Talk:Molecular Development - X Inactivation

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Cite this page: Hill, M.A. (2021, September 19) Embryology Molecular Development - X Inactivation. Retrieved from


Colognori D, Sunwoo H, Wang D, Wang CY & Lee JT. (2020). Xist Repeats A and B Account for Two Distinct Phases of X Inactivation Establishment. Dev. Cell , , . PMID: 32531209 DOI.

Xist Repeats A and B Account for Two Distinct Phases of X Inactivation Establishment

X chromosome inactivation (XCI) is a global silencing mechanism by which XX and XY mammals equalize X-linked gene dosages. XCI begins with an establishment phase during which Xist RNA spreads and induces de novo heterochromatinization across a female X chromosome and is followed by a maintenance phase when multiple epigenetic pathways lock down the inactive X (Xi) state. Involvement of Polycomb repressive complexes 1 and 2 in XCI has been intensively studied but with conflicting conclusions regarding their recruitment and role in Xi silencing. Here, we reveal that establishment of XCI has two phases and reconcile the roles that Xist repeats A and B play in gene silencing and Polycomb recruitment. Repeat A initiates both processes, whereas repeat B bolsters or stabilizes them thereafter. Once established, XCI no longer requires repeat A during maintenance. These findings integrate disparate studies and present a unified view of Xist's role in Polycomb-mediated silencing.


The bipartite TAD organization of the X-inactivation center ensures opposing developmental regulation of Tsix and Xist

Nat Genet. 2019 Jun;51(6):1024-1034. doi: 10.1038/s41588-019-0412-0. Epub 2019 May 27.

van Bemmel JG1,2,3, Galupa R4,5, Gard C4, Servant N6,7, Picard C4, Davies J8, Szempruch AJ9, Zhan Y10,11, Żylicz JJ4,12, Nora EP13, Lameiras S14, de Wit E15, Gentien D16, Baulande S14, Giorgetti L10, Guttman M9, Hughes JR8, Higgs DR8, Gribnau J17, Heard E18.

The mouse X-inactivation center (Xic) locus represents a powerful model for understanding the links between genome architecture and gene regulation, with the non-coding genes Xist and Tsix showing opposite developmental expression patterns while being organized as an overlapping sense/antisense unit. The Xic is organized into two topologically associating domains (TADs) but the role of this architecture in orchestrating cis-regulatory information remains elusive. To explore this, we generated genomic inversions that swap the Xist/Tsix transcriptional unit and place their promoters in each other's TAD. We found that this led to a switch in their expression dynamics: Xist became precociously and ectopically upregulated, both in male and female pluripotent cells, while Tsix expression aberrantly persisted during differentiation. The topological partitioning of the Xic is thus critical to ensure proper developmental timing of X inactivation. Our study illustrates how the genomic architecture of cis-regulatory landscapes can affect the regulation of mammalian developmental processes. PMID: 31133748 PMCID: PMC6551226 [Available on 2019-12-01] DOI: 10.1038/s41588-019-0412-0


The Implication of Early Chromatin Changes in X Chromosome Inactivation

Cell. 2018 Dec 21. pii: S0092-8674(18)31566-6. doi: 10.1016/j.cell.2018.11.041. [Epub ahead of print]

Żylicz JJ1, Bousard A2, Žumer K3, Dossin F2, Mohammad E3, da Rocha ST4, Schwalb B3, Syx L2, Dingli F5, Loew D5, Cramer P3, Heard E6.

Abstract During development, the precise relationships between transcription and chromatin modifications often remain unclear. We use the X chromosome inactivation (XCI) paradigm to explore the implication of chromatin changes in gene silencing. Using female mouse embryonic stem cells, we initiate XCI by inducing Xist and then monitor the temporal changes in transcription and chromatin by allele-specific profiling. This reveals histone deacetylation and H2AK119 ubiquitination as the earliest chromatin alterations during XCI. We show that HDAC3 is pre-bound on the X chromosome and that, upon Xist coating, its activity is required for efficient gene silencing. We also reveal that first PRC1-associated H2AK119Ub and then PRC2-associated H3K27me3 accumulate initially at large intergenic domains that can then spread into genes only in the context of histone deacetylation and gene silencing. Our results reveal the hierarchy of chromatin events during the initiation of XCI and identify key roles for chromatin in the early steps of transcriptional silencing.

