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Cited by 52Genomics and Chromatin DynamicsRNA Research and SplicingRNA and protein synthesis mechanisms

Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing

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Nepal, Chirag, Hadzhiev, Yavor, Balwierz, Piotr, Tarifeño-Saldivia, Estefanía, Cardenas, Ryan, Wragg, Joseph W., Suzuki, Ana-Maria, Carninci, Piero +4 more·2020·Nature Communications
DOI 10.1038/s41467-019-13687-0PMC PMC6954239

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Abstract

Variations in transcription start site (TSS) selection reflect diversity of preinitiation complexes and can impact on post-transcriptional RNA fates. Most metazoan polymerase II-transcribed genes carry canonical initiation with pyrimidine/purine (YR) dinucleotide, while translation machinery-associated genes carry polypyrimidine initiator (5’-TOP or TCT). By addressing the developmental regulation of TSS selection in zebrafish we uncovered a class of dual-initiation promoters in thousands of genes, including snoRNA host genes. 5’-TOP/TCT initiation is intertwined with canonical initiation and used divergently in hundreds of dual-initiation promoters during maternal to zygotic transition. Dual-initiation in snoRNA host genes selectively generates host and snoRNA with often different spatio-temporal expression. Dual-initiation promoters are pervasive in human and fruit fly, reflecting evolutionary conservation. We propose that dual-initiation on shared promoters represents a composite promoter architecture, which can function both coordinately and divergently to diversify RNAs.

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Authors
Nepal, C., Hadzhiev, Y., Balwierz, P., Tarifeño-Saldivia, E., Cardenas, R., Wragg, J. W., Suzuki, A.-M., Carninci, P., Peers, B., Lenhard, B., Andersen, J. B., & Müller, F.
Affiliations
  • University of Copenhagen (DK)
  • University of Birmingham (GB)
  • Hammersmith Hospital (GB)
  • University of Liège (BE)
  • RIKEN (JP)
Corresponding author
  • Nepal, Chirag
  • Müller, Ferenc
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2020-01-10
Volume
11
Issue
1
Pages
168-168
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-019-13687-0
PMC
PMC6954239
OpenAlex
W2999555406
Cited by
52
References
3
Citations by year
2026: 3 · 2025: 4 · 2024: 6 · 2023: 13 · 2022: 11 · 2021: 9 · 2020: 6
FWCI
3.24
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • University of Birmingham Research Portal (University of Birmingham) (publishedVersion, cc-by)
  • Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • ORBi (University of Liège) (submittedVersion, other-oa)
  • Research at the University of Copenhagen (University of Copenhagen) (submittedVersion, other-oa)
  • Spiral (Imperial College London) (submittedVersion, cc-by)
Funders
  • Wellcome Trust
  • RCUK | Biotechnology and Biological Sciences Research Council (BB/L010488/1)
  • Novo Nordisk Fonden (14040)
  • Danish Medical Research Council
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords
transcription start site selection, maternal-to-zygotic transition, zebrafish, preinitiation complex, divergent transcription, post-transcriptional processing, evolutionary conservation
MeSH terms
Animals, Base Sequence, Drosophila, Humans, Promoter Regions, Genetic, RNA, Transcription, Genetic, Zebrafish, Zygote, Gene Expression Regulation, Developmental, RNA, Small Nucleolar, RNA, Untranslated, Transcription Initiation Site, Regulatory Elements, Transcriptional, Gene Regulatory Networks, RNA, Small Untranslated

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