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Genome wide occupancy of SUMO machinery in proliferative and Ras-induced senescent human primary fibroblasts

ABSTRACT: Transcription factors represent one of the largest groups of proteins regulated by SUMO, and their modification has generally been correlated with transcriptional repression. However, as most of the studies focus on specific sumoylated transcriptional regulators, the distribution and global role of SUMO on chromatin in relation to transcription regulation remain largely unknown. To investigate this role, we determined the occupancy of SUMO machinery proteins on chromatin by ChIP coupled to sequencing in human primary cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE42211 | GEO | 2013/07/24

SECONDARY ACCESSION(S): PRJNA179304

REPOSITORIES: GEO

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Genome wide occupancy of SUMO machinery in proliferative and Ras-induced senescent human primary fibroblasts

Project description:Transcription factors represent one of the largest groups of proteins regulated by SUMO, and their modification has generally been correlated with transcriptional repression. However, as most of the studies focus on specific sumoylated transcriptional regulators, the distribution and global role of SUMO on chromatin in relation to transcription regulation remain largely unknown. To investigate this role, we determined the occupancy of SUMO machinery proteins on chromatin by ChIP coupled to sequencing in human primary cells. Examination of 3 histone modifications, Polymerase II, SUMO1, SUMO2, Ubc9 and PIASy in proliferative and Ras-induced senescent fibroblasts.

2013-07-24 | E-GEOD-42211 | biostudies-arrayexpress

Extensive SUMO modification of chromatin factors distinguishes pluripotent from somatic cells

Project description:The post-translational modification of proteins by SUMO acts as a key gatekeeper of cell identity. In mouse embryonic fibroblast (MEFs), SUMO impedes reprogramming to pluripotency, while in embryonic stem cells (ESCs), it represses the emergence of totipotent-like cells, suggesting that SUMO targets distinct sets of substrates to preserve the somatic and pluripotent states. Using MS-based proteomics, we show here that the composition of the endogenous SUMOylomes differs dramatically between MEFs and ESCs. In MEFs, SUMOylated proteins organize in a rather diffuse functional network enriched in nuclear factors with general cellular functions. In contrast, in ESCs, SUMOylated proteins form a tightly interconnected network mainly composed of repressive chromatin complexes. We also characterized several SUMOylated pluripotency factors and show that SUMO modification of Dppa2 and Dppa4 hampers their ability to induce a totipotent-like state. Altogether, we propose that rewiring the repertoire of SUMO target networks is a major driver of cell fate transition during embryonic development.

2020-09-04 | GSE144881 | GEO

Quantitative analysis of proliferative and Ras-induced senescent human primary fibroblasts transcriptomes

Project description:The goals of this study is to analyse transcriptionnal changes in senescent cells and to compare them with ChIPseq data for several histones marks and proteins of the SUMO machinery mRNA profiling of proliferative versus Ras-induced senescent humain primary fibroblasts 5 days post-infection

2013-07-24 | E-GEOD-42212 | biostudies-arrayexpress

Quantitative analysis of proliferative and Ras-induced senescent human primary fibroblasts transcriptomes

2013-07-24 | GSE42212 | GEO

Multifaceted down-regulation of the Srs2 helicase by the SUMO-like domain protein Esc2 promotes local recombination at sites of stalled replication

Project description:The SUMO-like domains-containing family of proteins to which Saccharomyces cerevisiae Esc2 belongs facilitates DNA damage tolerance (DDT) via elusive mechanisms. Here we report that Esc2 promotes recombination-mediated DDT by engaging in functional and physical interactions with Srs2 and Elg1, two readers of SUMOylated PCNA and modulators of DDT. These interactions depend on the SUMO Interacting Motifs of Elg1 and Srs2, and on the SUMO-like domains of Esc2. Mechanistically, Esc2 promotes Elg1 association to damaged and stalled forks and Srs2 turnover. Elg1 limits the levels of SUMOylated PCNA and subsequently of the anti-recombinase Srs2 at damaged sites, upholding local Rad51 binding. In conjunction with the SUMO–targeted ubiquitin ligase Slx5/Slx8, Esc2 also promotes proteasome-mediated Srs2 turnover, a process further enhanced by CDK-mediated Srs2 phosphorylation. Our results provide mechanistic insights into how SUMO- and DNA damage response-regulated pathways intersect to enable local error-free damage-bypass by recombination in the face of genotoxic stress. Proteins ChIP-chip analyses analysis were carried out as described (Bermejo et al., 2009). Labelled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

2015-02-16 | E-GEOD-65701 | biostudies-arrayexpress

The SUMO protease SENP6 regulates the constitutive centromere-associated network by group

Project description:Project 1: Identification of SUMOylated proteins which are regulated by the SUMO protease SENP6. SENP6 knockdown was performed by two independent shRNAs and SUMOylated proteins were purified from U2OS expressing His10-tagged SUMO2 by means of Ni-NTA pulldown. Purified SUMOylated proteins were identified and quantified by label-free quantification. Project 2: Dynamics of chromatin-associated proteins influenced by SENP6. After siRNA-mediated knockdown of SENP6, chromatin fractions of U2OS cells were isolated and abundances of proteins were quantified. Project 3: Analysis of in vitro SUMOylated CENP-T for the presence of SUMOylated SUMO peptides. For this aim purified CENP-T-HA was in vitro SUMOylated with a SUMO Q87R mutant to reduce the length of the tryptic peptide and therefore to be able to identified sit-specific SUMOylation.

