scholarly journals Single Cell Expression Data Reveal Human Genes that Escape X-Chromosome Inactivation

2016 ◽  
Author(s):  
Kerem Wainer-Katsir ◽  
Michal Linial
Keyword(s):  
X Chromosome ◽  
Direct Method ◽  
Single Cells ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
P Value ◽  
Expression Data ◽  
Rna Seq ◽  
Specific Expression ◽  
Biallelic Expression

ABSTRACTSex chromosomes pose an inherent genetic imbalance between genders. In mammals, one of the female’s X-chromosomes undergoes inactivation (Xi). Indirect measurements estimate that about 20% of Xi genes completely or partially escape inactivation. The identity of these escapee genes and their propensity to escape inactivation remain unsolved. A direct method for identifying escapees was applied by quantifying differential allelic expression from single cells. RNA-Seq fragments were assigned to informative SNPs which were labeled by the appropriate parental haplotype. This method was applied for measuring allelic specific expression from Chromosome-X (ChrX) and an autosomal chromosome as a control. We applied the protocol for measuring biallelic expression from ChrX to 104 primary fibroblasts. Out of 215 genes that were considered, only 13 genes (6%) were associated with biallelic expression. The sensitivity of escapees' identification was increased by combining SNP mapping for parental diploid genomes together with RNA-Seq from clonal single cells (25 lymphoblasts). Using complementary protocols, referred to as strict and relaxed, we confidently identified 25 and 31escapee genes, respectively. When pooled versions of 30 and 100 cells were used, <50% of these genes were revealed. We assessed the generality of our protocols in view of an escapee catalog compiled from indirect methods. The overlap between the escapee catalog and the genes’ list from this study is statistically significant (P-value of E-07). We conclude that single cells’ expression data are instrumental for studying X-inactivation with an improved sensitivity. Finally, our results support the emerging notion of the non-deterministic nature of genes that escape X-chromosome inactivation.

scholarly journals A Functional Chromatin Domain Does Not Resist X Chromosome Inactivation: Silencing of cLys Correlates with Methylation of a Dual Promoter-Replication Origin

2002 ◽  
Vol 22 (13) ◽  
pp. 4667-4676 ◽  
Author(s):  
Suyinn Chong ◽  
Joanna Kontaraki ◽  
Constanze Bonifer ◽  
Arthur D. Riggs
Keyword(s):  
X Chromosome ◽  
Copy Number ◽  
Cpg Island ◽  
Regulatory Elements ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Chromatin Domain ◽  
Specific Expression ◽  
Position Effects ◽  
Chicken Lysozyme

ABSTRACT To investigate the molecular mechanism(s) involved in the propagation and maintenance of X chromosome inactivation (XCI), the 21.4-kb chicken lysozyme (cLys) chromatin domain was inserted into the Hprt locus on the mouse X chromosome. The inserted fragment includes flanking matrix attachment regions (MARs), an origin of bidirectional replication (OBR), and all the cis-regulatory elements required for correct tissue-specific expression of cLys. It also contains a recently identified and widely expressed second gene, cGas41. The cLys domain is known to function as an autonomous unit resistant to chromosomal position effects, as evidenced by numerous transgenic mouse lines showing copy-number-dependent and development-specific expression of cLys in the myeloid lineage. We asked the questions whether this functional chromatin domain was resistant to XCI and whether the X inactivation signal could spread across an extended region of avian DNA. A generally useful method was devised to generate pure populations of macrophages with the transgene either on the active (Xa) or the inactive (Xi) chromosome. We found that (i) cLys and cGas41 are expressed normally from the Xa; (ii) the cLys chromatin domain, even when bracketed by MARs, is not resistant to XCI; (iii) transcription factors are excluded from lysozyme enhancers on the Xi; and (iv) inactivation correlates with methylation of a CpG island that is both an OBR and a promoter of the cGas41 gene.

