Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors [Cut&Run]

ABSTRACT: Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors [Cut&Run]

PROVIDER: PRJNA856256 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR20000600_1.fastq.gz	Fastqsanger.gz
	SRR20000600_2.fastq.gz	Fastqsanger.gz
	SRR20000601_1.fastq.gz	Fastqsanger.gz
	SRR20000601_2.fastq.gz	Fastqsanger.gz
	SRR20000602_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 72

Similar Datasets

Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors

Project description:Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors

| PRJNA856250 | ENA

Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors [Cut&Run]

Project description:Transcription factors (TFs) are classically attributed a modular construction, containing well-structured sequence specific DNA-binding domains (DBDs) paired with disordered activation domains (ADs) responsible for protein-protein interactions targeting cofactors or the core transcription initiation machinery. However, this simple division of labor model struggles to explain why TFs with identical DNA binding sequence specificity determined in vitro exhibit distinct binding profiles in vivo. The family of Hypoxia-Inducible Factors (HIFs) offer a stark example: aberrantly expressed in several cancer types, HIF-1α and HIF-2α subunit isoforms recognize the same DNA motif in vitro – the hypoxia response element (HRE) – but only share a subset of their target genes in vivo, while eliciting contrasting effects on cancer development and progression under certain circumstances. To probe the mechanisms mediating isoform-specific gene regulation, we used live cell single particle tracking (SPT) to investigate HIF nuclear dynamics and how they change upon genetic perturbation or drug treatment. We found that HIF-α subunits and their dimerization partner HIF-1β exhibit distinct diffusion and binding characteristics that are exquisitely sensitive to concentration and subunit stoichiometry. Using domain-swap variants, mutations, and a HIF-2α specific inhibitor, we found that although the DBD and dimerization domains are important, a major determinant of chromatin binding and diffusion behavior is dictated by the AD-containing intrinsically disordered regions (IDR). Using orthogonal genomic approaches such as Cut-and-Run and RNA-seq, we also confirmed IDR-dependent binding and activation for a specific subset of HIF-target genes. These findings reveal a previously unappreciated role of IDRs in regulating the TF search process that may play a role in selective functional target site binding on chromatin.

2022-07-08 | GSE207573 | GEO

Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors [RNA-seq]

Project description:Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors [RNA-seq]

| PRJNA856255 | ENA

Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors [ChIP-seq]

Project description:Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors [ChIP-seq]

| PRJNA762306 | ENA

Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors [RNA-seq]

2022-07-08 | GSE207574 | GEO

Activation of g-globin expression by hypoxia-inducible factor 1a [CUT&RUN]

Project description:Activation of g-globin expression by hypoxia-inducible factor 1a [CUT&RUN]

| PRJNA842691 | ENA

Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors

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

2022-07-07 | GSE207575 | GEO

Mechanisms Governing Target Search and Binding Dynamics of Hypoxia-Inducible Factors [ChIP-seq]

Project description:We performed ChIP-seq to compare genome-wide HIF-1b and HIF-2a occupancy in wild type 786-O cells to 786-O cells with either HIF-1b or HIF-2a endogenously tagged with a V5-Halo moiety.

2021-10-29 | GSE183900 | GEO

Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation [Cut&Run]

Project description:To investigate the regulation of human enteroendocrine cell differentiation, we established Neurog3ER inducible cell lines. We then analyzed ASCL1 and NEUROD1 binding using data obtained from CUT&RUN of at 96h.

2024-01-11 | GSE238272 | GEO

A Critical Role of RUNX1 in Governing Megakaryocyte-Primed Hematopoietic Stem Cell Differentiation [CUT&RUN Chip-seq]

Project description:A Critical Role of RUNX1 in Governing Megakaryocyte-Primed Hematopoietic Stem Cell Differentiation [CUT&RUN Chip-seq]

| PRJNA873136 | ENA