Integration of sperm ncRNA-directed DNA methylation and DNA methylation-directed histone retention in epigenetic transgenerational inheritance

Abstract

Background: Environmentally induced epigenetic transgenerational inheritance of pathology and phenotypic variation has been demonstrated in all organisms investigated from plants to humans. This non-genetic form of inheritance is mediated through epigenetic alterations in the sperm and/or egg to subsequent generations. Although the combined regulation of differential DNA methylated regions (DMR), non-coding RNA (ncRNA), and differential histone retention (DHR) have been shown to occur, the integration of these different epigenetic processes remains to be elucidated. The current study was designed to examine the integration of the different epigenetic processes.

Results: A rat model of transiently exposed F0 generation gestating females to the agricultural fungicide vinclozolin or pesticide DDT (dichloro-diphenyl-trichloroethane) was used to acquire the sperm from adult males in the subsequent F1 generation offspring, F2 generation grand offspring, and F3 generation great-grand offspring. The F1 generation sperm ncRNA had substantial overlap with the F1, F2 and F3 generation DMRs, suggesting a potential role for RNA-directed DNA methylation. The DMRs also had significant overlap with the DHRs, suggesting potential DNA methylation-directed histone retention. In addition, a high percentage of DMRs induced in the F1 generation sperm were maintained in subsequent generations.

Conclusions: Many of the DMRs, ncRNA, and DHRs were colocalized to the same chromosomal location regions. Observations suggest an integration of DMRs, ncRNA, and DHRs in part involve RNA-directed DNA methylation and DNA methylation-directed histone retention in epigenetic transgenerational inheritance.

Keywords: DNA methylation; Epigenetics; Histone; Non-genetic inheritance; Review; Sperm; Transgenerational; ncRNA.

Fig. 1

Generational epimutation overlap at high stringent statistical threshold. a F1 generation vinclozolin lineage DMR (p < 1e−06), DHR (p < 1e−06), and ncRNA (p < 1e−04). b F1 generation DDT lineage DMR (p < 1e−06), DHR (p < 1e−06), and ncRNA (p < 1e−04). c F2 generation vinclozolin lineage DMR (p < 1e−06), DHR (p < 1e−06), and ncRNA (p < 1e−04). d F2 generation DDT lineage DMR (p < 1e−06), DHR (p < 1e−06), and ncRNA (p < 1e−04). e F3 generation vinclozolin lineage DMR (p < 1e−06), DHR (p < 1e−06), and ncRNA (p < 1e−04). f F3 generation DDT lineage DMR (p < 1e−06), DHR (p < 1e−06), and ncRNA (p < 1e−04)

Fig. 2

Chromosomal colocalization of overlap epimutations. The overlap of one epimutation at high statistical stringency (DMR p < 1e−06, DHR p < 1e−06, or ncRNA p < 1e−04) overlap with others at p < 0.05. The epimutation at high stringency is identified with color and marked as indicated by the inset legend. The chromosomal number and size (megabase) are presented. a F1 generation vinclozolin lineage ncRNA and DMR. b F1 generation DDT lineage ncRNA and DMR. c F2 generation vinclozolin lineage ncRNA and DMR. d F2 generation DDT lineage ncRNA and DMR. e F3 generation vinclozolin lineage DMR, DHR and ncRNA. f F3 generation DDT lineage DMR, DHR and ncRNA

Fig. 3

Extended epimutation overlap. The epimutations at high stringency (DMR p < 1e−06, DHR p < 1e−06, and ncRNA p < 1e−04) in rows were compared to epimutations at p < 0.05 in columns. The number of overlap epimutations and percentage of the total are presented for each overlap. As anticipated, 100% overlap was observed for the same generation and epimutation indicated by shaded box. a Vinclozolin lineage epimutation and b DDT lineage epimutation overlap

Fig. 4

Epimutation overlaps. Generational DMR overlap with F1 generation ncRNA p < 0.05. A Venn diagram overlap of F1, F2, and F3 generation DMR (p < 1e−06) with F1 generation ncRNA (p < 0.05). a Vinclozolin lineage DMR and ncRNA overlap. b DDT lineage DMR and ncRNA overlap. Generational DMR overlap with F3 generation DHR p < 0.05. A Venn diagram overlap of F1, F2, and F3 generation DMR (p < 1e−06) with F3 generation DHR (p < 0.05). c Vinclozolin lineage DMR and DHR overlap. d DDT lineage DMR and DHR overlap. Generational DMR overlap. A Venn diagram overlap of F1 generation DMR (p < 1e−06) with F2 and F3 generation DMR (p < 0.05). e Vinclozolin lineage DMR overlap. f DDT lineage DMR overlap

Fig. 5

Genomic colocalization of DMR, DHR and ncRNA. The genomic and colocalized DMR, DHR and ncRNA presented. The region size (bp), genes present, and localization of DMR, DHR and ncRNA identified. The various examples include a nc-005100.4, b nc-005104.4, c nc-005111.4, and d nc-005113.4 from the NCBI Rattus norvegicus release 106 in 2016

Fig. 6

Extended epimutation overlap within a 10-kb region. The epimutations at high stringency (DMR p < 1e−06, DHR p < 1e−06, and ncRNA p < 1e−04) in rows were compared to epimutations at p < 0.05 in columns. The number of overlap epimutations and percentage of the total are presented for each overlap. As anticipated, 100% overlap was observed for the same generation and epimutation indicated by shaded box. a Vinclozolin lineage epimutation and b DDT lineage epimutation overlap

Fig. 7

Diagram of ncRNA-directed DNA methylation and DNA methylation-directed histone retention. The red dot identifies DNA methylation, green histone the nucleosome with modifications in histone tails indicated. The ncRNA association with cofactors and DNA methyltransferase (DNMT) promoting DNA methylation (red dot) for RNA-directed DNA methylation. The DNA methylation (red dot) association with chromatin remodeling proteins (CRP) to promote histone retention is indicated