Studying X chromosome inactivation in the single-cell genomic era

2018 ◽  
Vol 46 (3) ◽  
pp. 577-586 ◽  
Author(s):  
Andrew Keniry ◽  
Marnie E. Blewitt
Keyword(s):  
Single Cell ◽  
X Chromosome ◽  
Single Cells ◽  
Transcriptional Silencing ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
The Novel ◽  
Ideal Model ◽  
Single Cell Genomics ◽  
Silent State

Single-cell genomics is set to revolutionise our understanding of how epigenetic silencing works; by studying specific epigenetic marks or chromatin conformations in single cells, it is possible to ask whether they cause transcriptional silencing or are instead a consequence of the silent state. Here, we review what single-cell genomics has revealed about X chromosome inactivation, perhaps the best characterised mammalian epigenetic process, highlighting the novel findings and important differences between mouse and human X inactivation uncovered through these studies. We consider what fundamental questions these techniques are set to answer in coming years and propose that X chromosome inactivation is an ideal model to study gene silencing by single-cell genomics as technical limitations are minimised through the co-analysis of hundreds of genes.

scholarly journals Molecular signatures of X chromosome inactivation and associations with clinical outcomes in epithelial ovarian cancer

2018 ◽  
Vol 28 (8) ◽  
pp. 1331-1342 ◽  
Author(s):  
Stacey J Winham ◽  
Nicholas B Larson ◽  
Sebastian M Armasu ◽  
Zachary C Fogarty ◽  
Melissa C Larson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Dna Methylation ◽  
X Chromosome ◽  
Strong Association ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Specific Expression ◽  
Cluster Membership ◽  
Promoter Dna

AbstractX chromosome inactivation (XCI) is a key epigenetic gene expression regulatory process, which may play a role in women’s cancer. In particular tissues, some genes are known to escape XCI, yet patterns of XCI in ovarian cancer (OC) and their clinical associations are largely unknown. To examine XCI in OC, we integrated germline genotype with tumor copy number, gene expression and DNA methylation information from 99 OC patients. Approximately 10% of genes showed different XCI status (either escaping or being subject to XCI) compared with the studies of other tissues. Many of these genes are known oncogenes or tumor suppressors (e.g. DDX3X, TRAPPC2 and TCEANC). We also observed strong association between cis promoter DNA methylation and allele-specific expression imbalance (P = 2.0 × 10−10). Cluster analyses of the integrated data identified two molecular subgroups of OC patients representing those with regulated (N = 47) and dysregulated (N = 52) XCI. This XCI cluster membership was associated with expression of X inactive specific transcript (P = 0.002), a known driver of XCI, as well as age, grade, stage, tumor histology and extent of rl disease following surgical debulking. Patients with dysregulated XCI (N = 52) had shorter time to recurrence (HR = 2.34, P = 0.001) and overall survival time (HR = 1.87, P = 0.02) than those with regulated XCI, although results were attenuated after covariate adjustment. Similar findings were observed when restricted to high-grade serous tumors. We found evidence of a unique OC XCI profile, suggesting that XCI may play an important role in OC biology. Additional studies to examine somatic changes with paired tumor-normal tissue are needed.

scholarly journals Time-resolved structured illumination microscopy reveals key principles of Xist RNA spreading

2020 ◽  
Author(s):  
Lisa Rodermund ◽  
Heather Coker ◽  
Roel Oldenkamp ◽  
Guifeng Wei ◽  
Joseph Bowness ◽  
...  
Keyword(s):  
X Chromosome ◽  
Dynamic Properties ◽  
Single Cells ◽  
Super Resolution ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Rna Molecules ◽  
Xist Rna

