On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF.
Journal
NAR genomics and bioinformatics
ISSN: 2631-9268
Titre abrégé: NAR Genom Bioinform
Pays: England
ID NLM: 101756213
Informations de publication
Date de publication:
Sep 2020
Sep 2020
Historique:
received:
13
01
2020
revised:
07
05
2020
accepted:
10
06
2020
entrez:
12
2
2021
pubmed:
13
2
2021
medline:
13
2
2021
Statut:
epublish
Résumé
Cis2-His2 zinc finger (C2H2-ZF) proteins are the largest family of transcription factors in human and higher metazoans. To date, the DNA-binding preferences of many members of this family remain unknown. We have developed a computational method to predict their DNA-binding preferences. We have computed theoretical position weight matrices (PWMs) of proteins composed by C2H2-ZF domains, with the only requirement of an input structure. We have predicted more than two-third of a single zinc-finger domain binding site for about 70% variants of Zif268, a classical member of this family. We have successfully matched between 60 and 90% of the binding-site motif of examples of proteins composed by three C2H2-ZF domains in JASPAR, a standard database of PWMs. The tests are used as a proof of the capacity to scan a DNA fragment and find the potential binding sites of transcription-factors formed by C2H2-ZF domains. As an example, we have tested the approach to predict the DNA-binding preferences of the human chromatin binding factor CTCF. We offer a server to model the structure of a zinc-finger protein and predict its PWM.
Identifiants
pubmed: 33575598
doi: 10.1093/nargab/lqaa046
pii: lqaa046
pmc: PMC7671317
doi:
Types de publication
Journal Article
Langues
eng
Pagination
lqaa046Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.
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