Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

BANCseq for determination of genome-wide apparent transcription factor binding affinities [ATAC-Seq]

ABSTRACT: In vivo transcription factor binding is regulated by DNA sequence and chromatin features. However, the impact of chromatin context on genome-wide transcription factor binding affinities have not yet been characterized. Here we report the establishment of a quantitative protein-DNA binding assay to determine genome-wide binding affinities to native chromatinized DNA. We use this method to quantify apparent genome-wide binding affinities of both pioneering and non-pioneering transcription factors to uncover the regulatory role of chromatin on transcription factor binding. This revealed that DNA accessibility is the main determinant of transcription factor binding, which restricts nanomolar binding of non-pioneering factors to promoters. DNA binding motifs only appear to be important for very high-affinity binding, but are not essential for nanomolar binding. We uncover numerous biological processes enriched at specific binding affinities, suggesting they are regulated at defined transcription factor concentrations. Importantly, our method adds a new quantitative layer of transcription factor biology, enabling stratification of genomic targets based on transcription factor expression and prediction of transcription factor binding sites under non-physiological conditions, such as disease associated elevated expression of (onco)genes.

ORGANISM(S): Mus musculus

PROVIDER: GSE219034 | GEO | 2023/02/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

BANCseq for determination of genome-wide apparent transcription factor binding affinities

Project description:This SuperSeries is composed of the SubSeries listed below. In vivo transcription factor binding is regulated by DNA sequence and chromatin features. However, the impact of chromatin context on genome-wide transcription factor binding affinities have not yet been characterized. Here we report the establishment of a quantitative protein-DNA binding assay to determine genome-wide binding affinities to native chromatinized DNA. We use this method to quantify apparent genome-wide binding affinities of both pioneering and non-pioneering transcription factors to uncover the regulatory role of chromatin on transcription factor binding. This revealed that DNA accessibility is the main determinant of transcription factor binding, which restricts nanomolar binding of non-pioneering factors to promoters. DNA binding motifs only appear to be important for very high-affinity binding, but are not essential for nanomolar binding. We uncover numerous biological processes enriched at specific binding affinities, suggesting they are regulated at defined transcription factor concentrations. Importantly, our method adds a new quantitative layer of transcription factor biology, enabling stratification of genomic targets based on transcription factor expression and prediction of transcription factor binding sites under non-physiological conditions, such as disease associated elevated expression of (onco)genes.

2023-02-09 | GSE219035 | GEO

BANCseq for determination of genome-wide apparent transcription factor binding affinities [CUT&Run]

Project description:In vivo transcription factor binding is regulated by DNA sequence and chromatin features. However, the impact of chromatin context on genome-wide transcription factor binding affinities have not yet been characterized. Here we report the establishment of a quantitative protein-DNA binding assay to determine genome-wide binding affinities to native chromatinized DNA. We use this method to quantify apparent genome-wide binding affinities of both pioneering and non-pioneering transcription factors to uncover the regulatory role of chromatin on transcription factor binding. This revealed that DNA accessibility is the main determinant of transcription factor binding, which restricts nanomolar binding of non-pioneering factors to promoters. DNA binding motifs only appear to be important for very high-affinity binding, but are not essential for nanomolar binding. We uncover numerous biological processes enriched at specific binding affinities, suggesting they are regulated at defined transcription factor concentrations. Importantly, our method adds a new quantitative layer of transcription factor biology, enabling stratification of genomic targets based on transcription factor expression and prediction of transcription factor binding sites under non-physiological conditions, such as disease associated elevated expression of (onco)genes.

2023-02-09 | GSE193553 | GEO

BANCseq for determination of genome-wide apparent transcription factor binding affinities

Project description:BANCseq for determination of genome-wide apparent transcription factor binding affinities

| PRJNA906616 | ENA

BANCseq for determination of genome-wide apparent transcription factor binding affinities [ATAC-Seq]

Project description:BANCseq for determination of genome-wide apparent transcription factor binding affinities [ATAC-Seq]

| PRJNA906619 | ENA

BANCseq for determination of genome-wide apparent transcription factor binding affinities [CUT&Run]