KEYWORDS: PRC1; PRC2; Polycomb; X chromosome inactivation; Xist; embryonic stem cells; epigenetics; histone acetylation; histone deacetylase PMID: 30595450 DOI: 10.1016/j.cell.2018.11.041

Mammalian X Chromosome Dosage Compensation: Perspectives From the Germ Line

Bioessays. 2018 May 14. doi: 10.1002/bies.201800024. [Epub ahead of print]

Sangrithi MN1,2, Turner JMA3.


Sex chromosomes are advantageous to mammals, allowing them to adopt a genetic rather than environmental sex determination system. However, sex chromosome evolution also carries a burden, because it results in an imbalance in gene dosage between females (XX) and males (XY). This imbalance is resolved by X dosage compensation, which comprises both X chromosome inactivation and X chromosome upregulation. X dosage compensation has been well characterized in the soma, but not in the germ line. Germ cells face a special challenge, because genome wide reprogramming erases epigenetic marks responsible for maintaining the X dosage compensated state. Here we explain how evolution has influenced the gene content and germ line specialization of the mammalian sex chromosomes. We discuss new research uncovering unusual X dosage compensation states in germ cells, which we postulate influence sexual dimorphisms in germ line development and cause infertility in individuals with sex chromosome aneuploidy. KEYWORDS: X chromosome upregulation; X dosage compensation; genome-wide reprogramming; germ cells; sex chromosome aneuploidy; sex chromosomes PMID: 29756331 DOI: 10.1002/bies.201800024

Three-dimensional organization and dynamics of the genome

Cell Biol Toxicol. 2018 Mar 22. doi: 10.1007/s10565-018-9428-y.

Szalaj P1,2,3, Plewczynski D4,5,6.


Genome is a complex hierarchical structure, and its spatial organization plays an important role in its function. Chromatin loops and topological domains form the basic structural units of this multiscale organization and are essential to orchestrate complex regulatory networks and transcription mechanisms. They also form higher-order structures such as chromosomal compartments and chromosome territories. Each level of this intrinsic architecture is governed by principles and mechanisms that we only start to understand. In this review, we summarize the current view of the genome architecture on the scales ranging from chromatin loops to the whole genome. We describe cell-to-cell variability, links between genome reorganization and various genomic processes, such as chromosome X inactivation and cell differentiation, and the interplay between different experimental techniques. KEYWORDS: CTCF; Chromatin loops; Chromosome territories; Cohesin; Compartments; Genome organization; Topological domains PMID: 29568981 DOI: 10.1007/s10565-018-9428-y


X-chromosome inactivation in female newborns conceived by assisted reproductive technologies

Fertil Steril. 2014 Apr 10. pii: S0015-0282(14)00251-9. doi: 10.1016/j.fertnstert.2014.03.010. [Epub ahead of print]

Wu EX1, Stanar P1, Ma S2. Author information

Abstract OBJECTIVE: To investigate X-chromosome inactivation (XCI) skewing in female newborns conceived by intracytoplasmic sperm injection (ICSI), in vitro fertilization (IVF), and naturally. DESIGN: Case-control study. SETTING: Research institution. PATIENT(S): A total of 185 female newborns, including 60 conceived by intracytoplasmic sperm injection (ICSI), 73 by in vitro fertilization (IVF), and 52 naturally conceived (NC). INTERVENTION(S): DNA was extracted from umbilical cord blood after birth. MAIN OUTCOME MEASURE(S): XCI skewing values determined by assaying allelic ratio of methylated alleles at the androgen receptor (AR), fragile X mental retardation 1 (FMR1), and DXS6673E loci. RESULT(S): In the comparison of the ICSI, IVF, and NC populations, the frequency of skewing ≥75% (7.0% vs. 5.7% vs. 2.0%, respectively) or ≥90% (0 vs. 1.4% vs. 2.0%, respectively) was not statistically significantly different. The mean level of skewing between the ICSI, IVF, and NC groups also did not differ (63.7% vs. 61.8% vs. 60.7%, respectively). Skewing variability was observed in the placentas of the two extremely skewed cases. The parental origin of the preferentially inactivated X chromosome in the extremely skewed IVF and NC cases were maternal and paternal, respectively. CONCLUSION(S): The assisted reproductive technologies of ICSI and IVF do not appear to affect XCI skewing. Skewing variability within the placentas analyzed supports the theory that weaker selective pressures occur in the placenta that could result in skewed inactivation. Our study is the largest to date to investigate this epigenetic phenomenon in infants conceived by ICSI and IVF alongside age-matched NC controls. Copyright © 2014 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved. KEYWORDS: Assisted reproductive technology, ICSI, IVF, X-chromosome inactivation, epigenetics

