Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

69 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The RPB2 flap loop of human RNA polymerase II is dispensable for transcription initiation and elongation.

ABSTRACT: Deletion of the flap loop in the Rp2 subunit of human RNAPII did not alter the ability of human RNAPII to initiate transcription or elongate the initiated transcripts in vivo and in vitro, and was also dispensable for elongation factor-mediated enhancement and inhibition of transcript elongation in vitro. ChIP:chip of wild-type and flap deletion human RNAPII revealed that the mutant RNAPII was not defective for promoter binding, initiation and elongation in vivo. Eight ChIP datasets were generated as log2(IP/input) fluorescence intensities using anti-FLAG IP of wild-type RPB2-FLAG cells in biological triplicate, anti-FLAG IP of delta-FL RPB2 FLAG cells in biological triplicate, and anti-RPB1 CTD, 8WG16 of both wild-type and delta-FL cells in biological duplicate. The two 8WG16- IP datasets were combined to measure the distribution of RPB1 signal.

ORGANISM(S): Homo sapiens

SUBMITTER: jeff grass

PROVIDER: E-GEOD-29734 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

The RPB2 flap loop of human RNA polymerase II is dispensable for transcription initiation and elongation.

Palangat Murali M Grass Jeffrey A JA Langelier Marie-France MF Coulombe Benoit B Landick Robert R

Molecular and cellular biology 20110613 16

The flap domain of multisubunit RNA polymerases (RNAPs), also called the wall, forms one side of the RNA exit channel. In bacterial RNAP, the mobile part of the flap is called the flap tip and makes essential contacts with initiation and elongation factors. Cocrystal structures suggest that the orthologous part of eukaryotic RNAPII, called the flap loop, contacts transcription factor IIB (TFIIB), but the function of the flap loop has not been assessed. We constructed and tested a deletion of the ...[more]

PMID: 21670157

Similar Datasets

Next-generation sequencing for the fat mass and obesity-associated protein (FTO) binding mRNA

Project description:Purpose: The goals of this study are to investigate the mRNAs that bind to the FTO protein in the white fat tissue from mice. Methods: 1. White fat from CAG promoter driven transgenic Flag-tagged FTO mice were extracted with RNA protected. 2. Flag-FTO proteins were immunoprecipitated with control IP using IgG. 3. The immunoprecipitated RNAs were deep sequenced and analyzed. Results: We focused on the mRNAs which have functions related to lipid metabolism and homeostasis. Immunoprecipitated RNAs profiles from Flag-FTO IP and IgG IP were generated by deep sequencing.

2016-01-05 | E-GEOD-74255 | biostudies-arrayexpress

Genome-wide analysis of TIAR RNA ligands in mouse macrophages before and after LPS stimulation

Project description:TIA-1 related protein (TIAR) is a RNA-binding protein involved in several steps of gene expression such RNA splicing and translation. TIAR contains three RNA recognition motifs (RRMs) allowing its interaction with specific sequences localized in the untranslated regions (UTRs) of several mRNAs. In myeloid cells, TIAR has been shown to bind and regulate the translation and stability of various mRNAs encoding proteins important for the inflammatory response, such as TNFÎ±, Cox-2 or IL-8 . Here, we generated two macrophage-like RAW 264.7 cell lines expressing either a tagged full-length TIAR protein or a RRM2-truncated mutant unable to bind RNA with high affinity . By a combination of RNA-IP and microarray analysis (RIP-chip), we identified mRNAs specifically bound by the full-length protein both in basal conditions and in response to LPS. Microarray hybridization was performed on TIAR-FLAG-associated mRNAs or TIARÎRRM2-FLAG-associated mRNAs in unstimulated and LPS-stimulated RAW264.7 cells. Enrichment of TIAR-FLAG-associated mRNAs and TIARÎRRM2-FLAG-associated mRNAS were normalized to total transcriptome of TIAR-FLAG and TIARÎRRM2-FLAG expressing-RAW264.7 cells respectively. After amplification and labelling, sample pairs were hybridized onto Mouse Exonic Evidence Based Oligonucleotide (MEEBO) arrays containing on average 38784 mouse 70mer oligonucleotide probes (Stanford University, US). Hybridizations were replicated with dye swap.

