Expression changes in HeLa cells treated with siRNA against HCFC1 or control luciferase
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Viviane Praz
PROVIDER: E-GEOD-31412 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Analysis of transcriptional regulation in human cells has implicated a large number of promoter-specific DNA-binding proteins that regulate transcription via diverse mechanisms. In some cases, these DNA-sequence-specific factors associate with intermediaries that orchestrate interactions with the chromatin-modifying enzymes. One such intermediary is HCF-1 (host-cell factor-1; HCFC1). HCF-1, first identified for its involvement in herpes-simplex virus transcription and subsequently shown to be an important cell-cycle regulator, has a poorly defined role in genome-wide transcriptional regulation. We show here, by chromatin immunoprecipitation followed by high-throughput sequence analysis (ChIP-seq), that HCF-1 is a major transcriptional start site associated factor, whose promoter association correlates positively with transcriptional activity. Thus, in HeLa cells HCF-1 is observed on 5400 generally active CpG-island promoters. Examination of the DNA sequences underlying the HCF-1-binding sites revealed three sequence motifs associated with the binding of (i) ZNF143 and Ronin/THAP11, (ii) GABP, and (iii) YY1 sequence-specific transcription factors. Subsequent ChIP-seq analysis of these four transcription factors revealed a large co-association of HCF-1 with these four transcription factors at approximately 90% of HCF-1-bound promoters. These studies suggest that a relatively small number of transcription factors -- some (ZNF143 and Ronin/THAP11) in novel combinations -- play a major role in HeLa-cell transcriptional regulation in association with HCF-1. This experiment includes the sequencing data of material obtained from chromatin immunoprecipitation using antibodies against HCFC1(antibodies against the C-subunit and the N-subunit), PolII(antibody against the RPB2 subunit), H3K36ME3 and H3K4Me3 histone modifications, ZNF143, THAP11, GABPalpha and YY1. It also includes control data of the Input material. All of them were done using HeLa cycling cells.
2012-07-31 | E-GEOD-31417 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE31412: Expression changes in HeLa cells treated with siRNA against HCFC1 or control luciferase GSE31417: Genome-wide study of HCFC1 binding sites and its associated transcription factors in cycling Human HeLa cells Refer to individual Series
2012-07-30 | E-GEOD-31419 | biostudies-arrayexpress
Project description:To characterize the pol III transcriptome in actively growing human cells, we used MR90hTeIrt lung fibroblasts, which are immortal but not transformed, with an intact Rb pathway. After formaldehyde cross-linking, chromatin was extracted and submitted to immunoprecipitation. To identify actively transcribed RNAP-III transcription units, we used antibodies directed against the RPC4 subunit of RNAP-III. To identify promoter regions, we used antibodies directed against Bdp1, which is part of both Brf1-TFIIIB and Brf2-TFIIIB, and thus should mark all types of active RNAP-III promoters. Antibodies directed against Brf1 were used to mark type 1 and 2 promoters. For type 3 promoters, we engineered an IMR90hTert cell line expressing the SNAPc subunit SNAP45 tagged at its C-terminal end with the biotin acceptor domain as well as the biotin ligase BirA and performed M-bM-^@M-^\chromatin affinity purificationM-bM-^@M-^] (ChAP) with streptavidin beads. In each case, the precipitated material was then processed for deep sequencing. ChIP-enriched DNA or ChAP-enriched DNA from MR90hTeIrt cells were analyzed by Illumina high-throughput sequencing. This analysis includes ChIP data done with antibodies against : RPC4, Bfr1, Bdp1 and SNAP45. Two lanes were run for RPC4, Brf1 and SNAP45, and three for Bdp1. One lane was run with Input DNA for control.
2010-02-11 | E-GEOD-18184 | biostudies-arrayexpress
Project description:SNAPc-dependent promoters are unique among cellular promoters in being very similar to each other, even though some of them recruit RNA polymerase II and other RNA polymerase III. We have examined all SNAPc-bound promoters present in the human genome. We find that there is a surprisingly small number of them, some 70 promoters. Among these, the large majority is bound by either RNA polymerase II or RNA polymerase III, as expected, but one gene hitherto considered an RNA polymerase III gene is also occupied by significant levels of RNA polymerase II, which synthesizes an RNA distinct from that synthesized by RNA polymerase III. Both RNA polymerase II and RNA polymerase III SNAPc- dependent promoters use a largely overlapping set of a few transcription activators, including GABP, a novel factor implicated in snRNA gene transcription. SNAPc-dependent promoters in the human genome
2012-11-22 | E-GEOD-38303 | biostudies-arrayexpress
Project description:Cell type-specific master transcription factors (MTFs) play vital roles in defining cell identity and function. However, the roles ubiquitous factors play in the specification of cell identity remain underappreciated. Here we show that all three subunits of the ubiquitous heterotrimeric CCAAT-binding NF-Y complex are required for the maintenance of embryonic stem cell (ESC) identity, and establish NF-Y as a novel component of the core pluripotency network. Genome-wide occupancy and transcriptomic analyses in ESCs and neurons reveal that not only does NF-Y regulate genes with housekeeping functions through cell type-invariant promoter-proximal binding, but also genes required for cell identity by binding to cell type-specific enhancers with MTFs. Mechanistically, NF-Y's distinctive DNA-binding mode promotes MTF binding at enhancers by facilitating a permissive chromatin conformation. Our studies unearth a novel function for NF-Y in promoting chromatin accessibility, and suggest that other proteins with analogous structural and DNA-binding properties may function in similar ways. Genome-wide mapping of NF-YA, NF-YB, and NF-YC subunits of the NF-Y complex in mouse ESCs, and microarray gene expression profiling of control knockdown (KD), NF-YA KD, NF-YB KD, NF-YC KD, and NF-YA/NF-YB/NF-YC triple KD ESCs.