PMID 24726222


X Chromosome Inactivation and Epigenetic Responses to Cellular Reprogramming

Annu Rev Genomics Hum Genet. 2013 May 6. [Epub ahead of print]

Lessing D, Anguera MC, Lee JT. Source Howard Hughes Medical Institute, Department of Molecular Biology, and Department of Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114; email:


Reprogramming somatic cells to derive induced pluripotent stem cells (iPSCs) has provided a new method to model disease and holds great promise for regenerative medicine. Although genetically identical to their donor somatic cells, iPSCs undergo substantial changes in the epigenetic landscape during reprogramming. One such epigenetic process, X chromosome inactivation (XCI), has recently been shown to vary widely in human female iPSCs and embryonic stem cells (ESCs). XCI is a form of dosage compensation whose chief regulator is the noncoding RNA Xist. In mouse iPSCs and ESCs, Xist expression and XCI strictly correlate with the pluripotent state, but no such correlation exists in humans. Lack of XIST expression in human cells is linked to reduced developmental potential and an altered transcriptional profile, including upregulation of genes associated with cancer, which has therefore led to concerns about the safety of pluripotent stem cells for use in regenerative medicine. In this review, we describe how different states of XIST expression define three classes of female human pluripotent stem cells and explore progress in discovering the reasons for these variations and how they might be countered. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 14 is August 31, 2013. Please see for revised estimates.

PMID 23662665


Fifty years of X-inactivation research

Development. 2011 Dec;138(23):5049-55. Gendrel AV, Heard E. Source Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, CNRS UMR3215, INSERM U934, 75248 Paris, France.


The third X-inactivation meeting 'Fifty years of X-inactivation research', which celebrated the fiftieth anniversary of Mary Lyon's formulation of the X-inactivation hypothesis, was an EMBO workshop held in Oxford, UK, in July 2011. This conference brought together the usual suspects from the field, as well as younger researchers, to discuss recent advances in X-inactivation research. Here, we review the results presented at the meeting and highlight some of the exciting progress that has been made. We also discuss the future challenges for the field, which aim to further our understanding of the developmental regulation of X inactivation, the randomness (or skewing) of X inactivation, and the diverse strategies used by mammalian species to mediate X inactivation.

PMID 22069183

The demoiselle of X-inactivation: 50 years old and as trendy and mesmerising as ever

PLoS Genet. 2011 Jul;7(7):e1002212. Epub 2011 Jul 21. Morey C, Avner P. Source Institut Pasteur, Unité de Génétique Moléculaire Murine, CNRS, URA2578, Paris, France.


In humans, sexual dimorphism is associated with the presence of two X chromosomes in the female, whereas males possess only one X and a small and largely degenerate Y chromosome. How do men cope with having only a single X chromosome given that virtually all other chromosomal monosomies are lethal? Ironically, or even typically many might say, women and more generally female mammals contribute most to the job by shutting down one of their two X chromosomes at random. This phenomenon, called X-inactivation, was originally described some 50 years ago by Mary Lyon and has captivated an increasing number of scientists ever since. The fascination arose in part from the realisation that the inactive X corresponded to a dense heterochromatin mass called the "Barr body" whose number varied with the number of Xs within the nucleus and from the many intellectual questions that this raised: How does the cell count the X chromosomes in the nucleus and inactivate all Xs except one? What kind of molecular mechanisms are able to trigger such a profound, chromosome-wide metamorphosis? When is X-inactivation initiated? How is it transmitted to daughter cells and how is it reset during gametogenesis? This review retraces some of the crucial findings, which have led to our current understanding of a biological process that was initially considered as an exception completely distinct from conventional regulatory systems but is now viewed as a paradigm "par excellence" for epigenetic regulation.

PMID 21811421

Histone acetylation controls the inactive X chromosome replication dynamics

Nat Commun. 2011 Mar;2:222.

Casas-Delucchi CS, Brero A, Rahn HP, Solovei I, Wutz A, Cremer T, Leonhardt H, Cardoso MC. Source 1] Department of Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany. [2] Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany. [3].


