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Inactive or moderately active human promoters are enriched for inter-individual epialleles [Seq]

ABSTRACT: We first demonstrate that non-genetically determined inter-individual differentially methylated regions (iiDMRs) can be temporally stable for at least two years. Then, we show that iiDMRS are associated with concomitant changes in chromatin state as measured by inter-individual differences in the levels of the histone variant H2A.Z. However, the correlation of promoter iiDMRs with gene expression is negligible and this correlation is not improved even by integrating H2A.Z information. We find that most promoter epialleles, whether genetically or non-genetically determined, are associated with low levels of transcriptional activity, depleted for house keeping genes, and either depleted for H3K4me3/enriched for H3K27me3, or lacking both these marks in human embryonic stem cells. These findings validate in an independent cohort. Interestingly, the key features of iiDMRs are reminiscent of those previously observed for promoters that undergo hyper-methylation in various cancers, in vitro cell culture, and human chronological ageing. H2A.z ChIP-seq, RNA-seq, and DNA methylation data (submitted separately) were collected for five normal individuals. T21/T22 and T31/T32 are monozygotic twins.

ORGANISM(S): Homo sapiens

SUBMITTER: Thomas Down

PROVIDER: E-GEOD-46217 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Inactive or moderately active human promoters are enriched for inter-individual epialleles [Methylation BeadChip]

Project description:We first demonstrate that non-genetically determined inter-individual differentially methylated regions (iiDMRs) can be temporally stable for at least two years. Then, we show that iiDMRS are associated with concomitant changes in chromatin state as measured by inter-individual differences in the levels of the histone variant H2A.Z. However, the correlation of promoter iiDMRs with gene expression is negligible and this correlation is not improved even by integrating H2A.Z information. We find that most promoter epialleles, whether genetically or non-genetically determined, are associated with low levels of transcriptional activity, depleted for house keeping genes, and either depleted for H3K4me3/enriched for H3K27me3, or lacking both these marks in human embryonic stem cells. These findings validate in an independent cohort. Interestingly, the key features of iiDMRs are reminiscent of those previously observed for promoters that undergo hyper-methylation in various cancers, in vitro cell culture, and human chronological ageing. DNA Methylation, H2A.z ChIP-seq, RNA-seq (submitted) separately were collected for five normal individuals (samples with "T" prefixes). T21/T22 and T31/T32 are monozygotic twins. Further DNA methylation data was collected from and additional two pairs of MZ twins with technical replication (samples with "C" prefixes - the three digits are pair number, individual number, and replicate number). Bisulphite converted DNA was hybridised to the Illumina Infinium 450k Human Methylation Beadchip

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Inactive or moderately active human promoters are enriched for inter-individual epialleles [Seq]

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Project description:Variation in chromatin composition and organization often reflects differences in genome function. Histone variants, for example, replace canonical histones to contribute to regulation of numerous nuclear processes including transcription, DNA repair and chromosome segregation. Here we focus on H2A.Bbd, a rapidly evolving variant found in mammals but not in invertebrates. We report that in human cells, nucleosomes bearing H2A.Bbd form unconventional chromatin structures enriched within actively transcribed genes and characterized by shorter DNA protection and nucleosome spacing. Analysis of transcriptional profiles from cells depleted for H2A.Bbd demonstrated widespread changes in gene expression with a net down-regulation of transcription and disruption of normal mRNA splicing patterns. In particular, we observed changes in exon inclusion rates and increased presence of intronic sequences in mRNA products upon H2A.Bbd depletion. Taken together, our results indicate that H2A.Bbd is involved in formation of a specific chromatin structure that facilitates both transcription and initial mRNA processing. RNA-seq was used to examine changes in gene expression upon shRNA-assisted depletion of H2A.Bbd and H2A.Z histone variants in HeLa cells. The cells treated with shRNA with no homology to the human genome were used as control.

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