Genomic organization of human transcription initiation complexes

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 (BRE.sub.u), TATA, downstream TFIIB recognition element (BRE.sub.d), 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. The ChIP-exo technique is used to map the organization of transcription initiation complexes across the human genome at near-base-pair resolution; most of the transcription initiation complexes give rise to non-coding, non-polyadenylated RNA, indicating that pervasive non-coding transcription arise from specific promoters and is regulated. Promoter recognition In this study Bryan Venters and Frank Pugh use the ChIP-exo technique to map the organization of transcription initiation complexes across the human genome at near-base-pair resolution in four ENCODE human cancer cell lines. The resulting data reveal the in vivo organization of more than 160,000 transcription initiation complexes and provide insights into the role of core promoter motifs such as TATA boxes, the production of divergent transcripts, and the transition of RNA polymerase II from transcription initiation to a paused state. Strikingly, most of the transcription initiation complexes give rise to non-coding, non-polyadenylated RNA, indicating that pervasive non-coding transcription arises from specific promoters and is regulated.
Author(s): Bryan J. Venters [sup.1] [sup.2] , B. Franklin Pugh [sup.1] Author Affiliations: (1) Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University [...]