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ChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w sequenced by SOLiD

ABSTRACT: We determined DNA-binding sites of the yeast transcription factor Yfl052w by ChIP-exo. Cells were grown in the YP media containing palatinose. Yfl052w was tagged with HA tag and anti-HA antibody was used for the immunoprecipitation. Examination of Yfl052 trancription factor in HA-tagged and wt cells (as a control)

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Ksenia Pougach

PROVIDER: E-GEOD-57901 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network.

Pougach Ksenia K Voet Arnout A Kondrashov Fyodor A FA Voordeckers Karin K Christiaens Joaquin F JF Baying Bianka B Benes Vladimir V Sakai Ryo R Aerts Jan J Zhu Bo B Van Dijck Patrick P Verstrepen Kevin J KJ

Nature communications 20140910

The emergence of new genes throughout evolution requires rewiring and extension of regulatory networks. However, the molecular details of how the transcriptional regulation of new gene copies evolves remain largely unexplored. Here we show how duplication of a transcription factor gene allowed the emergence of two independent regulatory circuits. Interestingly, the ancestral transcription factor was promiscuous and could bind different motifs in its target promoters. After duplication, one paral ...[more]

PMID: 25204769

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ChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w sequenced by Illumina

Project description:We determined DNA-binding sites of the yeast transcription factor Yfl052w by ChIP-exo. Cells were grown in the YP media containing palatinose. Yfl052w was tagged with HA tag and anti-HA antibody was used for the immunoprecipitation. Examination of Yfl052 trancription factor in HA-tagged and wt cells (as a control)

2014-07-24 | E-GEOD-57900 | biostudies-arrayexpress

Single-molecule Dynamics of Enhanceosome Assembly In Embryonic Stem Cells

Project description:These ChIP-exo data were used to validate the predictions from our live-cell single-molecule imaging experiment The ChIP-exo mapping of ultra-fine localization of endogenous Sox2, halo-Sox2, and two halo-Sox2 mutants (halo-Sox2M and halo-Sox2D) in embryonic stem cells.

2014-03-12 | E-GEOD-54103 | biostudies-arrayexpress

ChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w

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

2014-07-22 | E-GEOD-57902 | biostudies-arrayexpress

High-resolution Brachyury DNA-binding Sites Mapping by ChIP-exo

Project description:Mapping ultra high resolution of Brachyury:DNA interaction would provide us with valuable new mechanistic insights into complex molecular transactions at Brachyury-bound enhancers. Embryonic stem cells were differentiated into Brachyury-positive mesoendoderm cells. And, ChIP-exo experiment was then performed to identify detailed Brachyury-DNA binding profiles.

2014-03-10 | E-GEOD-54963 | biostudies-arrayexpress

High-resolution Sp1 DNA-binding Site Mapping by ChIP-exo in STHdh Q7/Q7 cells

Project description:Mapping ultra-high resolution of Sp1:DNA interaction would provide us with valuable new mechanistic insights into Sp1-mediated gene regulatory network in Huntington Disease cell culture model. STHdh Q7/Q7 cells were directly fixed and used for the ChIP-exo experiment.

2016-07-15 | E-GEOD-84056 | biostudies-arrayexpress

Charting Brachyury-mediated Developmental Pathways During Early Mouse Embryogenesis

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

2014-03-10 | E-GEOD-54985 | biostudies-arrayexpress

Gene expression is a circular process

Project description:This study involves the role of yeast mRNA decay factors in transcription. The experiment included here are the ChIP-exo results of three decay factors: Xrn1, Dcp2 & Lsm1. Four experiments were made: Xrn1, Dcp2, Lsm1 and control (no-TAP tag), in two replicates.

2013-05-23 | E-GEOD-44312 | biostudies-arrayexpress

Discrete Functions of Rev-erba Couple Metabolism to the Clock [HTS]

Project description:Circadian and metabolic physiology are intricately intertwined, as illustrated by Rev-erb , a transcription factor (TF) that functions both as a core repressive component of the cell autonomous clock and as a regulator of metabolic genes. Here we show that Rev-erb modulates the clock and metabolism by different genomic mechanisms. Clock control requires Rev-erb to bind directly to the genome at its cognate sites, where it competes with activating ROR TFs. By contrast, Rev-erb regulates metabolic genes primarily by recruiting the HDAC3 corepressor to sites to which it is tethered by cell type-specific transcription factors. Thus, direct competition between Rev-erb and ROR TFs provides a universal mechanism for self-sustained control of molecular clock across all tissues, whereas Rev-erb utilizes lineage-determining factors to convey a tissue-specific epigenomic rhythm that regulates metabolism tailored to the specific need of that tissue. Biological replicates were uploaded in separated files and indicated in the file names.

2015-06-16 | E-GEOD-67962 | biostudies-arrayexpress

Permanganate ChIP-seq analysis of Pol II in nonheat shocked and heat shocked Drosophila S2R+ cells and nonheat shocked BG3 cells

Project description:The genomic distribution of transcriptionally engaged Pol II in control and heat shocked cells was determined by combining formaldehyde crosslinking and permanganate oxidation of transcription bubbles Cells treated in succession with formaldehyde and then permanganate, were subjected to chromatin precipitation with Rpb3 antibody, and then the pattern of permanganate modifications were mapped genome-wide

2013-07-02 | E-GEOD-46620 | biostudies-arrayexpress

Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPKMEF2 signaling [ChIP-seq]

Project description:Identfification of MEF2A target genes using ChIP-exo in skeletla muscle and primary cardiomyocytes. Identfification of MEF2A target genes using ChIP-exo and RNA-seq in skeletal muscle and primary cardiomyocytes. MEF2 plays a profound role in the regulation of transcription in cardiac and skeletal muscle lineages. To define the overlapping and unique MEF2A genomic targets, we utilized ChIP-exo analysis of cardiomyocytes and skeletal myoblasts. Of the 2783 and 1648 MEF2A binding peaks in skeletal myoblasts and cardiomyocytes, respectively, 294 common binding sites were identified. Genomic targets were compared to differentially expressed genes in RNA-seq analysis of MEF2A depleted myogenic cells. MEF2A target genes were identified in 48 hr DM C2C12 myoblasts cells and primary cardiomyocytes using ChIP-exo. Binding profiles on MEF2A in each cell type were compared. Cross sectional-analysis between ChIP-exo identified targets and RNA-seq analysis of MEF2A deplted myoblasts was also done.

2014-09-09 | E-GEOD-61204 | biostudies-arrayexpress

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