title: Association of 5-hydroxymethylation and 5-methylation of DNA cytosine with tissue-specific gene expression.
abstract: Differentially methylated or hydroxymethylated regions (DMRs) in mammalian DNA are often associated with tissue-specific gene expression but the functional relationships are still being unraveled. To elucidate these relationships, we studied 16 human genes containing myogenic DMRs by analyzing profiles of their epigenetics and transcription and quantitatively assaying 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) at specific sites in these genes in skeletal muscle (SkM), myoblasts, heart, brain, and diverse other samples. Although most human promoters have little or no methylation regardless of expression, more than half of the genes that we chose to study-owing to their myogenic DMRs-overlapped tissue-specific alternative or cryptic promoters displaying corresponding tissue-specific differences in histone modifications. The 5mC levels in myoblast DMRs were significantly associated with 5hmC levels in SkM at the same site. Hypermethylated myogenic DMRs within CDH15, a muscle- and cerebellum-specific cell adhesion gene, and PITX3, a homeobox gene, were used for transfection in reporter gene constructs. These intragenic DMRs had bidirectional tissue-specific promoter activity that was silenced by in vivo-like methylation. The CDH15 DMR, which was previously associated with an imprinted maternal germline DMR in mice, had especially strong promoter activity in myogenic host cells. These findings are consistent with the controversial hypothesis that intragenic DNA methylation can facilitate transcription and is not just a passive consequence of it. Our results support varied roles for tissue-specific 5mC- or 5hmC-enrichment in suppressing inappropriate gene expression from cryptic or alternative promoters and in increasing the plasticity of gene expression required for development and rapid responses to tissue stress or damage.
authors.affiliation: a New England Biolabs , Ipswich , MA , USA.
authors.forename: V K Chaithanya
authors.initials: VK
authors.lastname: Ponnaluri
authors.affiliation: b Center for Bioinformatics and Genomics, Tulane University Health Sciences Center , New Orleans , LA , USA.
authors.forename: Kenneth C
authors.initials: KC
authors.lastname: Ehrlich
authors.affiliation: a New England Biolabs , Ipswich , MA , USA.
authors.forename: Guoqiang
authors.initials: G
authors.lastname: Zhang
authors.affiliation: c Department of Mathematics , Tulane Health Sciences Center and Tulane University , New Orleans , LA , USA.
authors.forename: Michelle
authors.initials: M
authors.lastname: Lacey
authors.affiliation: d Department of Microbiology , Immunology and Parasitology, LSU Health Sciences Center , New Orleans , LA , USA.
authors.forename: Douglas
authors.initials: D
authors.lastname: Johnston
authors.affiliation: a New England Biolabs , Ipswich , MA , USA.
authors.forename: Sriharsa
authors.initials: S
authors.lastname: Pradhan
authors.affiliation: b Center for Bioinformatics and Genomics, Tulane University Health Sciences Center , New Orleans , LA , USA.|e Hayward Genetics Center and Tulane Cancer Center, Tulane University Health Sciences Center , New Orleans , LA , USA.
authors.forename: Melanie
authors.initials: M
authors.lastname: Ehrlich
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives* / Q000378:metabolism; D000328:Adult; D000368:Aged; D001921:Brain / Q000378:metabolism; D015820:Cadherins / Q000235:genetics / Q000378:metabolism; D002675:Child, Preschool; D019175:DNA Methylation; D005260:Female; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008297:Male; D018482:Muscle, Skeletal / Q000378:metabolism; D032446:Myoblasts / Q000378:metabolism; D009206:Myocardium / Q000378:metabolism; D009928:Organ Specificity; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D015820:Cadherins; D018398:Homeodomain Proteins; D014157:Transcription Factors; C433629:homeobox protein PITX3; C011865:5-hydroxymethylcytosine; C070896:M-cadherin; D044503:5-Methylcytosine
keywords: 5-hydroxymethylcytosine; DNA methylation; H3K36me3; alternative promoters; brain; cryptic promoters; heart; myoblasts; skeletal muscle; transcription factors