2016-02-05 | E-GEOD-77577 | biostudies-arrayexpress

A0913 interacts with CP47 of PSII and ApcF of PBS

Project description:Co-immunoprecipitation (CoIP) was performed to identify the proteins that A0913 interacts with. The thylakoid membranes were solubilized with the detergent n-Dodecyl-β-D-maltoside (DDM) before CoIP was performed using the monoclonal antibodies against the Flag tag to precipitate the target proteins. Four proteins were obtained by the CoIP as revealed by SDS-PAGE analysis . Immunoblotting with antibodies against CP47 and the Flag tag revealed that the top band in the gel was CP47 while the third band from the top down was A0913CF . Mass spectrometry revealed that these bands were CP47 of PSII。

2024-11-06 | PXD057430 | Pride

Genome-wide nucleosome, TFIIIC and TFIIIB occupancies in Saccharomyces cerevisiae

Project description:Paired-end sequencing study of nucleosomes and immuno-precipitated Tfc1 and Brf1 complexes from MNase-digested nuclei. Nucleosomal DNA, input DNA and DNA from immunopurified TFIIIB and TFIIIC complexes (IP) were subjected to paired-end sequencing.

2013-07-17 | E-GEOD-44586 | biostudies-arrayexpress

SgK269 Interactome - Homo- and Heterotypic Association Regulates Signalling by the SgK269/PEAK1 and SgK223 Pseudokinases

Project description:Anti Flag IP of Flag-SgK269 and control IP from MCF10A EcoR cells.

2016-08-24 | PXD004250 | Pride

TTC7A Localizes to Specific Regions of Chromatin

Project description:Inherited TTC7A loss of function mutations causes intestinal and immune deficiency. TTC7A is expressed in hematopoietic and epithelial cells however its cellular function remains poorly understood. In this work we provided evidence that TTC7A is an intrinsic nucleus factor. In an attempt to link the function of TTC7A in chromatin compaction, histone modifications and general transcriptional regulation we undertook to map the observed interaction of TTC7A to chromatin genome-wide by ChiP-Seq of Flag-tagged WT_TTC7A expressed in B lymphoblastoid cell lines using two anti-Flag antibodies (hereafter IP-Flag1 and IP-Flag2).

2018-10-19 | E-MTAB-5938 | biostudies-arrayexpress

ChIP-on-chip on BMP2 treated C2C12 cells transfected with FLAG tagged Alx3 expression vector

Project description:FLAG-binding DNA analysis using Agilent Mouse promoter 1M microarray Input vs FLAG-IP

2013-03-05 | E-GEOD-44822 | biostudies-arrayexpress

Senataxin associates with replication forks to protect fork integrity across RNAPII transcribed genes

Project description:Here we analysed the role of yeast Senataxin (Sen1) in coordinating replication with transcription and in protecting genome integrity. Senataxin is mutated in the two severe neurodegenerative diseases AOA2 and ALS4. We show that a fraction of Sen1/Senataxin DNA/RNA helicase associates with replication forks and protects the integrity of those fork encountering highly expressed RNAPII genes. sen1 mutants accumulate aberrant DNA structures and RNA-DNA hybrids while forks clash head-on with RNAPII transcription units and counteract recombinogenic events and accumulation of checkpoint signals. Nrd1, which acts togheter with Sen1 in trascription temination, is not recruited at replication forks. nrd1 mutants does not display replication defects, high genome instability and checkpoint activation observed in sen1 mutants The Sen1 function in replication can be therefore separable from its role in RNA processing. We propose a role for Sen1/Senataxin during chromosome replication in facilitating replisome progression across RNAPII transcribed genes thus preventing DNA-RNA hybrids accumulation when forks encounter nascent transcripts on the lagging strand template. Chip on chip analysis was carried out as described (Bermejo et al., 2011), employing anti-Flag monoclonal antibody M2 (Sigma-Aldrich) Labelled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.

2012-11-09 | E-GEOD-39139 | biostudies-arrayexpress

Proline hydroxylation of ChREBP

Project description:This project investigated proline hydroxylation of ChREBP. Proline hydroxylation was investigated in flag-IP enriched protein extracts from ChREBP-flag overexpressing HEK293 cells (A) and in ChREBP-IP enriched mouse liver protein (male, C57BL6/J) (B).

2020-10-19 | PXD019137 | Pride

Genome wide profiling of RNA polymerase III in Saccharomyces cerevisiae

Project description:Genome wide mapping of RNA polymearase III binding sites in Saccharomyces cerevisiae under normal growth and nutrient starved condition using ChIP-seq. Chromatin Immuno-precipitation (ChIP) was performed for FLAG tagged version of pol III subunit RPC128 after crosslinking the log-phase cells with formaldehyde. MOCK and IP DNA was sequenced and coverage of pol III was calculated at each base of the genome. RPC128-FLAG ChIP-seq single end seqquencing on Illumina GAII. 2 replicates of IP samples and 1 MOCK sample. Done in under normal growth and nutrient deprivation (4 hours).

2013-06-21 | E-GEOD-39566 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data