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LncRNA SNHG8d impedes chromatin condensation and epithelial differentiation by phase separating histone H1.

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

ORGANISM(S): Homo sapiens Homo

PROVIDER: GSE151626 | GEO | 2021/12/31

REPOSITORIES: GEO

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LncRNA SNHG8d impedes chromatin condensation and epithelial differentiation by phase separating histone H1 [RNA-seq]

Project description:Linker histone H1, the key chromatin structural protein facilitating higher order chromatin folding, isan important epigenetic mark and regulator for gene expression and cellular differentiation. However, mechanisms thatregulate H1 binding affinity to chromatin remain elusive. In an attempt to screen functionallong non-coding RNAs(lncRNAs), we designed a cell-type specific score (CTSS) algorithm on the basis of RNA-seq data derived fromcell lines of different origins, which leads to the identification of an epithelium-specific lncRNA designated assmall nucleolar RNA host gene 8 (SNHG8). In epithelial cells, loss of SNHG8d, a major transcriptof SNHG8, remodels the genomic expression profiletowards differentiation. Mechanistically, SNHG8d is localized in the nucleus and manifests stronginteraction withallthe histone H1 variants detected.Loss of SNHG8dleads to increasedH1 binding affinity to chromatinand subsequentchromatin condensationwhichdictates the epithelial differentiation-orientedgenomic expression remodeling.Further analysis proposes that SNHG8d regulates H1-chromatin affinityby competing with linker DNA forhistone H1 binding througha phase-separation mechanism. Thus, our study revealed a lncRNA-conducted mechanismthat sequesters histone H1 from chromatin through phase separation to sequentially regulatechromatin structure, gene expressionandepithelialdifferentiation.

2021-12-31 | GSE151625 | GEO

LncRNA SNHG8d impedes chromatin condensation and epithelial differentiation by phase separating histone H1 [ATAC-seq]

Project description:Linker histone H1, the key chromatin structural protein facilitating higher order chromatin folding, is an important epigenetic mark and regulator for gene expression and cellular differentiation. However, mechanisms thatregulate H1 binding affinity to chromatin remain elusive. In an attempt to screen functionallong non-coding RNAs(lncRNAs), we designed a cell-type specific score (CTSS) algorithm on the basis of RNA-seq data derived fromcell lines of different origins, which leads to the identification of an epithelium-specific lncRNA designated assmall nucleolar RNA host gene 8 (SNHG8). In epithelial cells, loss of SNHG8d, a major transcriptof SNHG8, remodels the genomic expression profiletowards differentiation. Mechanistically, SNHG8d is localized in the nucleus and manifests stronginteraction withallthe histone H1 variants detected.Loss of SNHG8dleads to increasedH1 binding affinity to chromatinand subsequentchromatin condensationwhichdictates the epithelial differentiation-orientedgenomic expression remodeling.Further analysis proposes that SNHG8d regulates H1-chromatin affinityby competing with linker DNA forhistone H1 binding througha phase-separation mechanism. Thus, our study revealed a lncRNA-conducted mechanismthat sequesters histone H1 from chromatin through phase separation to sequentially regulatechromatin structure, gene expressionandepithelialdifferentiation.

2021-12-31 | GSE151624 | GEO

LncRNA SNHG8d impedes chromatin condensation and epithelial differentiation by phase separating histone H1.

Project description:LncRNA SNHG8d impedes chromatin condensation and epithelial differentiation by phase separating histone H1.

| PRJNA636659 | ENA

LncRNA SNHG8d impedes chromatin condensation and epithelial differentiation by phase separating histone H1 [RNA-seq]

Project description:LncRNA SNHG8d impedes chromatin condensation and epithelial differentiation by phase separating histone H1 [RNA-seq]

| PRJNA636662 | ENA

LncRNA SNHG8d impedes chromatin condensation and epithelial differentiation by phase separating histone H1 [ATAC-seq]

Project description:LncRNA SNHG8d impedes chromatin condensation and epithelial differentiation by phase separating histone H1 [ATAC-seq]

| PRJNA636661 | ENA

PTEN interacts with histone H1 and controls chromatin condensation.

