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Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions [titration]

ABSTRACT: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions [titration]

PROVIDER: PRJNA686411 | ENA |

REPOSITORIES: ENA

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Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions [titration]

Project description:Most eukaryotic transcription factors (TFs) are part of large protein families, with members of the same family (i.e. paralogous TFs) recognizing similar DNA-binding motifs but performing different regulatory functions. Many TF paralogs are co-expressed in the cell, and thus can compete for target sites across the genome. Here, we show that direct competition for DNA binding between TF paralogs is a major determinant of their genomic binding patterns. Using yeast proteins Cbf1 and Pho4 as our model system, we designed a high-throughput quantitative assay to capture the genomic binding profiles of competing TFs in a cell-free system. Our data shows that Cbf1 and Pho4 greatly influence each other’s occupancy by competing for their common putative genomic binding sites. The competition is different at different genomic sites, as dictated by the TFs' expression levels and their divergence in DNA-binding specificity and affinity. Analyses of ChIP-seq data show that the biophysical rules that dictate the competitive TF binding patterns in vitro are also followed in vivo, in the complex cellular environment. Furthermore, the Cbf1-Pho4 competition for genomic sites, as characterized in vitro using our new assay, plays a critical role in the specific activation of their target genes in the cell. Overall, our study highlights the importance of direct TF-TF competition for genomic binding and gene regulation by TF paralogs, and proposes an approach for studying this competition in a quantitative and high-throughput manner.

2021-04-22 | GSE163511 | GEO

Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions [competition]

Project description:Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions [competition]

| PRJNA686408 | ENA

Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions

Project description:Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions

| PRJNA686407 | ENA

Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions [competition]

2021-04-22 | GSE163509 | GEO

Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions.

Project description:Most eukaryotic transcription factors (TFs) are part of large protein families, with members of the same family (i.e., paralogous TFs) recognizing similar DNA-binding motifs but performing different regulatory functions. Many TF paralogs are coexpressed in the cell and thus can compete for target sites across the genome. However, this competition is rarely taken into account when studying the in vivo binding patterns of eukaryotic TFs. Here, we show that direct competition for DNA binding between TF paralogs is a major determinant of their genomic binding patterns. Using yeast proteins Cbf1 and Pho4 as our model system, we designed a high-throughput quantitative assay to capture the genomic binding profiles of competing TFs in a cell-free system. Our data show that Cbf1 and Pho4 greatly influence each other's occupancy by competing for their common putative genomic binding sites. The competition is different at different genomic sites, as dictated by the TFs' expression levels and their divergence in DNA-binding specificity and affinity. Analyses of ChIP-seq data show that the biophysical rules that dictate the competitive TF binding patterns in vitro are also followed in vivo, in the complex cellular environment. Furthermore, the Cbf1-Pho4 competition for genomic sites, as characterized in vitro using our new assay, plays a critical role in the specific activation of their target genes in the cell. Overall, our study highlights the importance of direct TF-TF competition for genomic binding and gene regulation by TF paralogs, and proposes an approach for studying this competition in a quantitative and high-throughput manner.

| S-EPMC8256859 | biostudies-literature

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

Project description:MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

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Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-04-22 | GSE163512 | GEO

Competition between DNA methylation and transcription factors determines binding of NRF1

Project description:Competition between DNA methylation and transcription factors determines binding of NRF1

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In-culture titration experiment for sRSE

Project description:In order to test the transcriptome-wide functionality of the identified sRSE instances, we performed an in vivo titration experiment in which synthetic RNA oligonucleotides harboring tandem sRSE1 repeats were used as intracellular decoys that would bind the putative trans factor, preventing it from targeting endogenous transcripts. Capped and poly-adenylated RNAs carrying tandem sRSE elements were transfected along with scrambled RNA molecules as control. 48 hours post-transfection, samples were subjected to transcriptome profiling to measure the regulatory consequences of the in-vivo titration of the sRSE-binding trans factor.

2014-07-24 | E-GEOD-49609 | biostudies-arrayexpress

In-culture titration experiment for sRSE

2014-07-24 | GSE49609 | GEO