Renormalization of GSE32442 and GSE33128
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Tiandao Li
PROVIDER: E-GEOD-35878 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Functional association of Gdown1 with RNA polymerase II poised on human genes.
Cheng Bo B Li Tiandao T Rahl Peter B PB Adamson Todd E TE Loudas Nicholas B NB Guo Jiannan J Varzavand Katayoun K Cooper Jeffrey J JJ Hu Xiaopeng X Gnatt Averell A Young Richard A RA Price David H DH
Molecular cell 20120101 1
Most human genes are loaded with promoter-proximally paused RNA polymerase II (Pol II) molecules that are poised for release into productive elongation by P-TEFb. We present evidence that Gdown1, the product of the POLR2M gene that renders Pol II responsive to Mediator, is involved in Pol II elongation control. During in vitro transcription, Gdown1 specifically blocked elongation stimulation by TFIIF, inhibited the termination activity of TTF2, and influenced pausing factors NELF and DSIF, but d ...[more]
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Project description:Most human genes are loaded with promoter proximally paused RNA polymerase II (RNAP II) molecules that are poised for release into productive elongation by P-TEFb. Gdown1, a protein that renders RNAP II responsive to mediator, is involved in RNAP II elongation control. During in vitro transcription assays Gdown1 specifically blocked elongation stimulation by TFIIF, inhibited the termination activity of TTF2, and influenced pausing factors NELF and DSIF, but did not affect the function of TFIIS or the mRNA capping enzyme. Without P-TEFb, Gdown1 led to the production of stably paused polymerases in the presence of nuclear extract. ChIP-Seq data demonstrated that Gdown1 mapped over essentially all poised polymerases across the human genome. Gdown1 increases the stability of poised polymerases while maintaining their responsiveness to P-TEFb, and mediator overcomes a Gdown1-mediated block of initiation by allowing TFIIF function. 7 ChIP-Seq data for Pol II and Gdown1 in human HeLa cell. See associated publication.
2012-01-13 | E-GEOD-32442 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE35878: Renormalization of GSE32442 and GSE33128 GSE35882: Whole Cell Extract Refer to individual Series
2012-02-21 | E-GEOD-35886 | biostudies-arrayexpress
Project description:Most human genes are loaded with promoter proximally paused RNA polymerase II (RNAP II) molecules that are poised for release into productive elongation by P-TEFb. Gdown1, a protein that renders RNAP II responsive to mediator, is involved in RNAP II elongation control. During in vitro transcription assays Gdown1 specifically blocked elongation stimulation by TFIIF, inhibited the termination activity of TTF2, and influenced pausing factors NELF and DSIF, but did not affect the function of TFIIS or the mRNA capping enzyme. Without P-TEFb, Gdown1 led to the production of stably paused polymerases in the presence of nuclear extract. ChIP-Seq data demonstrated that Gdown1 mapped over essentially all poised polymerases across the human genome. Gdown1 increases the stability of poised polymerases while maintaining their responsiveness to P-TEFb, and mediator overcomes a Gdown1-mediated block of initiation by allowing TFIIF function. 1 whole cell extract sample in human HeLa cell. See associated publication.
2012-02-21 | E-GEOD-35882 | biostudies-arrayexpress
Project description:Purpose: Description of a spike-adjusting-method (SAM) to normalize ChIP-seq data . Methods: We performed ChIP-seq of POLR3D and POLR2B with mouse liver supplemented with 2.5% of human DNA. Human DNA will be used as an internal control for ChIP-seq quantification. Results: We show that using the SAM for ChIP-seq quantification improve similarity of POLR3D and POLR2B ChIP-seq replicates samples and improve difference between samples originate from different conditions. Conclusions: The SAM improves comparison of ChIP-seq samples, either by increasing similarity between replicates or by emphasise differences between conditions. Chromatin Immuno-precipitations were performed with antibodies directed against POLR3D (Pol III) and POLR2B (Pol II) using mouse liver material supplemented with human DNA. Immuno-precipitated DNA was next sequenced using Illumina HiSeq. Three different concentrations of human spiked DNA were tested for the Pol III ChIP (2.5%, 5% and 10%). We also sequenced the corresponding inputs (crosslinked DNA from mouse liver). Two concentrations of human spiked DNA (5% and 10%) were tested for the Pol 2 ChIP. We also sequenced the corresponding inputs (crosslinked DNA from mouse liver).
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Project description:The Tip60 (also known as Kat5) lysine acetyltransferase functions broadly as a transcriptional co-activator that acetylates histones. In contrast, Tip60 functions in embryonic stem cells (ESCs) both to silence genes that promote differentiation and to activate genes required for proliferation. The mechanism by which Tip60 functions as a repressor is unknown. Here we show that the class II histone deacetylase Hdac6 co-purifies with Tip60-p400 complex from ESCs and is necessary for complete silencing of most differentiation genes targeted by Tip60. In contrast to differentiated cells, where Hdac6 is mainly cytoplasmic and does not interact with Tip60, Hdac6 is largely nuclear in ESCs and neural stem cells (NSCs) and interacts with Tip60-p400 in both cell types. Hdac6 is enriched at promoters bound by Tip60-p400 in ESCs, but while Tip60 binds on both sides of transcription start sites (TSSs), Hdac6 binding overlaps with only the downstream Tip60 peak. Surprisingly, Hdac6 does not deacetylate histones at these sites, but rather is required for Tip60 binding. These data suggest that nuclear exclusion of Hdac6 during differentiation plays a major role in modulation of Tip60-p400 function. We determined the genome-wide localization of Tip60 and Hdac6 in mouse ES cells, and examined genomic binding profiles of Tip60 and Hdac6 upon indicated knockdown by ChIP-seq. We examined genomic binding profiles of p400 upon indicated knockdown by ChIP-seq.
