeobox - Revision history

Z8600021 at 01:51, 30 April 2020

2020-04-30T01:51:19Z

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

			==2020==

			{{#pmid:32138237}}

			'''The Hox Gene egl-5 Acts as a Terminal Selector for VD13 Development via Wnt Signaling'''

			Nervous systems are comprised of diverse cell types that differ functionally and morphologically. During development, extrinsic signals, e.g., growth factors, can activate intrinsic programs, usually orchestrated by networks of transcription factors. Within that network, transcription factors that drive the specification of features specific to a limited number of cells are often referred to as terminal selectors. While we still have an incomplete view of how individual neurons within organisms become specified, reporters limited to a subset of neurons in a nervous system can facilitate the discovery of cell specification programs. We have identified a fluorescent reporter that labels VD13, the most posterior of the 19 inhibitory GABA (γ-amino butyric acid)-ergic motorneurons, and two additional neurons, LUAL and LUAR. Loss of function in multiple Wnt signaling genes resulted in an incompletely penetrant loss of the marker, selectively in VD13, but not the LUAs, even though other aspects of GABAergic specification in VD13 were normal. The posterior Hox gene, egl-5, was necessary for expression of our marker in VD13, and ectopic expression of egl-5 in more anterior GABAergic neurons induced expression of the marker. These results suggest egl-5 is a terminal selector of VD13, subsequent to GABAergic specification.
			KEYWORDS:
			Hox genes; Wnt signaling; axon outgrowth; neuron specification
			PMCID: PMC7151087 DOI: 10.3390/jdb8010005

Z8600021 at 22:10, 19 November 2019

2019-11-19T22:10:53Z

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	==2019==		==2019==
			{{#pmid:31346080}}

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

Z8600021 at 00:03, 14 November 2019

2019-11-14T00:03:23Z

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	==2019==		==2019==

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

Z8600021 at 23:20, 13 November 2019

2019-11-13T23:20:30Z

Show changes

Z8600021 at 23:17, 13 November 2019

2019-11-13T23:17:34Z

← Older revision		Revision as of 10:17, 14 November 2019
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	PMID 20485555 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010600		PMID 20485555 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010600



			{\|
			! 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
			\|}


	==2019==		==2019==

Z8600021 at 21:39, 6 November 2019

2019-11-06T21:39:01Z

@@ Line 44: / Line 44: @@
 Cartilage; Hox proteins; Limb; Link protein; Promoter; Transcriptional regulation
 PMID: 31470976 DOI: 10.1016/j.bbrc.2019.08.104
 ==2018==

Z8600021 at 21:38, 6 November 2019

2019-11-06T21:38:15Z

← Older revision		Revision as of 08:38, 7 November 2019
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	PMID 20485555 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010600		PMID 20485555 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010600

			==2019==

			===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

	==2018==		==2018==

Z8600021 at 01:06, 5 Ocak 2019

2019-01-05T01:06:09Z

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	==2018==		==2018==
	nt J Dev Biol. 2018;62(11-12):775-783. doi: 10.1387/ijdb.180284jg.
	~~Hox genes in the pharyngeal region: how Hoxa3 controls early embryonic development of the pharyngeal organs.~~		===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.		Gordon J1.
	~~Author information~~
	Abstract		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.		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.

Z8600021 at 01:05, 5 Ocak 2019

2019-01-05T01:05:20Z

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

	==~~2017~~==		==2018==
			nt J Dev Biol. 2018;62(11-12):775-783. doi: 10.1387/ijdb.180284jg.
			Hox genes in the pharyngeal region: how Hoxa3 controls early embryonic development of the pharyngeal organs.
			Gordon J1.
			Author information
			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
	==2016==		==2016==
	===Diversity of human and mouse homeobox gene expression in development and adult tissues===		===Diversity of human and mouse homeobox gene expression in development and adult tissues===

Z8600021 at 01:40, 9 August 2017

2017-08-09T01:40:32Z

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	==2017==		==2017==

			==2016==
	===Diversity of human and mouse homeobox gene expression in development and adult tissues===		===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.		* 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.		* 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.		* 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		https://bmcdevbiol.biomedcentral.com/articles/10.1186/s12861-016-0140-y

	~~==2016==~~

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