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Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping

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

ORGANISM(S): Homo sapiens

PROVIDER: GSE190963 | GEO | 2023/02/18

REPOSITORIES: GEO

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Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [ATAC-seq]

Project description:Intrinsically disordered regions (IDRs) in DNA-associated proteins have recently been shown to play important roles in gene regulation. To better understand these domains we developed an antibody-independent assay to map disordered proteins genome-wide by combining b-isox mediated precipitation and next-generation sequencing (DisP-seq, disordered protein precipitation followed by DNA sequencing). We first analyzed Ewing sarcoma cells as a proof of principle given that the prion-like IDR of the oncogenic fusion protein EWS-FLI1 has been shown to play a critical role in this cancer. We find that DisP-seq produces thousands of strong peaks associated with diverse chromatin states in Ewing sarcoma and other cell types tested. These locations are highly enriched for DNA binding motifs matching EWS-FLI1 and other transcription factors with prominent IDRs. Moreover, depletion of EWS-FLI1 in Ewing sarcoma cells leads to a widespread reorganization of DisP-seq signals, including decreases at EWS-FLI1 binding sites and marked increases at sites associated with mesenchymal differentiation. Analysis of these new DisP-seq signals shows that they arise from redistribution of the transcription factor NFIB, which initially overlaps EWS-FLI1 and has an IDR that is required for proper localization and function. Our results thus show that antibody-independent precipitation mapping can enable genome-wide profiling and identification of disordered transcription factors to uncover their roles in complex gene regulation programs.

2023-02-20 | GSE190959 | GEO

Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [RNA-Seq]

2023-02-20 | GSE190962 | GEO

Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [DisP-Seq]

2023-02-20 | GSE190961 | GEO

Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [ChIP-seq]

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Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping

Project description:Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping

| PRJNA789181 | ENA

Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [RNA-Seq]

Project description:Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [RNA-Seq]

| PRJNA789189 | ENA

Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [DisP-Seq]

Project description:Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [DisP-Seq]

| PRJNA789186 | ENA

Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [ATAC-seq]

Project description:Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [ATAC-seq]

| PRJNA789188 | ENA

Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [ChIP-seq]

Project description:Genome-wide profiling and identification of disordered transcription factors through chemical precipitation mapping [ChIP-seq]

| PRJNA789187 | ENA

A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq.

Project description:Deciphering the structure of gene regulatory networks across the tree of life remains one of the major challenges in postgenomic biology. We present a novel ChIP-seq workflow for the archaea using the model organism Halobacterium salinarum sp. NRC-1 and demonstrate its application for mapping the genome-wide binding sites of natively expressed transcription factors. This end-to-end pipeline is the first protocol for ChIP-seq in archaea, with methods and tools for each stage from gene tagging to data analysis and biological discovery. Genome-wide binding sites for transcription factors with many binding sites (TfbD) are identified with sensitivity, while retaining specificity in the identification the smaller regulons (bacteriorhodopsin-activator protein). Chromosomal tagging of target proteins with a compact epitope facilitates a standardized and cost-effective workflow that is compatible with high-throughput immunoprecipitation of natively expressed transcription factors. The Pique package, an open-source bioinformatics method, is presented for identification of binding events. Relative to ChIP-Chip and qPCR, this workflow offers a robust catalog of protein-DNA binding events with improved spatial resolution and significantly decreased cost. While this study focuses on the application of ChIP-seq in H. salinarum sp. NRC-1, our workflow can also be adapted for use in other archaea and bacteria with basic genetic tools.

| S-EPMC3378898 | biostudies-other

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