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Regulation of histone H3 by the ubiquitin-conjugating enzyme UBE2K determines neurogenesis of human embryonic stem cells [RNA-Seq]

ABSTRACT: We find that loss of UBE2K leads to accumulation of histone leading to increase in overall load for epigenetic marks and thus hindering differentiation.Our results provide a novel link between ubiquitination, histone regulation and hESC differentiation into neurons. To test whether UBE2K knockdown also induces enrichment of H3K9me3 marks at specific genes, we performed chromatin immunoprecipitation (ChIP)-sequencing assays of hESCs using an antibody to H3K9me3.

ORGANISM(S): Homo sapiens

PROVIDER: GSE146701 | GEO | 2020/04/22

REPOSITORIES: GEO

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Regulation of histone H3 by the ubiquitin-conjugating enzyme UBE2K determines neurogenesis of human embryonic stem cells [ChIP-Seq]

Project description:We find that loss of UBE2K leads to accumulation of histone leading to increase in overall load for epigenetic marks and thus hindering differentiation.Our results provide a novel link between ubiquitination, histone regulation and hESC differentiation into neurons. To test whether UBE2K knockdown also induces enrichment of H3K9me3 marks at specific genes, we performed chromatin immunoprecipitation (ChIP)-sequencing assays of hESCs using an antibody to H3K9me3.

2020-04-22 | GSE146703 | GEO

Regulation of histone H3 by the ubiquitin-conjugating enzyme UBE2K determines neurogenesis of human embryonic stem cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-04-21 | GSE146704 | GEO

The ubiquitin-conjugating enzyme UBE2K determines neurogenic potential through histone H3 in human embryonic stem cells.

Project description:Histones modulate gene expression by chromatin compaction, regulating numerous processes such as differentiation. However, the mechanisms underlying histone degradation remain elusive. Human embryonic stem cells (hESCs) have a unique chromatin architecture characterized by low levels of trimethylated histone H3 at lysine 9 (H3K9me3), a heterochromatin-associated modification. Here we assess the link between the intrinsic epigenetic landscape and ubiquitin-proteasome system of hESCs. We find that hESCs exhibit high expression of the ubiquitin-conjugating enzyme UBE2K. Loss of UBE2K upregulates the trimethyltransferase SETDB1, resulting in H3K9 trimethylation and repression of neurogenic genes during differentiation. Besides H3K9 trimethylation, UBE2K binds histone H3 to induce its polyubiquitination and degradation by the proteasome. Notably, ubc-20, the worm orthologue of UBE2K, also regulates histone H3 levels and H3K9 trimethylation in Caenorhabditis elegans germ cells. Thus, our results indicate that UBE2K crosses evolutionary boundaries to promote histone H3 degradation and reduce H3K9me3 repressive marks in immortal cells.

| S-EPMC7248108 | biostudies-literature

Regulation of histone H3 by the ubiquitin-conjugating enzyme UBE2K determines neurogenesis of human embryonic stem cells

Project description:Regulation of histone H3 by the ubiquitin-conjugating enzyme UBE2K determines neurogenesis of human embryonic stem cells

| PRJNA611702 | ENA

Regulation of histone H3 by the ubiquitin-conjugating enzyme UBE2K determines neurogenesis of human embryonic stem cells [RNA-Seq]

Project description:Regulation of histone H3 by the ubiquitin-conjugating enzyme UBE2K determines neurogenesis of human embryonic stem cells [RNA-Seq]

| PRJNA611705 | ENA

Regulation of histone H3 by the ubiquitin-conjugating enzyme UBE2K determines neurogenesis of human embryonic stem cells [ChIP-Seq]

Project description:Regulation of histone H3 by the ubiquitin-conjugating enzyme UBE2K determines neurogenesis of human embryonic stem cells [ChIP-Seq]