Project description:Chromatin organization and dynamics are integral to global gene transcription. Histone modification influences chromatin status and gene expression. PTEN plays multiple roles in tumor suppression, development, and metabolism. Here, we report on the interplay of PTEN, histone H1, and chromatin. We show that loss of PTEN leads to dissociation of histone H1 from chromatin and decondensation of chromatin. PTEN deletion also results in elevation of histone H4 acetylation at lysine 16, an epigenetic marker for chromatin activation. We found that PTEN and histone H1 physically interact through their C-terminal domains. Disruption of the PTEN C terminus promotes the chromatin association of MOF acetyltransferase and induces H4K16 acetylation. Hyperacetylation of H4K16 impairs the association of PTEN with histone H1, which constitutes regulatory feedback that may reduce chromatin stability. Our results demonstrate that PTEN controls chromatin condensation, thus influencing gene expression. We propose that PTEN regulates global gene transcription profiling through histones and chromatin remodeling.

| S-EPMC4201947 | biostudies-literature

Epithelial cells-enriched lncRNA SNHG8 regulates chromatin condensation by binding to Histone H1s.

Project description:Linker histone H1 proteins contain many variants in mammalian and can stabilize the condensed state of chromatin by binding to nucleosomes and promoting a more inaccessible structure of DNA. However, it is poorly understood how the binding of histone H1s to chromatin DNA is regulated. Screened as one of a collection of epithelial cells-enriched long non-coding RNAs (lncRNAs), here we found that small nucleolar RNA host gene 8 (SNHG8) is a chromatin-localized lncRNA and presents strong interaction and phase separation with histone H1 variants. Moreover, SNHG8 presents stronger ability to bind H1s than linker DNA, and outcompetes linker DNA for H1 binding. Consequently, loss of SNHG8 increases the amount of H1s that bind to chromatin, promotes chromatin condensation, and induces an epithelial differentiation-associated gene expression pattern. Collectively, our results propose that the highly abundant SNHG8 in epithelial cells keeps histone H1 variants out of nucleosome and its loss contributes to epithelial cell differentiation.

| S-EPMC9345976 | biostudies-literature

Histone H1 acetylation at lysine 85 regulates chromatin condensation and genome stability upon DNA damage.

Project description:Linker histone H1 has a key role in maintaining higher order chromatin structure and genome stability, but how H1 functions in these processes is elusive. Here, we report that acetylation of lysine 85 (K85) within the H1 globular domain is a critical post-translational modification that regulates chromatin organization. H1K85 is dynamically acetylated by the acetyltransferase PCAF in response to DNA damage, and this effect is counterbalanced by the histone deacetylase HDAC1. Notably, an acetylation-mimic mutation of H1K85 (H1K85Q) alters H1 binding to the nucleosome and leads to condensed chromatin as a result of increased H1 binding to core histones. In addition, H1K85 acetylation promotes heterochromatin protein 1 (HP1) recruitment to facilitate chromatin compaction. Consequently, H1K85 mutation leads to genomic instability and decreased cell survival upon DNA damage. Together, our data suggest a novel model whereby H1K85 acetylation regulates chromatin structure and preserves chromosome integrity upon DNA damage.

| S-EPMC6125638 | biostudies-literature

Histone H1 subtypes differentially modulate chromatin condensation without preventing ATP-dependent remodeling by SWI/SNF or NURF.

Project description:Although ubiquitously present in chromatin, the function of the linker histone subtypes is partly unknown and contradictory studies on their properties have been published. To explore whether the various H1 subtypes have a differential role in the organization and dynamics of chromatin we have incorporated all of the somatic human H1 subtypes into minichromosomes and compared their influence on nucleosome spacing, chromatin compaction and ATP-dependent remodeling. H1 subtypes exhibit different affinities for chromatin and different abilities to promote chromatin condensation, as studied with the Atomic Force Microscope. According to this criterion, H1 subtypes can be classified as weak condensers (H1.1 and H1.2), intermediate condensers (H1.3) and strong condensers (H1.0, H1.4, H1.5 and H1x). The variable C-terminal domain is required for nucleosome spacing by H1.4 and is likely responsible for the chromatin condensation properties of the various subtypes, as shown using chimeras between H1.4 and H1.2. In contrast to previous reports with isolated nucleosomes or linear nucleosomal arrays, linker histones at a ratio of one per nucleosome do not preclude remodeling of minichromosomes by yeast SWI/SNF or Drosophila NURF. We hypothesize that the linker histone subtypes are differential organizers of chromatin, rather than general repressors.

| S-EPMC2748705 | biostudies-literature

Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis

Project description:We studied how H1 regulates higher-order chromatin architecture by performing Hi-C. In addition, we tested the effects of H1 domains on nucleosome organisation and DNA methylation by performing MNase-seq and Bisulfite-seq.

2024-02-15 | GSE176526 | GEO

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