X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils
Yukio Yasukochi,Osamu Maruyama,Milind Mahajan,Carolyn Padden,Ghia Euskirchen,Vincent P. Schulz,Hideki Hirakawa,Satoru Kuhara,Xinghua Pan,Peter E. Newburger,Michael Snyder,Sherman M. Weissman +11 more
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TLDR
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, suggesting that other factors are involved in the fine tuning of gene dosage compensation in neutrophils.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.read more
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Journal ArticleDOI
DNA methylation profiles of human active and inactive X chromosomes.
Andrew J. Sharp,Elisavet Stathaki,Eugenia Migliavacca,Manisha Brahmachary,Stephen B. Montgomery,Yann Dupré,Stylianos E. Antonarakis +6 more
TL;DR: This study provides a detailed analysis of the epigenetic profile of active and inactive X chromosomes, observing a global correlation between CGI methylation and the evolutionary age of X-chromosome strata, and that genes escaping XCI show increased methylation within gene bodies.
Journal ArticleDOI
Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation
Allison M. Cotton,Allison M. Cotton,Lucia Lam,Lucia Lam,Joslynn G. Affleck,Joslynn G. Affleck,Ian M. Wilson,Ian M. Wilson,Maria S. Peñaherrera,Maria S. Peñaherrera,Deborah E. McFadden,Michael S. Kobor,Michael S. Kobor,Wan L. Lam,Wan L. Lam,Wendy P. Robinson,Wendy P. Robinson,Carolyn J. Brown,Carolyn J. Brown +18 more
TL;DR: It is concluded that the XCI status predicted using methylation of X-linked promoters with CpG islands was usually the same as determined by expression analysis and that 12% ofX-linked genes examined show tissue-specific XCI whereby a gene has a different XCIstatus in at least one of the four tissues examined.
Journal ArticleDOI
Sexual epigenetic dimorphism in the human placenta: implications for susceptibility during the prenatal period.
Elizabeth M. Martin,Lisa Smeester,Paige A. Bommarito,Matthew R. Grace,Kim A. Boggess,Karl C.K. Kuban,Margaret R. Karagas,Carmen J. Marsit,T. Michael O'Shea,Rebecca C. Fry +9 more
TL;DR: These data highlight sex-dependent epigenetic patterning in the placenta and provide insight into differences in infant outcomes and responses to the perinatal environment.
Journal ArticleDOI
Dynamics of DNA methylation in aging and Alzheimer's disease.
Hasan A. Irier,Peng Jin +1 more
TL;DR: An overview of the literature on DNA methylation in neurodegenerative diseases is provided, with a special focus on methylation of 5-position of cytosine base (5mC) and hydroxymethylation (5hmC) in the context of Neurodegeneration associated with aging and Alzheimer's disease.
Journal ArticleDOI
Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model
Kyle M. Schachtschneider,Kyle M. Schachtschneider,Ole Madsen,Chankyu Park,Laurie A. Rund,Martien A. M. Groenen,Lawrence B. Schook,Lawrence B. Schook +7 more
TL;DR: This study provides baseline methylation and gene transcription profiles for a healthy adult pig, reports similar patterns to those observed in humans, and supports future porcine studies related to human disease and development.
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TL;DR: Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
Journal ArticleDOI
Gene Action in the X -chromosome of the Mouse ( Mus musculus L.)
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Journal ArticleDOI
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TL;DR: Low-throughput reduced representation bisulphite sequencing is established as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.