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NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [array]

ABSTRACT: NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [array]

PROVIDER: PRJNA510376 | ENA |

REPOSITORIES: ENA

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NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [array]

Project description:High-throughput (HT) in vitro methods for measuring protein-DNA binding have become invaluable for characterizing transcription factor (TF) complexes and modeling gene regulation. However, current methods do not utilize endogenous proteins and, therefore, do not quantify the impact of cell-specific post-translational modifications (PTMs) and cooperative cofactors. We introduce the HT nextPBM (nuclear extract protein-binding microarray) approach to study DNA binding of native cellular TFs that accounts for PTMs and cell-specific cofactors. We integrate immune-depletion and phosphatase-treatment steps into our nextPBM pipeline to characterize the impact of cofactors and phosphorylation on TF binding. We analyze binding of PU.1/SPI1 and IRF8 from human monocytes, delineate DNA-sequence determinants for their cooperativity, and show how PU.1 affinity correlates with enhancer status and the presence of cooperative and collaborative cofactors. We describe how nextPBMs, and our accompanying computational framework, can be used to discover cell-specific cofactors, screen for synthetic cooperative DNA elements, and characterize TF cooperativity at single-nucleotide resolution.

2018-12-18 | GSE123946 | GEO

NextPBM - A platform to study cell-specific transcription factor binding and cooperativity

Project description:NextPBM - A platform to study cell-specific transcription factor binding and cooperativity

| PRJNA510373 | ENA

NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [ChIP-Seq]

Project description:We analyzed binding of PU.1/SPI1 and IRF8 from human monocytes, delineate DNA-sequence determinants for their cooperativity using nextPBM, and show how PU.1 affinity correlates with enhancer status and the presence of cooperative and collaborative factors (C/EBPa)

2018-12-18 | GSE123872 | GEO

NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [ChIP-Seq]

Project description:NextPBM - A platform to study cell-specific transcription factor binding and cooperativity [ChIP-Seq]

| PRJNA510375 | ENA

NextPBM: a platform to study cell-specific transcription factor binding and cooperativity.

Project description: Not available

| S-EPMC6451091 | biostudies-literature

NextPBM - A platform to study cell-specific transcription factor binding and cooperativity

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

2018-12-18 | GSE123947 | GEO

Cross-platform study

Project description:Cross-platform study

| PRJNA95853 | ENA

Cross-Platform Array Comparative Genomic Hybridization (array CGH) Meta-Analysis

Project description:A series of studies have been published that evaluate the chromosomal copy number changes of different tumor classes using array Comparative Genomic Hybridization (array CGH), however the chromosomal aberrations that distinguish the different tumor classes have not been fully characterized. Therefore, we performed a meta-analysis of different array CGH data sets in an attempt to classify samples tested across different platforms. As opposed to RNA expression a common reference is used in dual channel CGH arrays: normal human DNA, theoretically facilitating cross-platform analysis. To this aim, cell line and primary cancer data sets from three different dual channel array CGH platforms obtained by four different institutes were integrated. The cell line data were used to develop preprocessing methods which performed noise reduction and transformed samples into a common format. The transformed array CGH profiles allowed perfect clustering by cell line, but importantly not by platform or institute. The same preprocessing procedures used for the cell line data were applied to data from 373 primary tumors profiled by array CGH, including controls. Results indicated that there is no apparent feature related to the institute or platform and that array CGH allows for unambiguous cross-platform meta-analysis. Major clusters with common tissue origin were identified. Interestingly, tumors of hematopoietic and mesenchymal origins cluster separately from tumors of epithelial origin. Therefore it can be concluded that chromosomal aberrations of tumors from hematopoietic and mesenchymal origin versus tumors of epithelial origin are distinct, and these differences can be picked up by metaanalysis of array CGH data. This suggests the possibility of prospectively using combined analysis of diverse copy number datasets for cancer subtype classification. Keywords: comparative genomic hybridization, meta-analysis, cancer

2006-08-29 | GSE5051 | GEO

DNA-guided transcription factor cooperativity shapes face and limb mesenchyme [CUT&RUN]

Project description:Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how ‘Coordinator’, a long DNA motif comprised of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, while HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in shared regulation of genes involved in cell-type and positional identities, and ultimately shapes facial morphology and evolution.

2023-05-30 | GSE230317 | GEO

DNA-guided transcription factor cooperativity shapes face and limb mesenchyme [ChIP-seq]

2023-05-30 | GSE230316 | GEO

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