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

Yukio Yasukochi, Osamu Maruyama, Milind C. Mahajan, Carolyn Padden, Ghia M. Euskirchen, Vincent Schulz, Hideki Hirakawa, Satoru Kuhara, Xing Hua Pan, Peter E. Newburger, Michael Snyder, Sherman M. Weissman

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Abstract

The DNA methylation status of human X chromosomes from male and female neutrophils was identified by high-throughput sequencing of HpaII and MspI digested fragments. In the intergenic and intragenic regions on the X chromosome, the sites outside CpG islands were heavily hypermethylated to the same degree in both genders. Nearly half of X chromosome promoters were either hypomethylated or hypermethylated in both females and males. Nearly one third of X chromosome promoters were a mixture of hypomethylated and heterogeneously methylated sites in females and were hypomethylated in males. Thus, a large fraction of genes that are silenced on the inactive X chromosome are hypomethylated in their promoter regions. These genes frequently belong to the evolutionarily younger strata of the X chromosome. The promoters that were hypomethylated at more than two sites contained most of the genes that escaped silencing on the inactive X chromosome. The overall levels of expression of X-linked genes were indistinguishable in females and males, regardless of the methylation state of the inactive X chromosome. Thus, in addition to DNA methylation, other factors are involved in the fine tuning of gene dosage compensation in neutrophils.

Original languageEnglish
Pages (from-to)3704-3709
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume107
Issue number8
DOIs
Publication statusPublished - Feb 23 2010

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X Chromosome
DNA Methylation
Neutrophils
Gene Expression
Chromosomes, Human, X
X-Linked Genes
CpG Islands
Intergenic DNA
Gene Silencing
Genetic Promoter Regions
Methylation
Genes

All Science Journal Classification (ASJC) codes

  • General

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X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils. / Yasukochi, Yukio; Maruyama, Osamu; Mahajan, Milind C.; Padden, Carolyn; Euskirchen, Ghia M.; Schulz, Vincent; Hirakawa, Hideki; Kuhara, Satoru; Pan, Xing Hua; Newburger, Peter E.; Snyder, Michael; Weissman, Sherman M.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 107, No. 8, 23.02.2010, p. 3704-3709.

Research output: Contribution to journalArticle

Yasukochi, Y, Maruyama, O, Mahajan, MC, Padden, C, Euskirchen, GM, Schulz, V, Hirakawa, H, Kuhara, S, Pan, XH, Newburger, PE, Snyder, M & Weissman, SM 2010, 'X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils', Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 8, pp. 3704-3709. https://doi.org/10.1073/pnas.0914812107
Yasukochi, Yukio ; Maruyama, Osamu ; Mahajan, Milind C. ; Padden, Carolyn ; Euskirchen, Ghia M. ; Schulz, Vincent ; Hirakawa, Hideki ; Kuhara, Satoru ; Pan, Xing Hua ; Newburger, Peter E. ; Snyder, Michael ; Weissman, Sherman M. / X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils. In: Proceedings of the National Academy of Sciences of the United States of America. 2010 ; Vol. 107, No. 8. pp. 3704-3709.
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