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Table 3  Enriched biological processes of key dibutyl-phthalate (DBP) responsive, paternally provided RNA Element (RE)-containing RNAs (RE-RNAs)

From: Phthalates impact on the epigenetic factors contributed specifically by the father at fertilization

RE-RNA

CRREW

CRREW class

Enriched biological process

Enriched MSigDB Gene Set

CAMTA2

No

–

Cellular stress

GOBP positive regulation of cellular biosynthetic process

Gene regulation

GOBP positive regulation of nucleobase containing compound metabolic process

GOBP positive regulation of RNA metabolic process

GOBP positive regulation of transcription by RNA polymerase II

GOCC chromosome

GOMF chromatin binding

GOMF transcription coactivator activity

GOMF transcription regulator activity

CUL2

Yes

Chromatin remodeler cofactor

Cellular stress

REACTOME cellular responses to stimuli

Apoptosis

Graessman apoptosis by doxorubicin dn

GOBP programmed cell death

DNA damage response to UV exposure

Dacosta UV response via ERCC3 dn

Gene regulation

GOCC transferase complex

Shen SMARCA2 targets up

PHF10

Yes

Chromatin remodeler cofactor

Cellular stress

GOBP negative regulation of biosynthetic process

GOBP positive regulation of cellular biosynthetic process

Martens tretinoin response dn

Gene regulation

GOBP negative regulation of nucleobase containing compound metabolic process

GOBP positive regulation of nucleobase containing compound metabolic process

GOBP positive regulation of RNA metabolic process

GOBP positive regulation of transcription by RNA polymerase II

GOCC chromosome

GOMF histone binding

GOMF transcription coregulator activity

GOMF transcription regulator activity

PSME4

No

–

Cellular stress

GOBP cellular response to DNA damage stimulus

GOBP cellular response to stress

REACTOME cellular responses to stimuli

Cell cycle

GOBP nucleus organization

REACTOME cell cycle

REACTOME cell cycle mitotic

DNA damage response to UV exposure

Dacosta UV response via ERCC3 dn

Gene regulation

GOBP chromatin organization

GOBP chromosome organization

GOMF histone binding

REACTOME metabolism of RNA

REACTOME RNA polymerase II transcription

Senese HDAC3 targets up

SMARCC1

Yes

Chromatin remodeler cofactor

Cellular stress

GOBP cellular response to endogenous stimulus

GOBP positive regulation of cellular biosynthetic process

GOBP regulation of catabolic process

GOBP response to endogenous stimulus

Martens tretinoin response dn

Cell cycle

Fischer DREAM targets

Hallmark G2M checkpoint

DNA damage response to UV exposure

Monnier postradiation tumor escape up

Gene regulation

GOBP chromatin organization

GOBP chromatin binding

GOBP chromosome organization

GOBP positive regulation of RNA metabolic process

GOBP positive regulation of nucleobase containing compound metabolic process

GOBP positive regulation of transcription by RNA polymerase II

GOCC chromosome

GOMF histone binding

GOMF transcription coactivator activity

GOMF transcription coregulator activity

GOMF transcription regulator activity

GSE17721 CPG vs gardiquimod 4 h BMDC dn

Hallmark MYC targets V1

Marson bound by FOXP3 stimulated

Marson bound by FOXP3 unstimulated

REACTOME chromatin modifying enzymes

REACTOME RNA polymerase II transcription

Senese HDAC3 targets up

  1. RE-RNAs are visually full-length using the UCSC genome browser. DNA damage response: DNA damage response to UV exposure. Paternally provided: fivefold paternally enriched or twofold paternally enriched; CRREW: chromatin remodeler cofactor, RNA interactor, reader, eraser and writer.