Project description:BANCseq for determination of genome-wide apparent transcription factor binding affinities [CUT&Run]

| PRJNA796587 | ENA

Global profiling of protein-DNA and protein-nucleosome binding affinities using quantitative mass spectrometry

Project description:Interaction proteomics studies have provided fundamental insights into multimeric biomolecular assemblies and cell-scale molecular networks. Significant recent developments in mass spectrometry-based interaction proteomics have been fueled by rapid advances in label-free, isotopic, and isobaric quantitation workflows. Here, we report a quantitative protein-DNA and protein-nucleosome binding assay that uses affinity purifications from nuclear extracts coupled with isobaric chemical labeling and mass spectrometry to quantify apparent binding affinities proteome-wide. We use this assay with a variety of DNA and nucleosome baits to quantify apparent binding affinities of monomeric and multimeric transcription factors and chromatin remodeling complexes.

2018-05-02 | PXD007132 | Pride

BANC-seq to identify genome-wide transcription factor binding affinities to native chromatin

Project description:BANC-seq (Binding Affinities to Native Chromatin by sequencing) allows determination of absolute apparent binding affinites of transcription factors to native chromatin in a genome-wide manner. In this study, we establish the method and show that chromatin and DNA sequence define binding affinites of FOXA1, SP1, YY1 and MYC/MAX complex. To relate the identified binding affinities to the actual transcriptional levels of these transcription factors in the cells used in this study, and to confirm that the nuclear isolation protocol used in the study does not lead to loss of nuclear proteins, we have generated whole proteomes including proteomics standards for absolute quantification of proteins. In addition, to validate some of the findings of the study, we have performed PAQMAN (Protein-nucleic acid affinity quantification by MAss spectrometry in nuclear extracts), as well as DNA pulldowns followed by mass spec.

2023-02-09 | PXD038502 | Pride

Determining DNA-protein binding affinities and specificities from crude lysates using a combined SILAC/TMT labeling strategy

Project description:Gene expression is driven by the binding of transcription factors to regulatory elements in the genome, such as enhancers and promoters. A powerful technique to study DNA-protein interactions is affinity purification followed by mass spectrometry. Classic affinity purifications coupled to quantitative mass spectrometry provide information about binding specificity. Binding of transcription factors to regulatory elements in vivo, however, also depends on binding affinity, so the strength of an interaction. To obtain this information, we recently developed a technique called PAQMAN that uses a series of DNA affinity purifications to quantify apparent binding affinities proteome-wide. Here, we expand our PAQMAN workflow to obtain information about binding specificity and affinity in a single experiment. To this end, we combine quantitation at the MS1 level with quantitation at the MS2 level, a strategy that is known as higher order multiplexing. This is, to our knowledge, the first time that higher order multiplexing is applied to affinity purification - mass spectrometry experiments. In the future, we anticipate that this new workflow will be a useful tool to investigate transcription factor biology.

2023-10-08 | PXD041674 | Pride

Genome-wide binding of transcription factor IRF3

Project description:Genome-wide binding of transcription factor IRF3

| PRJNA686372 | ENA

Nucleation of DNA Repair Factors by FOXA1 Links DNA Demethylation and Transcriptional Pioneering

Project description:We report that the winged helix transcription factor FOXA1 is unexpectedly associated with components of single and double stranded-DNA repair complexes. Biochemical studies and high-throughput approaches validated the hierarchical composition of this FOXA1-nucleated machinery and revealed the dependency on FOXA1 for global targeting of the key repair polymerase POLB. Genome-wide DNA methylomes at single-base resolution demonstrated that FOXA1-DNA repair complex is functionally linked to DNA demethylation in a lineage specific fashion. Loss-of-function studies indicate that a significant portion of FOXA1-bound regions display localized reestablishment of methylation and that the subsets with most consistent hypermethylation are represented by active promoters and enhancers that also exhibit the greatest depletion of POLB following FOXA1 removal. Consistently, forced expression of FOXA1 commits its binding sites to an active DNA demethylation in a POLB dependent manner. Finally, we showed that FOXA1-associated DNA demethylation is tightly coupled with genomic targeting of estrogen receptor and estrogen responsiveness. Together, our results link FOXA1-associated DNA demethylation to its transcriptional pioneering.

2016-06-08 | PXD004271 | Pride

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