AbstractXist RNA directs the process of X-chromosome inactivation in mammals by spreading in cis along the chromosome from which it is transcribed and recruiting chromatin modifiers to silence gene transcription. To elucidate mechanisms of Xist RNA cis-confinement, we established a sequential dual color labeling, super-resolution imaging approach to trace individual Xist RNA molecules over time, enabling us to define fundamental parameters of spreading. We demonstrate a feedback mechanism linking Xist RNA synthesis and degradation, and an unexpected physical coupling between preceding and newly synthesized Xist RNA molecules. Additionally, we show that the protein SPEN, a key factor for Xist-mediated gene-silencing, has a distinct function in Xist RNA localization, stability and in coupling behavior. Our results provide important insights towards understanding the unique dynamic properties of Xist RNA.One Sentence SummaryVisualizing Xist RNA dynamics in single cells during X chromosome inactivation

scholarly journals H3K9 methyltransferase EHMT2/G9a controls ERVK-driven noncanonical imprinted genes

Epigenomics ◽  
2021 ◽  
Author(s):  
Tie-Bo Zeng ◽  
Nicholas Pierce ◽  
Ji Liao ◽  
Piroska E Szabó
Keyword(s):  
Dna Methylation ◽  
X Chromosome ◽  
X Chromosome Inactivation ◽  
Paternal Allele ◽  
Imprinted Genes ◽  
Rna Seq ◽  
Maternal Allele ◽  
Specific Expression ◽  
Allele Specific ◽  
Ectoplacental Cone

Aim: Paternal allele-specific expression of noncanonical imprinted genes in the extraembryonic lineages depends on an H3K27me3-based imprint in the oocyte, which is not a lasting mark. We hypothesized that EHMT2, the main euchromatic H3K9 dimethyltransferase, also has a role in controlling noncanonical imprinting. Methods: We carried out allele-specific total RNA-seq analysis in the ectoplacental cone of somite-matched 8.5 days post coitum embryos using reciprocal mouse crosses. Results: We found that the maternal allele of noncanonical imprinted genes was derepressed from its ERVK promoter in the Ehmt2-/- ectoplacental cone. In Ehmt2-/- embryos, loss of DNA methylation accompanied biallelic derepression of the ERVK promoters. Canonical imprinting and imprinted X chromosome inactivation were generally undisturbed. Conclusion: EHMT2 is essential for repressing the maternal allele in noncanonical imprinting.

scholarly journals Diverse mechanisms for epigenetic imprinting in mammals

2021 ◽  
Author(s):  
Daniel Andergassen ◽  
Zachary D Smith ◽  
John L Rinn ◽  
Alexander Meissner
Keyword(s):  
Genomic Imprinting ◽  
X Chromosome ◽  
Gene Clusters ◽  
Endogenous Retrovirus ◽  
X Chromosome Inactivation ◽  
Polycomb Group ◽  
Chromosome Inactivation ◽  
Epigenetic Mechanisms ◽  
Specific Expression ◽  
Allele Specific

Genomic imprinting and X chromosome inactivation (XCI) require epigenetic mechanisms to direct allele-specific expression. Despite their critical roles in embryonic development, how universal epigenetic regulators coordinate these specific tasks from single locus to chromosome-scale remains understudied. Here, we systematically disrupted multiple essential epigenetic pathways within polymorphic F1 zygotes to examine postimplantation effects on canonical and non-canonical genomic imprinting as well as X chromosome inactivation. We find that DNA methylation and Polycomb group repressors are both indispensable for autosomal imprinting, albeit at distinct gene sets. Moreover, the extraembryonic ectoderm relies on a broader spectrum of unique imprinting mechanisms, including non-canonical targeting of maternal endogenous retrovirus (ERV) driven promoters by G9a. We further utilize our data to identify Polycomb dependent and independent gene clusters on the imprinted X chromosome, which appears to reflect distinct domains of Xist-mediated suppression. Our data has allowed us to assemble a comprehensive inventory of the epigenetic mechanisms utilized in eutherian mammals to maintain parent-specific imprinting, including an expanded view of the placental lineage that comprises multiple unique pathways.

scholarly journals Unusual maintenance of X chromosome inactivation predisposes female lymphocytes for increased expression from the inactive X