In mammals, dosage compensation between male and female cells is achieved by inactivating one female X chromosome (Xi). Late replication of Xi was proposed to be involved in the maintenance of its silenced state. Here, we show a highly synchronous replication of the Xi within 1 to 2 h during early-mid S-phase by following DNA replication in living mammalian cells with green fluorescent protein-tagged replication proteins. The Xi was replicated before or concomitant with perinuclear or perinucleolar facultative heterochromatin and before constitutive heterochromatin. Ectopic expression of the X-inactive-specific transcript (Xist) gene from an autosome imposed the same synchronous replication pattern. We used mutations and chemical inhibition affecting different epigenetic marks as well as inducible Xist expression and we demonstrate that histone hypoacetylation has a key role in controlling Xi replication. The epigenetically controlled, highly coordinated replication of the Xi is reminiscent of embryonic genome replication in flies and frogs before genome activation and might be a common feature of transcriptionally silent chromatin.

PMID: 21364561


Active Chromatin Marks Are Retained on X Chromosomes Lacking Gene or Repeat Silencing Despite XIST/Xist Expression in Somatic Cell Hybrids

Analysis of active and inactive X chromosome architecture reveals the independent organization of 30 nm and large-scale chromatin structures

Mol Cell. 2010 Nov 12;40(3):397-409.

Naughton C, Sproul D, Hamilton C, Gilbert N. S ource Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XR, UK. Abstract Using a genetic model, we present a high-resolution chromatin fiber analysis of transcriptionally active (Xa) and inactive (Xi) X chromosomes packaged into euchromatin and facultative heterochromatin. Our results show that gene promoters have an open chromatin structure that is enhanced upon transcriptional activation but the Xa and the Xi have similar overall 30 nm chromatin fiber structures. Therefore, the formation of facultative heterochromatin is dependent on factors that act at a level above the 30 nm fiber and transcription does not alter bulk chromatin fiber structures. However, large-scale chromatin structures on Xa are decondensed compared with the Xi and transcription inhibition is sufficient to promote large-scale chromatin compaction. We show a link between transcription and large-scale chromatin packaging independent of the bulk 30 nm chromatin fiber and propose that transcription, not the global compaction of 30 nm chromatin fibers, determines the cytological appearance of large-scale chromatin structures.

Copyright © 2010 Elsevier Inc. All rights reserved.

PMID: 21070966

Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse

BMC Genomics. 2010 Nov 3;11:614.

Reinius B, Shi C, Hengshuo L, Sandhu KS, Radomska KJ, Rosen GD, Lu L, Kullander K, Williams RW, Jazin E. Source Department of Evolution and Development, EBC, Uppsala University, Sweden. Abstract BACKGROUND: Sexual dimorphism in brain gene expression has been recognized in several animal species. However, the relevant regulatory mechanisms remain poorly understood. To investigate whether sex-biased gene expression in mammalian brain is globally regulated or locally regulated in diverse brain structures, and to study the genomic organisation of brain-expressed sex-biased genes, we performed a large scale gene expression analysis of distinct brain regions in adult male and female mice.

RESULTS: This study revealed spatial specificity in sex-biased transcription in the mouse brain, and identified 173 sex-biased genes in the striatum; 19 in the neocortex; 12 in the hippocampus and 31 in the eye. Genes located on sex chromosomes were consistently over-represented in all brain regions. Analysis on a subset of genes with sex-bias in more than one tissue revealed Y-encoded male-biased transcripts and X-encoded female-biased transcripts known to escape X-inactivation. In addition, we identified novel coding and non-coding X-linked genes with female-biased expression in multiple tissues. Interestingly, the chromosomal positions of all of the female-biased non-coding genes are in close proximity to protein-coding genes that escape X-inactivation. This defines X-chromosome domains each of which contains a coding and a non-coding female-biased gene. Lack of repressive chromatin marks in non-coding transcribed loci supports the possibility that they escape X-inactivation. Moreover, RNA-DNA combined FISH experiments confirmed the biallelic expression of one such novel domain.

CONCLUSION: This study demonstrated that the amount of genes with sex-biased expression varies between individual brain regions in mouse. The sex-biased genes identified are localized on many chromosomes. At the same time, sexually dimorphic gene expression that is common to several parts of the brain is mostly restricted to the sex chromosomes. Moreover, the study uncovered multiple female-biased non-coding genes that are non-randomly co-localized on the X-chromosome with protein-coding genes that escape X-inactivation. This raises the possibility that expression of long non-coding RNAs may play a role in modulating gene expression in domains that escape X-inactivation in mouse.