2019-09-13 | PXD011963 | Pride

Genome-wide localization of SUMO-modified proteins in untreated or heat-shocked budding yeast

Project description:Most SUMO-modified proteins in budding yeast and human cells are associated with chromatin. To determine specifically where sumoylated proteins are found across the genome, we performed ChIP-seq with a SUMO antibody in budding yeast. We identified 603 loci that each contain a stable SUMO peak. In agreement with a previous study, most of these sites correspond to tRNA genes or genes that encode ribosomal proteins (RPGs). However, 147 of the SUMO peaks in our analysis are found at promoters of protein-coding genes that are not RPGs (non-RPGs), many of which are among the most highly expressed genes. By comparing our data with other ChIP-seq studies, we determined that non-RPG SUMO peaks are situated precisely where general transcription factors (GTFs) assemble, but not where RNA polymerase II (RNAPII) or other promoter-proximal proteins bind. In support of this, we determined that the large subunit of TFIIF is the major SUMO target among GTFs and propose that its sumoylation controls the dynamics of RNAPII gene association. Additionally, we found that exposing yeast to a brief heat shock significantly reduces the intensity of SUMO peaks at most genes of all classes, which likely reflects the vast transcriptional reprogramming that occurs in response to temperature stress.

2021-09-21 | GSE167425 | GEO

SUMO-chain-regulated proteasomal degradation timing exemplified in DNA replication initiation

Project description:Similar to ubiquitin, SUMO forms chains, but the identity of SUMO-chain-modified factors and the purpose of this modification remain largely unknown. Here, we identify budding yeast SUMO protease Ulp2, able to disassemble SUMO chains, as a DDK interactor enriched at replication origins that promotes DNA replication initiation. Replication-engaged DDK is SUMOylated on chromatin, becoming a degradation-prone substrate when Ulp2 no longer protects it against SUMO-chain assembly. Specifically, SUMO chains channel DDK for SUMO-targeted ubiquitin ligase Slx5/Slx8-mediated and Cdc48 segregase-assisted proteasomal degradation. Importantly, the SUMOylation-defective ddk-KR mutant rescues inefficient replication onset and MCM activation in cells lacking Ulp2, suggesting that SUMO chains time DDK degradation. Using two unbiased proteomic approaches, we further identify subunits of the MCM helicase and other factors as SUMO-chain-modified degradation-prone substrates of Ulp2 and Slx5/Slx8. We thus propose SUMO-chain-/Ulp2-protease-regulated proteasomal degradation as a mechanism that times the availability of functionally-engaged SUMO-modified protein pools during replication and beyond.

2019-09-10 | GSE113835 | GEO

SUMO-2 Orchestrates Chromatin Modifiers in Response to DNA Damage

Project description:Small Ubiquitin-like Modifiers play critical roles in the DNA Damage Response (DDR). To increase our understanding of SUMOylation in the mammalian DDR, we employed a quantitative proteomics approach to identify dynamically regulated SUMO-2 conjugates and modification sites upon treatment with the DNA damaging agent MMS. We have uncovered a dynamic set of 20 upregulated and 33 downregulated SUMO-2 conjugates, and 755 SUMO-2 sites, of which 362 were dynamic in response to MMS. In contrast to yeast, where a response is centered on homologous recombination, we identified dynamically SUMOylated interaction networks of chromatin modifiers, transcription factors, DNA repair factors and nuclear body components. SUMOylated chromatin modifiers include JARID1B/KDM5B, JARID1C/KDM5C, p300, CBP, PARP1, SetDB1 and MBD1. Whereas SUMOylated JARID1B was ubiquitylated by the SUMO-targeted ubiquitin ligase RNF4 and degraded by the proteasome in response to DNA damage, JARID1C was SUMOylated and recruited to the chromatin to demethylate histone H3K4.

2015-03-16 | PXD001810 | Pride

Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes

Project description:We determined the occupancy of SUMO-1 on chromatin in HeLa cells by use of chromatin affinity purification coupled with next generation sequencing RNA-Seq: The goal is to compare differential gene expression in SUMO-1 depleted cells and control cells (GL2 depleted) to verify the observation in the paper, and to cross-check with RT-PCR results.

2012-10-02 | GSE41264 | GEO

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