Transcription Factor Binding in Embryonic Stem Cells Is Constrained by DNA Sequence Repeat Symmetry.

Base Sequence Binding Sites Embryonic Stem Cells / metabolism Protein Binding Transcription Factors / genetics

Journal

Biophysical journal
ISSN: 1542-0086
Titre abrégé: Biophys J
Pays: United States
ID NLM: 0370626

Informations de publication

Date de publication:
21 04 2020
Historique:
received: 02 12 2019
revised: 05 02 2020
accepted: 10 02 2020
pubmed: 27 2 2020
medline: 15 5 2021
entrez: 27 2 2020
Statut: ppublish

Résumé

Transcription factor (TF) recognition is dictated by the underlying DNA motif sequence specific for each TF. Here, we reveal that DNA sequence repeat symmetry plays a central role in defining TF-DNA-binding preferences. In particular, we find that different TFs bind similar symmetry patterns in the context of different developmental layers. Most TFs possess dominant preferences for similar DNA repeat symmetry types. However, in some cases, preferences of specific TFs are changed during differentiation, suggesting the importance of information encoded outside of known motif regions. Histone modifications also exhibit strong preferences for similar DNA repeat symmetry patterns unique to each type of modification. Next, using an in vivo reporter assay, we show that gene expression in embryonic stem cells can be positively modulated by the presence of genomic and computationally designed DNA oligonucleotides containing identified nonconsensus-repetitive sequence elements. This supports the hypothesis that certain nonconsensus-repetitive patterns possess a functional ability to regulate gene expression. We also performed a solution NMR experiment to probe the stability of double-stranded DNA via imino proton resonances for several double-stranded DNA sequences characterized by different repetitive patterns. We suggest that such local stability might play a key role in determining TF-DNA binding preferences. Overall, our findings show that despite the enormous sequence complexity of the TF-DNA binding landscape in differentiating embryonic stem cells, this landscape can be quantitatively characterized in simple terms using the notion of DNA sequence repeat symmetry.

Identifiants

DOI: 10.1016/j.bpj.2020.02.009 PMID: 32101712 PMC: PMC7175408
pubmed: 32101712
pii: S0006-3495(20)30129-6
doi: 10.1016/j.bpj.2020.02.009
pmc: PMC7175408
pii:
doi:

Substances chimiques

Transcription Factors 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

2015-2026

Commentaires et corrections

Type : CommentIn

Informations de copyright

Copyright © 2020 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Auteurs

Matan Goldshtein (M)

Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

Meir Mellul (M)

Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.

Gai Deutch (G)

Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.

Masahiko Imashimizu (M)

Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.

Koh Takeuchi (K)

Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.

Eran Meshorer (E)

Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel; The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.

Oren Ram (O)

Department of Biological Chemistry, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. Electronic address: oren.ram@mail.huji.ac.il.

David B Lukatsky (DB)

Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel. Electronic address: lukatsky@bgu.ac.il.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Séquence nucléotidique › Transcription Factor Binding in Embryonic Stem...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Sites de fixation › Transcription Factor Binding in Embryonic Stem...
questionsmedicales.fr › Cellules › Cellules souches › Cellules souches pluripotentes › Cellules souches embryonnaires › Transcription Factor Binding in Embryonic Stem...
questionsmedicales.fr › Métabolisme › Liaison aux protéines › Transcription Factor Binding in Embryonic Stem...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Facteurs de transcription › Transcription Factor Binding in Embryonic Stem...