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Mechanisms governing target search and binding dynamics of hypoxia-inducible factors

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 co-factors or the core transcription initiatio...

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Autores principales: Chen, Yu, Cattoglio, Claudia, Dailey, Gina M, Zhu, Qiulin, Tjian, Robert, Darzacq, Xavier
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9681212/
https://www.ncbi.nlm.nih.gov/pubmed/36322456
http://dx.doi.org/10.7554/eLife.75064
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author Chen, Yu
Cattoglio, Claudia
Dailey, Gina M
Zhu, Qiulin
Tjian, Robert
Darzacq, Xavier
author_facet Chen, Yu
Cattoglio, Claudia
Dailey, Gina M
Zhu, Qiulin
Tjian, Robert
Darzacq, Xavier
author_sort Chen, Yu
collection PubMed
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 co-factors 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, another main determinant of chromatin binding and diffusion behavior is the AD-containing intrinsically disordered region (IDR). Using Cut&Run and RNA-seq as orthogonal genomic approaches, we also confirmed IDR-dependent binding and activation of a specific subset of HIF target genes. These findings reveal a previously unappreciated role of IDRs in regulating the TF search and binding process that contribute to functional target site selectivity on chromatin.
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spelling pubmed-96812122022-11-23 Mechanisms governing target search and binding dynamics of hypoxia-inducible factors Chen, Yu Cattoglio, Claudia Dailey, Gina M Zhu, Qiulin Tjian, Robert Darzacq, Xavier eLife Chromosomes and Gene Expression 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 co-factors 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, another main determinant of chromatin binding and diffusion behavior is the AD-containing intrinsically disordered region (IDR). Using Cut&Run and RNA-seq as orthogonal genomic approaches, we also confirmed IDR-dependent binding and activation of a specific subset of HIF target genes. These findings reveal a previously unappreciated role of IDRs in regulating the TF search and binding process that contribute to functional target site selectivity on chromatin. eLife Sciences Publications, Ltd 2022-11-02 /pmc/articles/PMC9681212/ /pubmed/36322456 http://dx.doi.org/10.7554/eLife.75064 Text en © 2022, Chen et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Chromosomes and Gene Expression
Chen, Yu
Cattoglio, Claudia
Dailey, Gina M
Zhu, Qiulin
Tjian, Robert
Darzacq, Xavier
Mechanisms governing target search and binding dynamics of hypoxia-inducible factors
title Mechanisms governing target search and binding dynamics of hypoxia-inducible factors
title_full Mechanisms governing target search and binding dynamics of hypoxia-inducible factors
title_fullStr Mechanisms governing target search and binding dynamics of hypoxia-inducible factors
title_full_unstemmed Mechanisms governing target search and binding dynamics of hypoxia-inducible factors
title_short Mechanisms governing target search and binding dynamics of hypoxia-inducible factors
title_sort mechanisms governing target search and binding dynamics of hypoxia-inducible factors
topic Chromosomes and Gene Expression
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9681212/
https://www.ncbi.nlm.nih.gov/pubmed/36322456
http://dx.doi.org/10.7554/eLife.75064
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