Genomic organization of human transcription initiation complexes

Nature. 2013 Oct 3;502(7469):53-8. doi: 10.1038/nature12535. Epub 2013 Sep 18.

Abstract

The human genome is pervasively transcribed, yet only a small fraction is coding. Here we address whether this non-coding transcription arises at promoters, and detail the interactions of initiation factors TATA box binding protein (TBP), transcription factor IIB (TFIIB) and RNA polymerase (Pol) II. Using ChIP-exo (chromatin immunoprecipitation with lambda exonuclease digestion followed by high-throughput sequencing), we identify approximately 160,000 transcription initiation complexes across the human K562 genome, and more in other cancer genomes. Only about 5% associate with messenger RNA genes. The remainder associates with non-polyadenylated non-coding transcription. Regardless, Pol II moves into a transcriptionally paused state, and TBP and TFIIB remain at the promoter. Remarkably, the vast majority of locations contain the four core promoter elements- upstream TFIIB recognition element (BREu), TATA, downstream TFIIB recognition element (BREd), and initiator element (INR)-in constrained positions. All but the INR also reside at Pol III promoters, where TBP makes similar contacts. This comprehensive and high-resolution genome-wide detection of the initiation machinery produces a consolidated view of transcription initiation events from yeast to humans at Pol II/III TATA-containing/TATA-less coding and non-coding genes.

Publication types

  • Research Support, N.I.H., Extramural
  • Retracted Publication

MeSH terms

  • Chromatin / metabolism
  • Genome, Human / genetics*
  • HeLa Cells
  • Hep G2 Cells
  • Humans
  • K562 Cells
  • MCF-7 Cells
  • Nucleotide Motifs
  • Polyadenylation
  • Promoter Regions, Genetic / genetics
  • RNA, Messenger / genetics
  • RNA, Transfer / chemistry
  • RNA, Transfer / genetics
  • TATA Box / genetics
  • Transcription Factors / genetics
  • Transcription Factors / metabolism*
  • Transcription Initiation, Genetic / physiology*

Substances

  • Chromatin
  • RNA, Messenger
  • Transcription Factors
  • RNA, Transfer