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Genomic organization of human transcription initiation complexes

Author

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  • Bryan J. Venters

    (Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park
    Present address: Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.)

  • B. Franklin Pugh

    (Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park)

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.

Suggested Citation

  • Bryan J. Venters & B. Franklin Pugh, 2013. "Genomic organization of human transcription initiation complexes," Nature, Nature, vol. 502(7469), pages 53-58, October.
    • Handle: RePEc:nat:nature:v:502:y:2013:i:7469:d:10.1038_nature12535
    DOI: 10.1038/nature12535
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