Evolution of binding preferences among whole-genome duplicated transcription factors.
DNA binding
S. cerevisiae
evolutionary biology
functional divergence
gene regulation
genetics
genomics
paralogs
transcription factors
whole genome duplication
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
11 04 2022
11 04 2022
Historique:
received:
22
08
2021
accepted:
20
01
2022
entrez:
11
4
2022
pubmed:
12
4
2022
medline:
14
4
2022
Statut:
epublish
Résumé
Throughout evolution, new transcription factors (TFs) emerge by gene duplication, promoting growth and rewiring of transcriptional networks. How TF duplicates diverge was studied in a few cases only. To provide a genome-scale view, we considered the set of budding yeast TFs classified as whole-genome duplication (WGD)-retained paralogs (~35% of all specific TFs). Using high-resolution profiling, we find that ~60% of paralogs evolved differential binding preferences. We show that this divergence results primarily from variations outside the DNA-binding domains (DBDs), while DBD preferences remain largely conserved. Analysis of non-WGD orthologs revealed uneven splitting of ancestral preferences between duplicates, and the preferential acquiring of new targets by the least conserved paralog (biased neo/sub-functionalization). Interactions between paralogs were rare, and, when present, occurred through weak competition for DNA-binding or dependency between dimer-forming paralogs. We discuss the implications of our findings for the evolutionary design of transcriptional networks.
Identifiants
pubmed: 35404235
doi: 10.7554/eLife.73225
pii: 73225
pmc: PMC9000951
doi:
pii:
Substances chimiques
Transcription Factors
0
DNA
9007-49-2
Banques de données
GEO
['GSE179430']
Dryad
['10.5061/dryad.xgxd254j6']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2022, Gera et al.
Déclaration de conflit d'intérêts
TG, FJ, RM No competing interests declared, NB Senior editor, eLife
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