2013-11-20 | E-GEOD-42209 | biostudies-arrayexpress
Project description:SMORE-seq (Simultaneous Mapping Of RNA Ends by sequencing) is developted to simultaneously identify the strongest TSS (Transcription Start Site) and PAS (Polyadenylation Site) SMORE-seq were performed in wild type Saccharomyces cerevisiae
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2015-09-12 | E-GEOD-72948 | biostudies-arrayexpress
Project description:Commitment of hematopoietic stem cells to B lineage precursors and development of B lineage precursors into mature B cells is attained through the coordinated function of multiple signaling networks, which are in turn controlled through stringent functioning of stage-specific transcription factors. Here, we describe the essential role of Sox4, an HMG (high mobility group)-box-containing transactivator, in B cell development. In the absence of Sox4, differentiation from pre-pro B to pro-B, from pro-B fraction B to pro-B fraction C and further to the immature B cell stage was severely impaired. Loss of differentiation was associated with reduced expression of Rag1 and Rag2 and markedly reduced DJ (diverse, joining) and VDJ (variable DJ) recombination at immunoglobulin heavy chain gene loci. We uncovered Sox4-regulated transcriptional circuits and a landscape of Sox4-chromatin interactions in pro-B cells. Sox4 ensured the negative regulation of Wnt signaling, which is critical for self-renewal of hematopoietic stem cells and early progenitors, by inducing one of its downstream effectors, casein kinase 1 epsilon. Our findings suggest that Sox4 orchestrates a unique transcriptional program and coordinates multilevel control in the differentiation of early-stage B cells. One sample of BAP-Sox4 bioChIP DNA and one sample of BAP-Sox4 input chromatin DNA were used.
2014-07-02 | E-GEOD-50066 | biostudies-arrayexpress
Project description:Investigation of DNAse Hypersensitivity changes in podocytes cultured under normal or high glucose conditions transfected with a miR-93 mimic or a nontargeting mimic. Examination of the changes in hypersensitivity induced by high glucose culture conditions compared to normal glucose conditions to mimic the diabetic millieu. Further, to see if miR-93 overexpression can reverse these changes.
2016-06-28 | E-GEOD-63975 | biostudies-arrayexpress
Project description:Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs (lncRNAs), as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-type specific biomarkers. However, despite the potential importance of lncRNAs to the cancer field, no comprehensive survey of lncRNA expression across various cancers has been reported. We used 3'-End Sequencing for Expression Quantification (3SEQ) to quantify transcript abundance across 64 solid tumors representing 17 diagnostic subtypes of adenocarcinomas, squamous cell carcinomas, and sarcomas. We identified hundreds of transcripts from among the known 1,065 lncRNAs surveyed that show variability in transcript levels between the tumor types, and therefore, make potential biomarker candidates. We discovered 1,071 novel intergenic transcribed regions and demonstrate that these show similar patterns of variability between tumor types. We find that many of these differentially expressed cancer transcripts are also expressed in normal tissues. One such novel transcript specifically expressed in breast tissue was further evaluated using RNA in situ hybridization on a panel of breast tumors and shown to correlate with low tumor grade and estrogen receptor expression, thereby representing a potentially important new breast cancer biomarker. This study provides the first large survey of lncRNA expression within a panel of solid cancers and also identifies a number of novel transcribed regions differentially expressed across distinct cancer types that represent candidate biomarkers for future research. 3SEQ was performed on 64 formalin-fixed, paraffin-embedded (FFPE) human tumors representing 17 diagnostic cancer subtypes. Duplicate libraries were prepared for two of the tumors (ESS STT5520 and LMS STT516). 3SEQ was also performed on 27 normal human tissue samples. RNA-Seq was performed on 6 breast cancer cell lines for the examination of the breast-specific transcript on chr10. Series supplementary files: 'GSE28866_raw_counts_54511_peaks_cancer_and_normal.txt': Raw_counts: Total 3SEQ reads in each peak for each sample. File includes read counts for 54,511 peaks for the 66 cancer libraries and the 27 normal libraries. 'GSE28866_36048_normalized_peaks_cancer_and_normal.txt': Normalized_peaks: Normalized 3SEQ expression data for the 36,048 filtered peaks for the 66 cancer libraries and the 27 normal libraries. Peaks were classified as coding, lncRNA (Rinn, Bartel, Hughes, Gencode_lnc), other known transcripts (ref_known_Gencode_nc, all_mrna, other known), downstream, intron, promoter, or novel_intergenic. Peaks determined to be differentially expressed in one of the 17 cancer subtypes using a series of 2-Class SAM analyses are noted along with the type of cancer showing upregulation. Expression data was normalized using the sequencing depth of each sample by scaling the data using the mean value of each sample. Data was further compressed to reduce outliers by taking the square root of each value.
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