Mechanisms of binding specificity among bHLH transcription factors

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• dc.contributor.author de Martin, Xabier
• dc.contributor.author Sodaei, Reza, 1988-
• dc.contributor.author Santpere Baró, Gabriel, 1981-
• dc.date.accessioned 2022-06-16T06:18:59Z
• dc.date.available 2022-06-16T06:18:59Z
• dc.date.issued 2021
• dc.description.abstract The transcriptome of every cell is orchestrated by the complex network of interaction between transcription factors (TFs) and their binding sites on DNA. Disruption of this network can result in many forms of organism malfunction but also can be the substrate of positive natural selection. However, understanding the specific determinants of each of these individual TF-DNA interactions is a challenging task as it requires integrating the multiple possible mechanisms by which a given TF ends up interacting with a specific genomic region. These mechanisms include DNA motif preferences, which can be determined by nucleotide sequence but also by DNA's shape; post-translational modifications of the TF, such as phosphorylation; and dimerization partners and co-factors, which can mediate multiple forms of direct or indirect cooperative binding. Binding can also be affected by epigenetic modifications of putative target regions, including DNA methylation and nucleosome occupancy. In this review, we describe how all these mechanisms have a role and crosstalk in one specific family of TFs, the basic helix-loop-helix (bHLH), with a very conserved DNA binding domain and a similar DNA preferred motif, the E-box. Here, we compile and discuss a rich catalog of strategies used by bHLH to acquire TF-specific genome-wide landscapes of binding sites.
• dc.description.sponsorship G.S. received the support of a fellowship from “la Caixa” Foundation (ID 100010434). The fellowship code is LCF/BQ/PI19/11690010. G.S. is also supported by Ministerio de Ciencia e Innovación, Spain (PID2019-104700GA-I00) and by the NIH grant R01HG010898-01.
• dc.format.mimetype application/pdf
• dc.identifier.citation de Martin X, Sodaei R, Santpere G. et al. Mechanisms of binding specificity among bHLH transcription factors. Int J Mol Sci. 2021 Aug 24; 22(17): 9150. DOI: 10.3390/ijms22179150
• dc.identifier.doi http://dx.doi.org/10.3390/ijms22179150
• dc.identifier.issn 1422-0067
• dc.identifier.uri http://hdl.handle.net/10230/53506
• dc.language.iso eng
• dc.publisher MDPI
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2019-104700GA-I00
• dc.rights Copyright © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword ChIP-seq
• dc.subject.keyword E-box
• dc.subject.keyword bHLH
• dc.subject.keyword Co-factors
• dc.subject.keyword Dimerization
• dc.subject.keyword Pioneer factors
• dc.subject.keyword Transcription factor binding sites
• dc.title Mechanisms of binding specificity among bHLH transcription factors
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion