Nucleosome mapping in 20 kb upstream regions of microRNAs
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE9029 | GEO | 2008/11/16
SECONDARY ACCESSION(S): PRJNA102529
REPOSITORIES: GEO
Similar Datasets
Project description:We mapped the nucleosome locations in upstream regions of all known microRNAs in 3 cell lines using the method described in Nature Biotechnology 2007 Feb;25(2):244-8. Keywords: Nucleosome Mapping Study 20 kb upstream regions of microRNAs were tiled at 10 bp spacing using mostly 50-mer probes. Duplicate experiments were performed in MCF7, MALME, and UACC62 cell lines.
2008-11-15 | E-GEOD-9029 | biostudies-arrayexpress
Project description:Nucleosome organization is critical for the regulation of gene expression, and genome-scale mapping of nucleosomes has revealed a conserved, highly ordered pattern in nucleosome positioning. Most genome-wide studies have been performed in model organisms and little is known about nucleosome positioning in evolutionarily divergent eukaryotes. We generated a high-resolution nucleosome map of the protozoan parasite Toxoplasma gondii from four high quality MNase-Seq datasets. T. gondii nucleosomes are organised in phase around the transcription start sites (TSSs) with a canonical pattern that is conserved across eukaryotes. Nucleosome occupancy in exons is influenced by several factors, including GC content, length of exons and strength of splice sites. Poly(dA:dT) is enriched at the +1 nucleosome rather than nucleosome-free regions (NFRs) and serves as the key sequence associated with nucleosome formation in T. gondii. Motif analysis of sequences in NFR1, adjacent to the transcription start site, revealed enrichment of DNA-binding motifs recognized by members of the plant-like ApiAP2 transcription factor family that is conserved across Apicomplexa. Genes associated with the two most common motifs are enriched in genes upregulated during two major waves of mRNA accumulation within the cell cycle. Genome-wide peaks from T. gondii assays for transposase-accessible chromatin using sequencing (ATAC-seq) coincide with NFR1, consistent with the enrichment of T. gondii open chromatin regulatory regions localizing to close to transcription initiation sites. Finally, by integrating the map of nucleosome positions with ChIP-seq we suggest that nucleosome positioning and placement of histone variants and histone modifications play roles in splicing of genes in T. gondii.
2017-09-08 | GSE86620 | GEO
Project description:BackgroundUnderstanding the regulation mechanism of var gene expression is crucial for explaining antigenic variation in Plasmodium falciparum. Recent work observed that while all var genes produce transcripts, only a few var genes exhibit high expression levels. However, the global regulation of var expression and the relationship between epigenetic and genetic control remains to be established.ResultWe have systematically reanalyzed the existing genomic data including chromatin configurations and gene expressions; and for the first time used robust statistical methods to show that the intron and 2 kb upstream regions of each endogenous var gene always maintain high chromatin accessibility, with high potential to bind transcription factors (TFs). The levels of transcripts for different var gene family members are associated with this chromatin accessibility. Any given var gene thus shows punctuated chromatin states throughout the asexual life cycle. This is demonstrated by three independent transcript datasets. Chromatin accessibility in the var intron and 2 kb upstream regions are also positively correlated with their GC content, suggesting the level of var genes silencing might be encoded in their intron sequences. Interestingly, both var intron and 2 kb upstream regions exhibit higher chromatin accessibility when the genes have relatively lower transcription levels, suggesting a punctuated repressive function for these regulatory elements.ConclusionBy integrating and analyzing epigenomic, genomic and transcriptomic data, our work reveals a novel distal element in var control. We found dynamic modulations of specific epigenetic marks around the var intron and distal upstream regions are involved in the general var gene expression patterns in malarial antigenic variation.
