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

Research output: Contribution to journalArticlepeer-review


  • Chirag Nepal
  • Estefanía Tarifeño-Saldivia
  • Joseph W Wragg
  • Ana-Maria Suzuki
  • Piero Carninci
  • Bernard Peers
  • Boris Lenhard
  • Jesper B Andersen

External organisations

  • Imperial College London
  • University of Copenhagen
  • University of Concepcion
  • RIKEN Center for Life Science Technologies
  • Université de Liège


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.


Original languageEnglish
Article number168
JournalNature Communications
Issue number1
Publication statusPublished - 10 Jan 2020