PMID: 21047393

Variations of X chromosome inactivation occur in early passages of female human embryonic stem cells

PLoS One. 2010 Jun 25;5(6):e11330.

Dvash T, Lavon N, Fan G. Source Department of Human Genetics and The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America. Abstract X chromosome inactivation (XCI) is a dosage compensation mechanism essential for embryonic development and cell physiology. Human embryonic stem cells (hESCs) derived from inner cell mass (ICM) of blastocyst stage embryos have been used as a model system to understand XCI initiation and maintenance. Previous studies of undifferentiated female hESCs at intermediate passages have shown three possible states of XCI; 1) cells in a pre-XCI state, 2) cells that already exhibit XCI, or 3) cells that never undergo XCI even upon differentiation. In this study, XCI status was assayed in ten female hESC lines between passage 5 and 15 to determine whether XCI variations occur in early passages of hESCs. Our results show that three different states of XCI already exist in the early passages of hESC. In addition, we observe one cell line with skewed XCI and preferential expression of X-linked genes from the paternal allele, while another cell line exhibits random XCI. Skewed XCI in undifferentiated hESCs may be due to clonal selection in culture instead of non-random XCI in ICM cells. We also found that XIST promoter methylation is correlated with silencing of XIST transcripts in early passages of hESCs, even in the pre-XCI state. In conclusion, XCI variations already take place in early passages of hESCs, which may be a consequence of in vitro culture selection during the derivation process. Nevertheless, we cannot rule out the possibility that XCI variations in hESCs may reflect heterogeneous XCI states in ICM cells that stochastically give rise to hESCs.

PMID: 20593031


Meiotic sex chromosome inactivation

Development. 2007 May;134(10):1823-31. Epub 2007 Feb 28.

Turner JM.

Division of Stem Cell Biology and Developmental Genetics, MRC NIMR, The Ridgeway, Mill Hill, London NW7 1AA, UK. Abstract X chromosome inactivation is most commonly studied in the context of female mammalian development, where it performs an essential role in dosage compensation. However, another form of X-inactivation takes place in the male, during spermatogenesis, as germ cells enter meiosis. This second form of X-inactivation, called meiotic sex chromosome inactivation (MSCI) has emerged as a novel paradigm for studying the epigenetic regulation of gene expression. New studies have revealed that MSCI is a special example of a more general mechanism called meiotic silencing of unsynapsed chromatin (MSUC), which silences chromosomes that fail to pair with their homologous partners and, in doing so, may protect against aneuploidy in subsequent generations. Furthermore, failure in MSCI is emerging as an important etiological factor in meiotic sterility.

PMID: 17329371


The X chromosome is organized into a gene-rich outer rim and an internal core containing silenced nongenic sequences

Proc Natl Acad Sci U S A. 2006 May 16;103(20):7688-93. Epub 2006 May 8.

Clemson CM, Hall LL, Byron M, McNeil J, Lawrence JB. Department of Cell Biology, University of Massachusetts Medical Center, 55 Lake Avenue North, Worcester, MA 01655, USA.


We investigated whether genes escape X chromosome inactivation by positioning outside of the territory defined by XIST RNA. Results reveal an unanticipated higher order organization of genes and noncoding sequences. All 15 X-linked genes, regardless of activity, position on the border of the XIST RNA territory, which resides outside of the DAPI-dense Barr body. Although more strictly delineated on the inactive X chromosome (Xi), all genes localized predominantly to the outer rim of the Xi and active X chromosome. This outer rim is decorated only by X chromosome DNA paints and is excluded from both the XIST RNA and dense DAPI staining. The only DNA found well within the Barr body and XIST RNA territory was centromeric and Cot-1 DNA; hence, the core of the X chromosome essentially excludes genes and is composed primarily of noncoding repeat-rich DNA. Moreover, we show that this core of repetitive sequences is expressed throughout the nucleus yet is silenced throughout Xi, providing direct evidence for chromosome-wide regulation of "junk" DNA transcription. Collective results suggest that the Barr body, long presumed to be the physical manifestation of silenced genes, is in fact composed of a core of silenced noncoding DNA. Instead of acting at a local gene level, XIST RNA appears to interact with and silence core architectural elements to effectively condense and shut down the Xi.

PMID: 16682630