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

Author

Listed:
  • Chirag Nepal

    (University of Copenhagen)

  • Yavor Hadzhiev

    (University of Birmingham)

  • Piotr Balwierz

    (University of Birmingham
    Imperial College London
    MRC Clinical Sciences Centre)

  • Estefanía Tarifeño-Saldivia

    (Université de Liège
    University of Concepcion)

  • Ryan Cardenas

    (University of Birmingham)

  • Joseph W. Wragg

    (University of Birmingham)

  • Ana-Maria Suzuki

    (RIKEN Center for Life Science Technologies)

  • Piero Carninci

    (RIKEN Center for Life Science Technologies
    RIKEN Center for Integrative Medical Sciences)

  • Bernard Peers

    (Université de Liège)

  • Boris Lenhard

    (Imperial College London
    MRC Clinical Sciences Centre)

  • Jesper B. Andersen

    (University of Copenhagen)

  • Ferenc Müller

    (University of Birmingham)

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.

Suggested Citation

  • Chirag Nepal & Yavor Hadzhiev & Piotr Balwierz & Estefanía Tarifeño-Saldivia & Ryan Cardenas & Joseph W. Wragg & Ana-Maria Suzuki & Piero Carninci & Bernard Peers & Boris Lenhard & Jesper B. Andersen , 2020. "Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-019-13687-0
    DOI: 10.1038/s41467-019-13687-0
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    Cited by:

    1. Chirag Nepal & Jesper B. Andersen, 2023. "Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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