SUMO2 ChIP-seq in the starved U2OS cells
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 4000
ORGANISM(S): Homo sapiens
SUBMITTER: Yaoyong Li
PROVIDER: E-MTAB-12293 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Chromatin immuno-precipitation using SUMO2 (Life Technologies) antibody in U2OS cell line.
2015-08-07 | E-MTAB-3084 | biostudies-arrayexpress
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Project description:In order to investigate the functions of the zinc finger transcription regulator ZMYM2 and the different types of ZMYM2 binding complex with TRIM28 or ADNP, we generated the ChIP-seq data of ADNP or TRIM28 in U2OS cells.
2023-06-01 | E-MTAB-12292 | biostudies-arrayexpress
Project description:Chromatin immuno-precipitation using anti-H3K18ac antibodies in U2OS cells.
2016-04-27 | E-MTAB-3695 | biostudies-arrayexpress
Project description:Chromatin immuno-precipitation using anti-Flag (Sigma) or control IgG (Millipore) antibodies in a U2OS stable cell line. ZMYM2 has the synonym ZNF198. Note: paired-end sequencing libraires were created in this experiment but only the forward (R1) reads are available in this submission. The 'LIBRARY_LAYOUT' attribute is therefore set to be 'SINGLE' ather than 'PAIRED'.
2015-06-23 | E-MTAB-2701 | biostudies-arrayexpress
Project description:Chromatin immuno-precipitation using anti-Flag (Sigma) antibodies in a U2OS stable cell line. Paired-end R1 and R2 reads are provided, but the processed (mapped) reads are from a single-end (R1 read only) mapping.
2015-12-03 | E-MTAB-3687 | biostudies-arrayexpress
Project description:Gene expression changes were measured between mouse ES cells of three genotypes: WT Chd7, Heterzygous Chd7 Null, Homozygous Chd7 Null. The hypothesis being tested was that CHD7, a chromatin remodeling protein, functions as a transcriptional regulator. This experiment was performed to detect gene targets of CHD7-mediated regulation. We report the genome-wide binding profile of CHD7, the protein implicated in CHARGE syndrome, in mouse ES cells using ChIP-Seq technology. Combining these data with other genomic datasets, we discover CHD7 to colocalize with other transcription factors including Oct4, Nanog, Sox2, and p300 at gene enhancer elements to regulate ES cell specific gene expression. Chd7 wildtype, heterozygous, and homozygous ES cells derived from preimplantation embryos were grown on feeder cells and total RNA was isolated using Trizol. The ratio of ES to feeder cells was estimated at 5:1. ChIP sequencing of CHD7 and p300 in mouse ES cells
2010-06-15 | E-GEOD-22341 | biostudies-arrayexpress
Project description:SUMOylation is a form of post-translational modification involving covalent attachment of SUMO (Small Ubiquitin-like Modifier) polypeptides to specific lysine residues in the target protein. In human cells, there are four SUMO proteins, SUMO1–4, with SUMO2 and SUMO3 forming a closely related subfamily. SUMO2/3, in contrast to SUMO1, are predominantly involved in the cellular response to certain stresses, including heat shock. Substantial evidence from studies in yeast has shown that SUMOylation plays an important role in the regulation of DNA replication and repair. Here, we report a proteomic analysis of proteins modified by SUMO2 in response to DNA replication stress in S phase in human cells. We have identified a panel of 22 SUMO2 targets with increased SUMOylation during DNA replication stress, many of which play key functions within the DNA replication machinery and/or in the cellular response to DNA damage. Interestingly, POLD3 was found modified most significantly in response to a low dose aphidicolin treatment protocol that promotes common fragile site (CFS) breakage. POLD3 is the human ortholog of POL32 in budding yeast, and has been shown to act during break-induced recombinational repair. We have also shown that deficiency of POLD3 leads to an increase in RPA-bound ssDNA when cells are under replication stress, suggesting that POLD3 plays a role in the cellular response to DNA replication stress. Considering that DNA replication stress is a source of genome instability, and that excessive replication stress is a hallmark of pre-neoplastic and tumor cells, our characterization of SUMO2 targets during a perturbed S-phase should provide a valuable resource for future functional studies in the fields of DNA metabolism and cancer biology.
2014-12-09 | PXD000716 | Pride
Project description:Purpose: To determine SUMO1 and SUMO2 chromatin profile in a static and dynamic manner in BMDC before and after LPS stimulation, and to determine RNAPolII chromatin occupancy in sumoylation-deficient BMDC compared to wild-type cells. Methods: SUMO1, SUMO2 and RNAPolII chromatin profiles were determined by sequencing BMDC chromatin immunoprecipitated with antibodies specific for SUMO1, SUMO2 and RNAPolII before and after LPS stimulation. Results: We show dynamic occupancy of three distal sites upstream of Ifnb1 gene by SUMO1 and SUMO2, as well as increased RNAPolII recruitment on selected genes. Conclusions: SUMO acts as a regulator of inflammatory and anti-viral gene programs. A study of SUMO and RNAPolII chromatin profile in Bone Marrow derived Dendritic Cells.
2015-12-14 | E-GEOD-66315 | biostudies-arrayexpress
Project description:Posttranslational modification with small ubiquitin-like modifiers (SUMOs) alters the function of proteins involved in diverse cellular processes. SUMOs are conjugated to lysine residues in target proteins by SUMO-specific enzymes. Although proteomic studies have identified hundreds of sumoylated substrates, methods to identify the modified lysines on a proteome-wide scale are lacking. We developed a method that enabled large-scale identification of sumoylated lysines and involved the expression of polyhistidine (6His)–tagged SUMO2 with Thr90 mutated to Lys. Digestion of 6His-SUMO2(T90K)–modified proteins with an endoproteinase Lys-C produces a diGly remnant on SUMO2(T90K)-conjugated lysines, enabling a specific immunoprecipitation of modified peptides with diGly-Lys-specific antibody and producing a unique mass-to-charge signature. Mass spectrometry analysis of SUMO2-enriched peptides from human cell lysates revealed more than 1000 sumoylated lysines in 539 proteins, including many functionally related proteins involved in cell cycle, transcription, and DNA repair. Not only can this strategy be used to study the dynamics of sumoylation and other potentially similar posttranslational modifications, but also, these data provide an unprecedented resource for future research on the role of sumoylation in cellular physiology and disease.
2014-10-15 | PXD001281 | Pride