| S-EPMC4990864 | biostudies-literature
Project description:Interventions: Case series:Nucleosome Complex CAR-T cells
Primary outcome(s): Tumor markers
Study Design: Sequential
| 2684952 | ecrin-mdr-crc
Project description:Nuclear proteins bind chromatin to execute and regulate genome-templated processes. While structural and biochemical studies of individual nucleosome interactions have suggested that an acidic patch on the nucleosome disk surface may be a common site for recruitment to chromatin, the pervasiveness of acidic patch binding and whether other nucleosome surface binding hot-spots exist remains unclear. Here, we use nucleosome affinity proteomics with a library of nucleosomes that collectively disrupts all exposed histone surfaces to establish the universal principles of nucleosome binding. We find that the acidic patch and two adjacent surfaces are the primary hot-spots for nucleosome disk binding and are critical for the majority of nucleosome-protein interactions. In contrast, nearly half of the nucleosome disk surface participates only minimally in protein binding. In addition to establishing the fundamental principles of chromatin binding, our screen defines nucleosome surface requirements of nearly 300 nucleosome interacting proteins implicated in diverse nuclear processes including transcription, DNA damage repair, cell cycle regulation, and nuclear architecture. Building from our screen, we demonstrate that the Anaphase-Promoting Complex/Cyclosome directly binds the acidic patch and elucidate a redundant charge-based mechanism of acidic patch binding by nuclear pore protein ELYS. Overall, our interactome screen illuminates a highly competitive nucleosome binding hub for chromatin-targeted activities and curates a list of nucleosome interacting proteins that will enable mechanistic exploration of many unexpected chromatin-templated nuclear processes.
2020-06-24 | PXD018690 | Pride
Project description:The genome-wide distributions of STAT1, STAT2 and IRF9 in mock and interferon alpha (IFN) stimulated human cells was generated using high throughput sequencing to identify ISGF3 genomic occupancy. In combination, the nucleosome occupancy of 20 select IFN-stimulated gene regions were analyzed by direct selection MNase sequencing to determine the nucleosome positions and changes in nucleosome occupancy levels following IFN treatment over time. IFN stimulation resulted in decreased nucleosome positioning strength, with clear disruption over the course of IFN treatment followed by a return to steady state, and prominently at most ISGF3-bound regions.
2018-07-26 | GSE110067 | GEO
Project description:Analysis performed on protein samples submitted by Zhe Hu of the John E. Cronan Laboratory by the Protein Sciences Facility of the Biotechnology Center of the University of Illinois at Urbana-Champaign
2021-01-29 | PXD023486 | Pride
Project description:Goal of this project was the identification of chromatin interacting proteins whose binding is differentially regulated by di-methylation of lysine 20 on histone H4 (H4K20me2). To achieve this unodified and H4K20me2-modified histone H4 were generated by native chemical ligation and assembled into recombinant di-nucleosomes. The di-nucleosomes were immobilized on streptavidin-coated beads via the biotinylated di-nucleosomal DNA and used for nucleosome affinity purifications to identify proteins regulated by H4K20me2 from SILAC-labelled HeLaS3 nuclear extracts (Arg10 and Lys8). SILAC affinity purifications were carried out in "forward" (heavy extract on modified nucleosome and light extract on unmodified nucleosome) and "reverse" (light extract on modified nucleosome and heavy extract on unmodified nucleosome) label-swap experiments and protein abundances were quantified by MaxQuant.
2019-02-27 | PXD009281 | Pride
Project description:BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. Despite previous structural studies and recent advance of SWI/SNF family complexes, it remains incompletely understood how PBAF-nucleosome complex is organized. Here we determined structure of 13-subunit human PBAF in complex with acetylated nucleosome in ADP-BeF3-bound state. Four PBAF-specific subunits work together with nine BAF/PBAF-shared subunits to generate PBAF-specific modular organization, distinct from that of BAF at various regions. PBAF-nucleosome structure reveals six histone-binding domains and four DNA-binding domains/modules, the majority of which directly bind histone/DNA. This multivalent nucleosome-binding pattern, not observed in previous studies, suggests that PBAF may integrate comprehensive chromatin information to target genomic loci for function. Our study reveals molecular organization of subunits and histone/DNA-binding domains/modules in PBAF-nucleosome complex and provides structural insights into PBAF-mediated nucleosome association complimentary to the recently reported PBAF-nucleosome structure.
2023-03-11 | PXD036708 | Pride
Project description:Normal human epidermal keratinocytes (NHEK) from neonatal foreskin were cultured in serum-free EpiLife medium with human KC growth supplement (0.2% bovine pituitary extract (v/v), 5ug bovine insulin, 5ug/ml bovine transferrin, 0.5ng/ml human EGF, and 0.18 ug/ml hydrocortisone) from Cascade Biologics. Cultures were treated with recombinant cytokines from R&D Systems. J Immunol. 2007 Feb 15;178(4):2229-40. Keywords: cytokine response
2007-03-09 | GSE7216 | GEO