Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CETCh-Seq of Mammalian Transcription Factors

ABSTRACT: CETCh-Seq of Mammalian Transcription Factors

PROVIDER: PRJNA293987 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

CETCh-Seq of Mammalian Transcription Factors

Project description:Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) is a widely used technique for identifying transcription factor (TF) binding events throughout an entire genome. However, ChIP-seq is limited by the availability of suitable ChIP-seq grade antibodies, and the vast majority of commercially available antibodies fail to generate usable datasets. To ameliorate these technical obstacles, we present a robust methodological approach for performing ChIP-seq through epitope tagging of endogenous TFs. We used Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-based genome editing technology to develop CRISPR Epitope Tagging ChIP-seq (CETCh-seq) of DNA-binding proteins. We assessed the feasibility of CETCh-seq by tagging several TFs spanning a wide range of endogenous expression levels in the hepatocellular carcinoma cell line HepG2. Our data exhibit strong correlations between both replicate types as well as with standard ChIP-seq approaches that use TF antibodies. Notably, we also observed minimal changes to the cellular transcriptome and to the expression of the tagged TF. To examine the robustness of our technique, we further performed CETCh-seq in the breast adenocarcinoma cell line MCF7 as well as mouse embryonic stem cells and observed similarly high correlations. Collectively, these data highlight the applicability of CETCh-seq to accurately define the genome-wide binding profiles of DNA-binding proteins, allowing for a straightforward methodology to potentially assay the complete repertoire of TFs, including the large fraction for which ChIPquality antibodies are not available. CRISPR/Cas9 mediated epitope tagging of transcription factors in human cell types

2015-08-31 | E-GEOD-72082 | biostudies-arrayexpress

Synthetic transcription elongation factors

Project description:Synthetic transcription elongation factors

| PRJNA388392 | ENA

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (HiC-seq data sets)

Project description:Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (HiC-seq data sets)

| PRJNA445201 | ENA

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (Bis-seq data sets)

Project description:Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (Bis-seq data sets)

| PRJNA445196 | ENA

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (ATAC-seq data sets)

Project description:Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (ATAC-seq data sets)

| PRJNA445198 | ENA

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (ChIP-seq data sets)

Project description:Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (ChIP-seq data sets)

| PRJNA445200 | ENA

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (MNase-seq data sets)

Project description:Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (MNase-seq data sets)

| PRJNA445202 | ENA

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (RNA-seq data sets)

Project description:Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (RNA-seq data sets)

| PRJNA445203 | ENA

Mammalian NET-seq reveals genome-wide nascent transcription coupled to RNA processing

Project description:We have generated single-nucleotide resolution, nascent transcription profiles from HeLa cells by developing Native Elongation Transcript sequencing technology for mammalian chromatin (mNET-seq). Our extensive data sets provide a substantial resource to study mammalian nascent transcript profiles. We reveal unanticipated phosphorylation states for RNA polymerase II C-terminal domain (Pol II CTD) at both gene ends. We also observe that following 5’ splice site cleavage by the spliceosome, upstream exon transcripts are tethered to Pol II CTD phosphorylated on the serine 5 position (S5P) which is accumulated over downstream exons. We further show that depletion of termination factors substantially reduces Pol II pausing at gene ends leading to termination defects. Remarkably termination factors play an additional promoter role by restricting non-productive RNA synthesis and redistributing Pol II CTD S2P to promoters. These data demonstrate that CTD phosphorylation is more dynamic and variably distributed across mammalian transcription units than previously envisaged. To monitor nascent RNA within the mammalian Pol II complex, and its association with different CTD phosphorylation states, we employed mNET-seq methodology on HeLa cells, complemented with direct sequencing of chromatin-bound RNA (ChrRNA-seq). mNET-seq was preformed using the antibodies 8WG16, CMA602, CMA603 and CMA601, which are specific for unphosphorylated CTD, Ser2 phosphorylation, Ser5 phosphorylation and all CTD isoforms, respectively. In another experiment, to evaluate the effect of transcription termination factors in nascent RNA production by Pol II, mNET-seq and complemented with ChrRNA-seq was preformed on HeLa cells transfected with siRNA against PTBP1, CPSF73, CstF64+CstF64tau or Xrn2, and the gene profiles were compared with profiles from HeLa transfected with siRNA for Luciferase generated by the same protocol.

2015-04-23 | E-GEOD-60358 | biostudies-arrayexpress

Mammalian apoptotic factors regulate bacterial gene expression

Project description:Mammalian apoptotic factors regulate bacterial gene expression

| PRJNA734340 | ENA