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Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE211058 | GEO | 2025/08/01

REPOSITORIES: GEO

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Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs [RIP-seq]

Project description:The mechanisms by which epigenetic modifications are established in gene regulatory regions of active genes remain elusive. The data presented show that the establishment and recycling of a major epigenetic mark, the acetylated form of the replacement histone H2A.Z, is regulated by cell cycle-specific long noncoding RNAs encoded in regions adjacent to the promoters of active genes. These transcripts, termed SPEARs (S Phase EArly RNAs), are induced in early S phase: their expression precedes that of the downstream genes on which they exert their regulatory action. SPEARs drive the modification and deposition of the acetylated form of histone H2A.Z by bringing together the replacement histone and the histone acetyl transferase TIP60. This widespread bimodal pathway constitutes a novel RNA-mediated mechanism for the establishment of epigenetic marks and cell-specific epigenetic profiles, thereby providing a unifying explanation for the accuracy and persistence of epigenetic marks on chromatin.

2025-08-01 | GSE211056 | GEO

Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs [ChIP-seq]

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Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs [RNA-seq]

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Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs

Project description:Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs

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Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs [ChIP-seq]

Project description:Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs [ChIP-seq]

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Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs [RNA-seq]

Project description:Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs [RNA-seq]

| PRJNA868745 | ENA

Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs [RIP-seq]

Project description:Formation of an active epigenetic mark and its recycling is mediated by cell cycle-specific RNAs [RIP-seq]

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Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq.

Project description:Long noncoding RNAs (lncRNAs) localize in the cell nucleus and influence gene expression through a variety of molecular mechanisms. Chromatin-enriched RNAs (cheRNAs) are a unique class of lncRNAs that are tightly bound to chromatin and putatively function to locally cis-activate gene transcription. CheRNAs can be identified by biochemical fractionation of nuclear RNA followed by RNA sequencing, but until now, a rigorous analytic pipeline for nuclear RNA-seq has been lacking. In this study, we survey four computational strategies for nuclear RNA-seq data analysis and develop a new pipeline, Tuxedo-ch, which outperforms other approaches. Tuxedo-ch assembles a more complete transcriptome and identifies cheRNA with higher accuracy than other approaches. We used Tuxedo-ch to analyze benchmark datasets of K562 cells and further characterize the genomic features of intergenic cheRNA (icheRNA) and their similarity to enhancer RNAs (eRNAs). We quantify the transcriptional correlation of icheRNA and adjacent genes and show that icheRNA is more positively associated with neighboring gene expression than eRNA or cap analysis of gene expression (CAGE) signals. We also explore two novel genomic associations of cheRNA, which indicate that cheRNAs may function to promote or repress gene expression in a context-dependent manner. IcheRNA loci with significant levels of H3K9me3 modifications are associated with active enhancers, consistent with the hypothesis that enhancers are derived from ancient mobile elements. In contrast, antisense cheRNA (as-cheRNA) may play a role in local gene repression, possibly through local RNA:DNA:DNA triple-helix formation.

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Enhancer Transcripts Mark Active Estrogen Receptor Binding Sites using GRO-seq

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-01-28 | E-GEOD-43836 | biostudies-arrayexpress

Formation of an active tissue-specific chromatin domain initiated by epigenetic marking at the embryonic stem cell stage.

Project description:The differentiation potential of stem cells is determined by the ability of these cells to establish and maintain developmentally regulated gene expression programs that are specific to different lineages. Although transcriptionally potentiated epigenetic states of genes have been described for haematopoietic progenitors, the developmental stage at which the formation of lineage-specific gene expression domains is initiated remains unclear. In this study, we show that an intergenic cis-acting element in the mouse lambda5-VpreB1 locus is marked by histone H3 acetylation and histone H3 lysine 4 methylation at a discrete site in embryonic stem (ES) cells. The epigenetic modifications spread from this site toward the VpreB1 and lambda5 genes at later stages of B-cell development, and a large, active chromatin domain is established in pre-B cells when the genes are fully expressed. In early B-cell progenitors, the binding of haematopoietic factor PU.1 coincides with the expansion of the marked region, and the region becomes a center for the recruitment of general transcription factors and RNA polymerase II. In pre-B cells, E2A also binds to the locus, and general transcription factors are distributed across the active domain, including the gene promoters and the intergenic region. These results suggest that localized epigenetic marking is important for establishing the transcriptional competence of the lambda5 and VpreB1 genes as early as the pluripotent ES cell stage.

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