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Cell type‐specific methylation profiles occurring disproportionately in CpG‐less regions that delineate developmental similarity
Author(s) -
Sakamoto Hideki,
Suzuki Masako,
Abe Tetsuya,
Hosoyama Tohru,
Himeno Emi,
Tanaka Satoshi,
Greally John M,
Hattori Naka,
Yagi Shintaro,
Shiota Kunio
Publication year - 2007
Publication title -
genes to cells
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.912
H-Index - 115
eISSN - 1365-2443
pISSN - 1356-9597
DOI - 10.1111/j.1365-2443.2007.01120.x
Subject(s) - biology , dna methylation , cpg site , methylation , computational biology , similarity (geometry) , evolutionary biology , genetics , cell type , cell , microbiology and biotechnology , dna , gene , gene expression , artificial intelligence , computer science , image (mathematics)
Our previous studies using restriction landmark genomic scanning (RLGS) defined tissue‐ or cell‐specific DNA methylation profiles. It remains to be determined whether the DNA sequence compositions in the genomic contexts of the Not I loci tested by RLGS influence their tendency to change with differentiation. We carried out 3834 methylation measurements consisting of 213 Not I loci in the mouse genome in 18 different tissues and cell types, using quantitative real‐time PCR based on a V irtual image rlgs database. Loci were categorized as CpG islands or other, and as unique or repetitive sequences, each category being associated with a variety of methylation categories. Strikingly, the tissue‐dependently and differentially methylated regions (T‐DMRs) were disproportionately distributed in the non‐CpG island loci. These loci were located not only in 5′‐upstream regions of genes but also in intronic and non‐genic regions. Hierarchical clustering of the methylation profiles could be used to define developmental similarity and cellular phenotypes. The results show that distinctive tissue‐ and cell type‐specific methylation profiles by RLGS occur mostly at Not I sites located at non‐CpG island sequences, which delineate developmental similarity of different cell types. The finding indicates the power of Not I methylation profiles in evaluating the relatedness of different cell types.