Epigenetic profile of the euchromatic region of human Y chromosome.
The genome of a multi-cellular organism acquires various functional capabilities in different cell types by means of distinct chromatin modifications and packaging states. Acquired during early development, the cell type-specific epigenotype is maintained by cellular memory mechanisms that involve epigenetic modifications. Here we present the epigenetic status of the euchromatic region of the human Y chromosome that has mostly been ignored in earlier whole genome epigenetic mapping studies. Using ChIP-on-chip approach, we mapped H3K9ac, H3K9me3, H3K27me3 modifications and CTCF binding sites while DNA methylation analysis of selected CpG islands was done using bisulfite sequencing. The global pattern of histone modifications observed on the Y chromosome reflects the functional state and evolutionary history of the sequences that constitute it. The combination of histone and DNA modifications, along with CTCF association in some cases, reveals the transcriptional potential of all protein coding genes including the sex-determining gene SRY and the oncogene TSPY. We also observe preferential association of histone marks with different tandem repeats, suggesting their importance in genome organization and gene regulation. Our results present the first large scale epigenetic analysis of the human Y chromosome and link a number of cis-elements to epigenetic regulatory mechanisms, enabling an understanding of such mechanisms in Y chromosome linked disorders.
Centre for Cellular and Molecular Biology, Council for Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India.
Narendra Pratap
NP
Singh
Sri Ranganayaki
SR
Madabhushi
Surabhi
S
Srivastava
R
R
Senthilkumar
C
C
Neeraja
Sanjeev
S
Khosla
Rakesh K
RK
Mishra
D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D018797:Cell Cycle Proteins / Q000235:genetics; D041322:Chromosomes, Human, Y / Q000737:chemistry / Q000378:metabolism*; D044127:Epigenesis, Genetic; D022041:Euchromatin / Q000737:chemistry / Q000378:metabolism*; D015870:Gene Expression; D024282:Genes, sry; D056426:Genetic Loci; D006657:Histones / Q000378:metabolism; D006801:Humans; D008297:Male; D012097:Repressor Proteins / Q000378:metabolism; D020080:Tandem Repeat Sequences
D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D018797:Cell Cycle Proteins; D022041:Euchromatin; D006657:Histones; D012097:Repressor Proteins; C497749:TSPY1 protein, human
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