| PRJNA611708 | ENA

Identification of ubiquitination sites of purified histone H3

Project description:Histones modulate gene expression by chromatin compaction, regulating numerous processes such as differentiation. However, the mechanisms underlying histone degradation remain elusive. When compared with their differentiated counterparts, immortal human embryonic stem cells (hESCs) have a unique chromatin architecture and low levels of trimethylated histone H3 at lysine 9 (H3K9me3), a heterochromatin-associated modification. Here we assess a link between the intrinsic epigenetic landscape and ubiquitin-proteasome system of hESCs. We find that hESCs exhibit high expression of UBE2K, a ubiquitin-conjugating enzyme. Loss of UBE2K increases the levels of H3K9 trimethyltransferase SETDB1, resulting in H3K9 trimethylation and repression of neurogenic genes during differentiation. Concomitantly, loss of UBE2K impairs the ability of hESCs to differentiate into neural progenitors with neurogenic properties. Besides H3K9 trimethylation, we find that UBE2K binds histone H3 to induce its polyubiquitination and degradation by the proteasome. Notably, ubc-20, the worm orthologue of UBE2K, also regulates both histone H3 levels and H3K9 trimethylation in C. elegans germline. Thus, our results indicate that UBE2K crosses evolutionary boundaries to promote histone H3 degradation and reduce H3K9me3 repressive marks in immortal cells.

2020-06-01 | PXD018621 | Pride

The ubiquitin-conjugating enzyme HR6B is required for maintenance of X chromosome silencing in mouse spermatocytes and spermatids

Project description:Background: The ubiquitin-conjugating enzyme HR6B is required for spermatogenesis in mouse. Loss of HR6B results in aberrant histone modification patterns on the trancriptionally silenced X and Y chromosomes (XY body) and on centromeric chromatin in meiotic prophase. We studied the relationship between these chromatin modifications and their effects on global gene expression patterns, in spermatocytes and spermatids. Results: HR6B is enriched on the XY body and on centromeric regions in pachytene spermatocytes. Global gene expression analyses revealed that spermatid-specific single- and multicopy X-linked genes are prematurely expressed in Hr6b knockout spermatocytes. Very few other differences in gene expression were observed in these cells, except for upregulation of major satellite repeat transcription. In contrast, in Hr6b knockout spermatids, 7298 genes were differentially expressed; 65% of these genes was downregulated, but we observed a global upregulation of gene transcription from the X chromosome. In wildtype spermatids, approximately 20% of the single-copy X-linked genes reach an average expression level that is similar to the average expression from autosomes. Conclusions: Spermatids maintain an enrichment of repressive chromatin marks on the X chromosome, originating from meiotic prophase, but this does not interfere with transcription of the single-copy X-linked genes that are reactivated or specifically activated in spermatids. HR6B represses major satellite repeat transcription in spermatocytes, and functions in the maintenance of X chromosome silencing in spermatocytes and spermatids. It is discussed that these functions involve modification of chromatin structure, possibly including H2B ubiquitylation. 8 Affymetrix microarrays were generated: 4 from wildtype and HR6B knockout spermatocytes (2 replicates each), and 4 from wildtype and HR6B knockout spermatids (2 replicates each).

2010-05-27 | E-GEOD-21749 | biostudies-arrayexpress

Ubiquitin in motion: structural studies of the ubiquitin-conjugating enzyme?ubiquitin conjugate.

Project description:Ubiquitination of proteins provides a powerful and versatile post-translational signal in the eukaryotic cell. The formation of a thioester bond between ubiquitin (Ub) and the active site of a ubiquitin-conjugating enzyme (E2) is critical for the transfer of Ub to substrates. Assembly of a functional ubiquitin ligase (E3) complex poised for Ub transfer involves recognition and binding of an E2?Ub conjugate. Therefore, full characterization of the structure and dynamics of E2?Ub conjugates is required for further mechanistic understanding of Ub transfer reactions. Here we present characterization of the dynamic behavior of E2?Ub conjugates of two human enzymes, UbcH5c?Ub and Ubc13?Ub, in solution as determined by nuclear magnetic resonance and small-angle X-ray scattering. Within each conjugate, Ub retains great flexibility with respect to the E2, indicative of highly dynamic species that adopt manifold orientations. The population distribution of Ub conformations is dictated by the identity of the E2: the UbcH5c?Ub conjugate populates an array of extended conformations, and the population of Ubc13?Ub conjugates favors a closed conformation in which the hydrophobic surface of Ub faces helix 2 of Ubc13. We propose that the varied conformations adopted by Ub represent available binding modes of the E2?Ub species and thus provide insight into the diverse E2?Ub protein interactome, particularly with regard to interaction with Ub ligases.

| S-EPMC3056393 | biostudies-literature

The ubiquitin-conjugating enzyme HR6B is required for maintenance of X chromosome silencing in mouse spermatocytes and spermatids

2010-05-08 | GSE21749 | GEO