Exploring the Link between Nucleosome Occupancy and DNA Methylation
Near promoters, both nucleosomes and CpG sites form characteristic spatial patterns. Previously, nucleosome depleted regions were observed upstream of transcription start sites and nucleosome occupancy was reported to correlate both with CpG density and the level of CpG methylation. Several studies...
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Frontiers Media S.A.
2018-01-01
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Online Access: | http://journal.frontiersin.org/article/10.3389/fgene.2017.00232/full |
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author | Cecilia Lövkvist Kim Sneppen Jan O. Haerter |
author_facet | Cecilia Lövkvist Kim Sneppen Jan O. Haerter |
author_sort | Cecilia Lövkvist |
collection | DOAJ |
description | Near promoters, both nucleosomes and CpG sites form characteristic spatial patterns. Previously, nucleosome depleted regions were observed upstream of transcription start sites and nucleosome occupancy was reported to correlate both with CpG density and the level of CpG methylation. Several studies imply a causal link where CpG methylation might induce nucleosome formation, whereas others argue the opposite, i.e., that nucleosome occupancy might influence CpG methylation. Correlations are indeed evident between nucleosomes, CpG density and CpG methylation—at least near promoter sites. It is however less established whether there is an immediate causal relation between nucleosome occupancy and the presence of CpG sites—or if nucleosome occupancy could be influenced by other factors. In this work, we test for such causality in human genomes by analyzing the three quantities both near and away from promoter sites. For data from the human genome we compare promoter regions with given CpG densities with genomic regions without promoters but of similar CpG densities. We find the observed correlation between nucleosome occupancy and CpG density, respectively CpG methylation, to be specific to promoter regions. In other regions along the genome nucleosome occupancy is statistically independent of the positioning of CpGs or their methylation levels. Anti-correlation between CpG density and methylation level is however similarly strong in both regions. On promoters, nucleosome occupancy is more strongly affected by the level of gene expression than CpG density or CpG methylation—calling into question any direct causal relation between nucleosome occupancy and CpG organization. Rather, our results suggest that for organisms with cytosine methylation nucleosome occupancy might be primarily linked to gene expression, with no strong impact on methylation. |
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language | English |
last_indexed | 2024-04-12T18:29:49Z |
publishDate | 2018-01-01 |
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series | Frontiers in Genetics |
spelling | doaj.art-0af6d9fed2f84be6ac304dd344cb9b2e2022-12-22T03:21:07ZengFrontiers Media S.A.Frontiers in Genetics1664-80212018-01-01810.3389/fgene.2017.00232306636Exploring the Link between Nucleosome Occupancy and DNA MethylationCecilia LövkvistKim SneppenJan O. HaerterNear promoters, both nucleosomes and CpG sites form characteristic spatial patterns. Previously, nucleosome depleted regions were observed upstream of transcription start sites and nucleosome occupancy was reported to correlate both with CpG density and the level of CpG methylation. Several studies imply a causal link where CpG methylation might induce nucleosome formation, whereas others argue the opposite, i.e., that nucleosome occupancy might influence CpG methylation. Correlations are indeed evident between nucleosomes, CpG density and CpG methylation—at least near promoter sites. It is however less established whether there is an immediate causal relation between nucleosome occupancy and the presence of CpG sites—or if nucleosome occupancy could be influenced by other factors. In this work, we test for such causality in human genomes by analyzing the three quantities both near and away from promoter sites. For data from the human genome we compare promoter regions with given CpG densities with genomic regions without promoters but of similar CpG densities. We find the observed correlation between nucleosome occupancy and CpG density, respectively CpG methylation, to be specific to promoter regions. In other regions along the genome nucleosome occupancy is statistically independent of the positioning of CpGs or their methylation levels. Anti-correlation between CpG density and methylation level is however similarly strong in both regions. On promoters, nucleosome occupancy is more strongly affected by the level of gene expression than CpG density or CpG methylation—calling into question any direct causal relation between nucleosome occupancy and CpG organization. Rather, our results suggest that for organisms with cytosine methylation nucleosome occupancy might be primarily linked to gene expression, with no strong impact on methylation.http://journal.frontiersin.org/article/10.3389/fgene.2017.00232/fullCpG sitesDNA methylationnucleosome occupancyepigeneticsgene expression |
spellingShingle | Cecilia Lövkvist Kim Sneppen Jan O. Haerter Exploring the Link between Nucleosome Occupancy and DNA Methylation Frontiers in Genetics CpG sites DNA methylation nucleosome occupancy epigenetics gene expression |
title | Exploring the Link between Nucleosome Occupancy and DNA Methylation |
title_full | Exploring the Link between Nucleosome Occupancy and DNA Methylation |
title_fullStr | Exploring the Link between Nucleosome Occupancy and DNA Methylation |
title_full_unstemmed | Exploring the Link between Nucleosome Occupancy and DNA Methylation |
title_short | Exploring the Link between Nucleosome Occupancy and DNA Methylation |
title_sort | exploring the link between nucleosome occupancy and dna methylation |
topic | CpG sites DNA methylation nucleosome occupancy epigenetics gene expression |
url | http://journal.frontiersin.org/article/10.3389/fgene.2017.00232/full |
work_keys_str_mv | AT cecilialovkvist exploringthelinkbetweennucleosomeoccupancyanddnamethylation AT kimsneppen exploringthelinkbetweennucleosomeoccupancyanddnamethylation AT janohaerter exploringthelinkbetweennucleosomeoccupancyanddnamethylation |