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Genome wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE60918 | GEO | 2014/08/29

SECONDARY ACCESSION(S): PRJNA259804

REPOSITORIES: GEO

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Genome-wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I.

Project description:CCCTC-binding factor (CTCF) is a key regulator of nuclear chromatin structure and gene regulation. The impact of CTCF on transcriptional output is highly varied, ranging from repression to transcriptional pausing and transactivation. The multifunctional nature of CTCF may be directed solely through remodeling chromatin architecture. However, another hypothesis is that the multifunctional nature of CTCF is mediated, in part, through differential association with protein partners having unique functions. Consistent with this hypothesis, our mass spectrometry analyses of CTCF interacting partners reveal a previously undefined association with the transcription factor general transcription factor II-I (TFII-I). Biochemical fractionation of CTCF indicates that a distinct CTCF complex incorporating TFII-I is assembled on DNA. Unexpectedly, we found that the interaction between CTCF and TFII-I is essential for directing CTCF to the promoter proximal regulatory regions of target genes across the genome, particularly at genes involved in metabolism. At genes coregulated by CTCF and TFII-I, we find knockdown of TFII-I results in diminished CTCF binding, lack of cyclin-dependent kinase 8 (CDK8) recruitment, and an attenuation of RNA polymerase II phosphorylation at serine 5. Phenotypically, knockdown of TFII-I alters the cellular response to metabolic stress. Our data indicate that TFII-I directs CTCF binding to target genes, and in turn the two proteins cooperate to recruit CDK8 and enhance transcription initiation.

| S-EPMC4343169 | biostudies-literature

Genome wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-08-29 | E-GEOD-60918 | biostudies-arrayexpress

Genome wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I [gene expression]

Project description:Analysis of the effect of TFII-I depletion on gene expression Wehi-231 cell lines. Total RNA were extract from shCT and shTFII-I Wehi-231 cells.

2014-08-29 | E-GEOD-60915 | biostudies-arrayexpress

Genome wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I [ChIP-Seq]

Project description:Analysis of CTCF binding in Wehi-231 with TFII-I knockdown compare to Wehi-231 wt. ChIP experiment of CTCF in Wehi-231-CT and Wehi-231-shTFII-I

2014-08-29 | E-GEOD-60917 | biostudies-arrayexpress

Genome wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I [ChIP-Seq]

Project description:Analysis of CTCF binding in Wehi-231 with TFII-I knockdown compare to Wehi-231 wt.

2014-08-29 | GSE60917 | GEO

Genome wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I [gene expression]

Project description:Analysis of the effect of TFII-I depletion on gene expression Wehi-231 cell lines.

2014-08-29 | GSE60915 | GEO

Genome wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I

Project description:Genome wide targeting of the epigenetic regulatory protein CTCF to gene promoters by the transcription factor TFII-I

| PRJNA259804 | ENA

CTCF blocks antisense transcription initiation at divergent promoters.

Project description:Transcription at most promoters is divergent, initiating at closely spaced oppositely oriented core promoters to produce sense transcripts along with often unstable upstream antisense transcripts (uasTrx). How antisense transcription is regulated and to what extent it is coordinated with sense transcription is not well understood. Here, by combining acute degradation of the multi-functional transcription factor CTCF and nascent transcription measurements, we find that CTCF specifically suppresses antisense but not sense transcription at hundreds of divergent promoters. Primary transcript RNA-FISH shows that CTCF lowers burst fraction but not burst intensity of uasTrx and that co-bursting of sense and antisense transcripts is disfavored. Genome editing, chromatin conformation studies and high-resolution transcript mapping revealed that precisely positioned CTCF directly suppresses the initiation of uasTrx, in a manner independent of its architectural function. In sum, CTCF shapes the transcriptional landscape in part by suppressing upstream antisense transcription.

| S-EPMC10015438 | biostudies-literature

Solution structure of the general transcription factor 2I domain in mouse TFII-I protein.

Project description:The general transcription factor TFII-I, with the corresponding gene name GTF2I, is an unusual transcriptional regulator that associates with both basal and signal-induced transcription factors. TFII-I consists of six GTF2I repeat domains, called I-repeats R1-R6. The structure and function of the GTF2I domain are not clearly understood, even though it contains a helix-loop-helix motif, which is considered to be the protein-protein interaction area, based on biochemical analyses. Here, we report the solution structure of the fifth repeat of the six GTF2I repeat domains from murine TFII-I, which was determined by heteronuclear multidimensional NMR spectroscopy (PDB code 1Q60). The three-dimensional structure of the GTF2I domain is classified as a new fold, consisting of four helices (residues 8-24, 34-39, 63-71, and 83-91), two antiparallel beta strands (residues 44-47 and 77-80), and a well-defined loop containing two beta-turns between sheet 1 and helix 3. All of the repeats probably have similar folds to that of repeat 5, because the conserved residues in the GTF2I repeat domains are assembled on the hydrophobic core, turns, and secondary structure elements, as revealed by a comparison of the sequences of the first through the sixth GTF2I repeats in TFII-I.

| S-EPMC2203370 | biostudies-literature

A novel archaeal regulatory protein, Sta1, activates transcription from viral promoters.

Project description:While studying gene expression of the rudivirus SIRV1 in cells of its host, the hyperthermophilic crenarchaeon Sulfolobus, a novel archaeal transcriptional regulator was isolated. The 14 kDa protein, termed Sulfolobus transcription activator 1, Sta1, is encoded on the host chromosome. Its activating effect on transcription initiation from viral promoters was demonstrated in in vitro transcription experiments using a reconstituted host system containing the RNA polymerase, TATA-binding protein (TBP) and transcription factor B (TFB). Most pronounced activation was observed at low concentrations of either of the two transcription factors, TBP or TFB. Sta1 was able to bind viral promoters independently of any component of the host pre-initiation complex. Two binding sites were revealed by footprinting, one located in the core promoter region and the second approximately 30 bp upstream of it. Comparative modeling, NMR and circular dichroism of Sta1 indicated that the protein contained a winged helix-turn-helix motif, most probably involved in DNA binding. This strategy of the archaeal virus to co-opt a host cell regulator to promote transcription of its genes resembles eukaryal virus-host relationships.

| S-EPMC1635249 | biostudies-literature

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