DNA Methylation and the Control of Gene Expression on the Human X Chromosome

1983 ◽  
Vol 47 (0) ◽  
pp. 631-637 ◽  
Author(s):  
L.J. Shapiro ◽  
T. Mohandas
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
X Chromosome ◽  
Control Of Gene Expression

scholarly journals X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils

2010 ◽  
Vol 107 (8) ◽  
pp. 3704-3709 ◽  
Author(s):  
Yukio Yasukochi ◽  
Osamu Maruyama ◽  
Milind C. Mahajan ◽  
Carolyn Padden ◽  
Ghia M. Euskirchen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
X Chromosome ◽  
Genomic Dna ◽  
Male And Female

Changes in DNA methylation during mouse embryonic development in relation to X-chromosome activity and imprinting

1990 ◽  
Vol 326 (1235) ◽  
pp. 299-312 ◽  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Embryonic Development ◽  
X Chromosome ◽  
De Novo ◽  
Germ Line ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Chromatin Configuration ◽  
Methylation Patterns

Changing DNA methylation patterns during embryonic development are discussed in relation to differential gene expression, changes in X-chromosome activity and genomic imprinting. Sperm DNA is more methylated than oocyte DNA, both overall and for specific sequences. The methylation difference between the gametes could be one of the mechanisms (along with chromatin structure) regulating initial differences in expression of parental alleles in early development. There is a loss of methylation during development from the morula to the blastocyst and a marked decrease in methylase activity. De novo methylation becomes apparent around the time of implantation and occurs to a lesser extent in extra-embryonic tissue DNA. In embryonic DNA, de novo methylation begins at the time of random X-chromosome inactivation but it continues to occur after X-chromosome inactivation and may be a mechanism that irreversibly fixes specific patterns of gene expression and X-chromosome inactivity in the female. The germ line is probably delineated before extensive de novo methylation and hence escapes this process. The marked undermethylation of the germ line DNA may be a prerequisite for X-chromosome reactivation. The process underlying reactivation and removal of parent-specific patterns of gene expression may be changes in chromatin configuration associated with meiosis and a general reprogramming of the germ line to developmental totipotency.

scholarly journals Long-range control of gene expression via RNA-directed DNA methylation

PLoS Genetics ◽  
2017 ◽  
Vol 13 (5) ◽  
pp. e1006749 ◽  
Author(s):  
M. Jordan Rowley ◽  
M. Hafiz Rothi ◽  
Gudrun Böhmdorfer ◽  
Jan Kuciński ◽  
Andrzej T. Wierzbicki
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Long Range ◽  
Control Of Gene Expression

scholarly journals AFF3-DNA methylation interplay in maintaining the mono-allelic expression pattern of XIST in terminally differentiated cells

2018 ◽  
Vol 11 (9) ◽  
pp. 761-769 ◽  
Author(s):  
Yue Zhang ◽  
Chao Wang ◽  
Xiaoxu Liu ◽  
Qian Yang ◽  
Hongliang Ji ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Expression Pattern ◽  
X Chromosome ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Allelic Expression ◽  
Elongation Complex ◽  
Regulatory Processes ◽  
Differentiated Cells

Abstract X chromosome inactivation and genomic imprinting are two classic epigenetic regulatory processes that cause mono-allelic gene expression. In female mammals, mono-allelic expression of the long non-coding RNA gene X-inactive specific transcript (XIST) is essential for initiation of X chromosome inactivation upon differentiation. We have previously demonstrated that the central factor of super elongation complex-like 3 (SEC-L3), AFF3, is enriched at gamete differentially methylated regions (DMRs) of the imprinted loci and regulates the imprinted gene expression. Here, we found that AFF3 can also bind to the DMR downstream of the XIST promoter. Knockdown of AFF3 leads to de-repression of the inactive allele of XIST in terminally differentiated cells. In addition, the binding of AFF3 to the XIST DMR relies on DNA methylation and also regulates DNA methylation level at DMR region. However, the KAP1-H3K9 methylation machineries, which regulate the imprinted loci, might not play major roles in maintaining the mono-allelic expression pattern of XIST in these cells. Thus, our results suggest that the differential mechanisms involved in the XIST DMR and gDMR regulation, which both require AFF3 and DNA methylation.

scholarly journals Parent-of-origin differences in DNA methylation of X chromosome genes in T lymphocytes

2019 ◽  
Vol 116 (52) ◽  
pp. 26779-26787 ◽  
Author(s):  
Lisa C. Golden ◽  
Yuichiro Itoh ◽  
Noriko Itoh ◽  
Sonia Iyengar ◽  
Patrick Coit ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Sex Differences ◽  
T Lymphocytes ◽  
Immune Responses ◽  
X Chromosome ◽  
F1 Hybrid ◽  
Parent Of Origin ◽  
X Gene ◽  
Global Increase

Many autoimmune diseases are more frequent in females than in males in humans and their mouse models, and sex differences in immune responses have been shown. Despite extensive studies of sex hormones, mechanisms underlying these sex differences remain unclear. Here, we focused on sex chromosomes using the “four core genotypes” model in C57BL/6 mice and discovered that the transcriptomes of both autoantigen and anti-CD3/CD28 stimulated CD4+T lymphocytes showed higher expression of a cluster of 5 X genes when derived from XY as compared to XX mice. We next determined if higher expression of an X gene in XY compared to XX could be due to parent-of-origin differences in DNA methylation of the X chromosome. We found a global increase in DNA methylation on the X chromosome of paternal as compared to maternal origin. Since DNA methylation usually suppresses gene expression, this result was consistent with higher expression of X genes in XY cells because XY cells always express from the maternal X chromosome. In addition, gene expression analysis of F1 hybrid mice from CAST × FVB reciprocal crosses showed preferential gene expression from the maternal X compared to paternal X chromosome, revealing that these parent-of-origin effects are not strain-specific. SJL mice also showed a parent-of-origin effect on DNA methylation and X gene expression; however, which X genes were affected differed from those in C57BL/6. Together, this demonstrates how parent-of-origin differences in DNA methylation of the X chromosome can lead to sex differences in gene expression during immune responses.

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.

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