Locus- and cell type-specific epigenetic switching during cellular differentiation in mammals

doi:10.1007/s11515-016-1411-5

Front. Biol.

2016, Vol. 11

Issue (4) : 311-322 https://doi.org/10.1007/s11515-016-1411-5

RESEARCH ARTICLE

Locus- and cell type-specific epigenetic switching during cellular differentiation in mammals

Ying-Tao Zhao,Maria Fasolino,Zhaolan Zhou(

)

Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA

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Abstract

BACKGROUND: Epigenomic reconfiguration, including changes in DNA methylation and histone modifications, is crucial for the differentiation of embryonic stem cells (ESCs) into somatic cells. However, the extent to which the epigenome is reconfigured and the interplay between components of the epigenome during cellular differentiation remain poorly defined.

METHODS: We systematically analyzed and compared DNA methylation, various histone modification, and transcriptome profiles in ESCs with those of two distinct types of somatic cells from human and mouse.

RESULTS: We found that global DNA methylation levels are lower in somatic cells compared to ESCs in both species. We also found that 80% of regions with histone modification occupancy differ between human ESCs and the two human somatic cell types. Approximately 70% of the reconfigurations in DNA methylation and histone modifications are locus- and cell type-specific. Intriguingly, the loss of DNA methylation is accompanied by the gain of different histone modifications in a locus- and cell type-specific manner. Further examination of transcriptional changes associated with epigenetic reconfiguration at promoter regions revealed an epigenetic switching for gene regulation—a transition from stable gene silencing mediated by DNA methylation in ESCs to flexible gene repression facilitated by repressive histone modifications in somatic cells.

CONCLUSIONS: Our findings demonstrate that the epigenome is reconfigured in a locus- and cell type-specific manner and epigenetic switching is common during cellular differentiation in both human and mouse.

Keywords DNA methylation histone modifications epigenome epigenetic switch cellular differentiation

Corresponding Author(s): Zhaolan Zhou

Just Accepted Date: 23 June 2016 Online First Date: 18 July 2016 Issue Date: 30 August 2016

Cite this article:

Ying-Tao Zhao,Maria Fasolino,Zhaolan Zhou. Locus- and cell type-specific epigenetic switching during cellular differentiation in mammals[J]. Front. Biol., 2016, 11(4): 311-322.

URL:

https://academic.hep.com.cn/fib/EN/10.1007/s11515-016-1411-5
https://academic.hep.com.cn/fib/EN/Y2016/V11/I4/311

Fig.1 Global DNA hypomethylation in somatic cells in both human and mouse. (A) Methylation levels (ML) of differentially methylated CpGs (diff-mCpGs) between ESCs and two somatic cell types in human and mouse. Each circle represents a CpG. The deeper the shade of blue, the higher the point density (number of CpGs). (B) The percentage of diff-mCpGs (FDR<0.05, two-tailed Fisher’s exact test, B-H correction) that are hypomethylated or hypermethylated during cellular differentiation. Confident CpGs are those with 10 or more read coverage in both ESCs and somatic cells.

Fig.2 DNA hypomethylation during cellular differentiation is locus- and cell type-specific. (A) A schematic of the enrichment-based statistical approach used to identify differentially methylated genomic regions (e.g. promoters). Confident CpG, CpGs with 10 or more read coverage in both data sets; diff-mCpGs, differentially methylated CpGs. (B) Heat maps of differentially methylated genomic regions between hESC and the two human somatic cell types after clustering analysis. (C) Browser representation of methylation profiles of the genes with changes in methylation levels at their promoter regions during cellular differentiation. Each green vertical bar represents a CpG, and the height of the bar represents its methylation level (from 0 to 100%). Grey arrows indicate the transcriptional orientation of each gene. Regions marked by orange bars indicate the locus- and cell type-specific DNA methylation changes.

Fig.3 Changes in histone modifications during cellular differentiation are locus- and cell type-specific. (A) The percentage of enriched sites for each histone modification that were gained (gain), lost (lose), and remained (remain) during differentiation of hESC to hFB and hEP. (B) Heat maps of changes of enriched sites for 11 histone modifications during cellular differentiation in human after clustering analysis.(C) The width of H3K27me3 and H3K9me3 enriched sites in hESC and hFB. ★★★, p-value<2.2 × 10^-¹⁶, Student’s t-test. (D) Browser representation of two regions with H3K27me3 and H3K9me3 expansion during cellular differentiation in human.

Fig.4 A switching from DNA methylation to histone modifications during cellular differentiation. (A) DNA methylation changes in the highly dynamic regions that gain histone modifications during the differentiation of hESC to hFB. Green regions, histone modifications that are associated with a decrease in DNA methylation; Gray regions, histone modifications that are not associated with a change in DNA methylation; Red regions, histone modifications that are associated with an increase in DNA methylation. (B) DNA methylation changes in the highly dynamic gain regions during the differentiation of hESC to hEP. (C) DNA methylation changes in the highly dynamic regions that gain or lose H3K4me3 and H3K27ac during the differentiation of mESC to mFC. Enrichment score for each region was calculated by dividing the number of normalized reads aligned in a particular region in mFC by that in mESC. (D) Browser representation of three regions that exhibit switching from DNA methylation to histone modifications during cellular differentiation in human. Regions marked by gray bars indicate the cell type-specific switching. The track scale for all histone modifications is from 0 to 50 normalized reads.

Fig.5 Switching from DNA methylation to repressive histone modifications at promoter regions uncovers a change of gene regulation from ESCs to somatic cells. (A) Scatter plots of the number of genomic CpGs, the ratio of mCpG, and the ratio of diif-mCpG in 10 bp bins within the region 5 kb upstream and 1 kb downstream of known transcription start site (TSS). (B) Heat map-pie charts of the expression changes of the genes with hypomethylated promoters. FC, fold change, gene expression levels in somatic cell types divided by that in ESCs. (C) Pie charts of percentages of genes, which are hypomethylated at the promoter regions but with no expression changes during cellular differentiation, marked by H3K27me3 or H3K9me3 or both in somatic cells. (D) Browser representation of four genes with epigenomic reconfiguration at their promoter regions. These genes were silent in both hESC and somatic cell types. The track scale for all mRNA-seq is from 0 to 45 normalized reads. The track scale for all histone modifications is from 0 to 50 normalized reads. (E) A model depicting gene regulation changes during cellular differentiation.

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