2016 ◽  
Vol 113 (14) ◽  
pp. E2029-E2038 ◽  
Author(s):  
Jianle Wang ◽  
Camille M. Syrett ◽  
Marianne C. Kramer ◽  
Arindam Basu ◽  
Michael L. Atchison ◽  
...  
Keyword(s):  
B Cells ◽  
X Chromosome ◽  
Lupus Erythematosus ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Fish Analysis ◽  
Biallelic Expression ◽  
Xist Rna

Females have a greater immunological advantage than men, yet they are more prone to autoimmune disorders. The basis for this sex bias lies in the X chromosome, which contains many immunity-related genes. Female mammals use X chromosome inactivation (XCI) to generate a transcriptionally silent inactive X chromosome (Xi) enriched with heterochromatic modifications and XIST/Xist RNA, which equalizes gene expression between the sexes. Here, we examine the maintenance of XCI in lymphocytes from females in mice and humans. Strikingly, we find that mature naïve T and B cells have dispersed patterns of XIST/Xist RNA, and they lack the typical heterochromatic modifications of the Xi. In vitro activation of lymphocytes triggers the return of XIST/Xist RNA transcripts and some chromatin marks (H3K27me3, ubiquitin-H2A) to the Xi. Single-cell RNA FISH analysis of female T cells revealed that the X-linked immunity genes CD40LG and CXCR3 are biallelically expressed in some cells. Using knockout and knockdown approaches, we find that Xist RNA-binding proteins, YY1 and hnRNPU, are critical for recruitment of XIST/Xist RNA back to the Xi. Furthermore, we examined B cells from patients with systemic lupus erythematosus, an autoimmune disorder with a strong female bias, and observed different XIST RNA localization patterns, evidence of biallelic expression of immunity-related genes, and increased transcription of these genes. We propose that the Xi in female lymphocytes is predisposed to become partially reactivated and to overexpress immunity-related genes, providing the first mechanistic evidence to our knowledge for the enhanced immunity of females and their increased susceptibility for autoimmunity.

scholarly journals Inferring genes that escape X-Chromosome inactivation reveals important contribution of variable escape genes to sex-biased diseases

2021 ◽  
Author(s):  
Renan Sauteraud ◽  
Jill M. Stahl ◽  
Jesica James ◽  
Marisa Englebright ◽  
Fang Chen ◽  
...  
Keyword(s):  
X Chromosome ◽  
Association Studies ◽  
Large Population ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Autosomal Gene ◽  
Homologous Gene ◽  
Data Sets ◽  
Rna Seq ◽  
Data Set

The X Chromosome plays an important role in human development and disease. However, functional genomic and disease association studies of X genes greatly lag behind autosomal gene studies, in part owing to the unique biology of X-Chromosome inactivation (XCI). Because of XCI, most genes are only expressed from one allele. Yet, ∼30% of X genes “escape” XCI and are transcribed from both alleles, many only in a proportion of the population. Such interindividual differences are likely to be disease relevant, particularly for sex-biased disorders. To understand the functional biology for X-linked genes, we developed X-Chromosome inactivation for RNA-seq (XCIR), a novel approach to identify escape genes using bulk RNA-seq data. Our method, available as an R package, is more powerful than alternative approaches and is computationally efficient to handle large population-scale data sets. Using annotated XCI states, we examined the contribution of X-linked genes to the disease heritability in the United Kingdom Biobank data set. We show that escape and variable escape genes explain the largest proportion of X heritability, which is in large part attributable to X genes with Y homology. Finally, we investigated the role of each XCI state in sex-biased diseases and found that although XY homologous gene pairs have a larger overall effect size, enrichment for variable escape genes is significantly increased in female-biased diseases. Our results, for the first time, quantitate the importance of variable escape genes for the etiology of sex-biased disease, and our pipeline allows analysis of larger data sets for a broad range of phenotypes.

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