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. 2015 Mar 15;24(6):1528-39.
doi: 10.1093/hmg/ddu564. Epub 2014 Nov 7.

Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation

Allison M Cotton  1 , E Magda Price  2 , Meaghan J Jones  3 , Bradley P Balaton  1 , Michael S Kobor  3 , Carolyn J Brown  4
Affiliations

Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation

Allison M Cotton et al. Hum Mol Genet. .

Abstract

X-chromosome inactivation (XCI) achieves dosage compensation between males and females through the silencing of the majority of genes on one of the female X chromosomes. Thus, the female X chromosomes provide a unique opportunity to study euchromatin and heterochromatin of allelic regions within the same nuclear environment. We examined the interplay of DNA methylation (DNAm) with CpG density, transcriptional activity and chromatin state at genes on the X chromosome using over 1800 female samples analysed with the Illumina Infinium Human Methylation450 BeadChip. DNAm was used to predict an inactivation status for 63 novel transcription start sites (TSSs) across 27 tissues. There was high concordance of inactivation status across tissues, with 62% of TSSs subject to XCI in all 27 tissues examined, whereas 9% escaped from XCI in all tissues, and the remainder showed variable escape from XCI between females in subsets of tissues. Inter-female and twin data supported a model of predominately cis-acting influences on inactivation status. The level of expression from the inactive X relative to the active X correlated with the amount of female promoter DNAm to a threshold of ∼30%, beyond which genes were consistently subject to inactivation. The inactive X showed lower DNAm than the active X at intragenic and intergenic regions for genes subject to XCI, but not at genes that escape from inactivation. Our categorization of genes that escape from X inactivation provides candidates for sex-specific differences in disease.

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Figures

Figure 1.
Figure 1.
DNAm landscape of the X chromosome by CpG density and chromatin state. (A) Average male versus average female DNAm at X-linked CpGs demonstrates two major clusters of DNAm. Each grey square represents a single CpG (n = 8527); thick black kernel density lines help visualize the number of CpGs. (B) Box and whisker plots of the average female (F = light grey) and male (M = dark grey) DNAm based on CpG density (number of CpGs, HC: n = 3725, ICshore: n = 849, IC: n = 1402, LC: n = 2551). Significance based on a Wilcox test comparison of means is as follow: *P-values 0.05–0.001, **P-values 0.001–2.2E−16 and ***P-values < 2.2E − 16. (C) Summary of the influence of CpG density and chromatin marks on different X-linked genomic regions. Xi≤≥Xa indicates that there is not a clear relationship explaining the interaction between DNAm, X inactivation density and chromatin marks.
Figure 2.
Figure 2.
Female DNAm at TSSs shows a continuous range from subject to escape. (A) The average level of female DNAm in PB ranked from highest to lowest. XCI status of each TSS is denoted by colour (red: subject, purple: variable escape, grey: uncallable and green: escape) with error bars representing 1 SD. (B) Linear regression of AI and average female PB DNAm (red: subject, and green: escape). (C) Linear regression of average female DNAm on PB and BU. (D) Variable escape TSSs rarely disagreed in XCI status within a twin pair. A comparison of the DNAm within twin pairs and coloured according to WB twin XCI status revealed a high level of agreement in average twin TSS DNAm. Most TSSs had the same XCI status within a twin pair [subject in both: solid red circle, uncallable in both (solid grey circle) or escape in both (solid green circle)] or were uncallable in one twin but subject (open red circle) or escaped (open green circle) in the other twin. A limited number of variable escape TSSs were subject in one twin but escaped from XCI in the other (solid black circle). R2 and P-values for each linear regression are given on their respective graphs.
Figure 3.
Figure 3.
The majority of TSSs have the same XCI status in all examined tissues. (A) XCI status: escape (dark grey), variable escape (VE) (white), subject (black) and uncallable (light grey) in 27 tissues. Two letter tissue codes are found in Supplementary Material, Table S2 along with the complete tissue names. The number of female samples per tissue (n F) is given within each subject bar. (B) XCI status of the 489 TSSs that are informative in all 27 tissues, with the number of TSSs that had not been examined previously for XCI status listed in brackets (novel).
Figure 4.
Figure 4.
Transcription level has significant correlation with promoter DNAm as well as heterochromatin DNAm. Box and whisker plots comparing the average male (Xa) DNAm (PB) of the genes from the highest expression quartile and the lowest expression quartile by CpG density class (HIC, IC, LC; Ref. 22). (A) Promoters, (B) enhancers and insulators, (C) transcribed regions of genes and (D) repressed and heterochromatic regions were defined based on the chromatin states in Ref. . Significance based on a Wilcox test comparison of means is as follow: *P-values 0.05–0.001, **P-values 0.001–2.2E − 16 and ***P-values < 2.2E − 16). (E) Summary of X-linked DNAm patterns. The Xa and Xi DNAm patterns of females are summarized for genes that are subject to XCI and genes that escape from XCI. The average Xa and Xi DNAm values given are an average of all CpGs used in this analysis within the denoted category. The presence of individual CpGs (ovals) is meant only as a graphical representation and does not accurately denote CpG density. Chromatin states were combined with intergenic and intragenic data to separate CpGs within the gene body from CpGs between genes.
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References

    1. Carrel L., Willard H.F. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature. 2005;434:400–404. - PubMed
    1. Cotton A.M., Ge B., Light N., Adoue V., Pastinen T., Brown C.J. Analysis of expressed SNPs identifies variable extents of expression from the human inactive X chromosome. Genome Biol. 2013;14:R122. - PMC - PubMed
    1. Bellott D.W., Hughes J.F., Skaletsky H., Brown L.G., Pyntikova T., Cho T.J., Koutseva N., Zaghlul S., Graves T., Rock S., et al. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature. 2014;508:494–499. - PMC - PubMed
    1. Deng X., Berletch J.B., Nguyen D.K., Disteche C.M. X chromosome regulation: diverse patterns in development, tissues and disease. Nat. Rev. Genet. 2014;15:367–378. - PMC - PubMed
    1. Xu J., Deng X., Disteche C.M. Sex-specific expression of the X-linked histone demethylase gene Jarid1c in brain. PLoS ONE. 2008;3:e2553. - PMC - PubMed

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