2014-08-14 | E-GEOD-56839 | biostudies-arrayexpress
Project description:Recent transcriptome analysis indicates that >90% of human genes undergoes alternative splicing, underscoring the contribution of differential RNA processing to diverse proteomes in higher eukaryotic cells. The polypyrimidine tract binding protein PTB is a well-characterized splicing repressor, but PTB knockdown causes both exon inclusion and skipping. Genome-wide mapping of PTB-RNA interactions and construction of a functional RNA map now revealed that dominant PTB binding near a competing constitutive splice site generally induces exon inclusion whereas prevalent binding close to an alternative site often causes exon skipping. This positional effect was further demonstrated by disrupting or creating a PTB binding site on minigene constructs and testing their responses to PTB knockdown or overexpression. These findings suggest a mechanism for PTB to modulate splice site competition to produce opposite functional consequences, which may be generally applicable to RNA binding splicing factors to positively or negatively regulate alternative splicing in mammalian cells. Examination of PTB-RNA binding in Hela cells using CLIP-seq (Cross-Linking ImmunoPrecipitation coupled with high-throughput sequencing) method. Peaks: The four alignment files (linked as supplementary files on Sample records) were combined together for peak finding, as we found that most of the monomeric and dimeric tags are similarly distributed in the genome with high pearson correlation coefficient. The method to detect the peaks above gene-specific randomized background was similar to (Yeo et al., 2009) and described in the paper (Xue et al., 2009).
2009-12-24 | E-GEOD-19323 | biostudies-arrayexpress
Project description:We compared in triplicate mRNA levels from cells treated with siRNA against either HCF-1 or, as a negative control, luciferase. We observed that 19% of Refseq annotated genes are differentially expressed (either up or down regulated with a multiple testing corrected p value of ≤ 0.05) upon depletion of HCF-1. This large number of differentially expressed genes upon HCF-1 depletion demonstrates a broad role of HCF-1 in the regulation of gene expression.
2012-07-31 | GSE31412 | GEO
Project description:TOP2B is involved in transcriptional initiation in response to nuclear hormone ligands and plays a role in transcriptional elongation. Whole genome TOP2B ChIP-seq was carried out on human MCF7 cells in the presence and absence of the nuclear hormone estradiol. Three peak calling methods were used and the peaks identified by at least two methods were analyzed further. Approximately half of the peaks fell either within a gene or within 5Kb of a transcription start site. The coincidence of TOP2B peaks and gene promoters was analyzed; TOP2B peaks were less frequently associated with promoters in estradiol treated than in control cells, suggesting a role of TOP2B in repression of transcription or a transient role in estradiol induced transcriptional changes. Whole genome TOP2B ChIP-seq was carried out on human MCF7 cells in the presence (30 mins exposure) and absence of the nuclear hormone estradiol. "Input" control samples were also sequenced for background detection and comparison.
2015-09-21 | E-GEOD-66753 | biostudies-arrayexpress
Project description:We report the genome wide binding sites of BAP1, HCF1 and OGT in bone marrow derived macrophages. De-ubiquitinating enzyme BAP1 is mutated in a hereditary cancer syndrome with increased risk of mesothelioma and uveal melanoma. Somatic BAP1 mutations occur in various malignancies. We show that mouse Bap1 gene deletion is lethal during embryogenesis, but systemic or hematopoietic-restricted deletion in adults recapitulates features of human myelodysplastic syndrome (MDS). Knockin mice expressing BAP1 with a 3xFlag tag revealed that BAP1 interacts with host cell factor–1 (HCF-1), O-linked N-acetylglucosamine transferase (OGT), and the polycomb group proteins ASXL1 and ASXL2 in vivo. OGT and HCF-1 levels were decreased by Bap1 deletion, indicating a critical role for BAP1 in stabilizing these epigenetic regulators. Human ASXL1 is mutated frequently in chronic myelomonocytic leukemia (CMML) so an ASXL/BAP1 complex may suppress CMML. A BAP1 catalytic mutation found in a MDS patient implies that BAP1 loss of function has similar consequences in mice and humans. For BAP1, bone marrow derived macrophages were used differentiated from bone marrow cells of BAP1-3X Flag Tagged KI mice we generated. For OGT and HCF1, bone marrow derived macrophages were used from BAP1 WT mice.
2012-11-07 | E-GEOD-40723 | biostudies-arrayexpress
Project description:Transcriptome analysis of depletion of DYRK1A in HeLa cells Global gene expression profiling has shown upregulation of many genes in the context of DYRK1A depletion in HeLa cells. Many of these genes deregulated by DYRK1A are involved in immune response system. Transcriptome analysis of siRNA against DYRK1A transfected in HeLa cells on GeneChipM-BM-. Human Exon 1.0 ST Arrays (Affimetrix). Control HeLa cells have been transfected with the same concentration of siRNA non-targeting (siNT). Experiment has been done experimental triplicates.
2014-05-01 | E-GEOD-43259 | biostudies-arrayexpress