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Genomic organization of human transcription initiation complexes

Nature volume 502, pages 53–58 (2013)Cite this article

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A Retraction to this article was published on 23 July 2014

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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.

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Figure 1: Transcription machinery organization at human mRNA promoters.
Figure 2: TATA elements at most mRNA genes.
Figure 3: BRE and INR at most mRNA genes.
Figure 4: Non-coding TFIIB locations have chromatin marks and non-polyadenylated RNA.
Figure 5: Restricted spacing of CPEs.
Figure 6: TATA and BRE elements at most tRNA genes.

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Accession codes

Accessions

Sequence Read Archive

Data deposits

Sequencing data have been deposited at the NCBI Sequence Read Archive under accession number SRA067908.

Change history

  • 02 October 2013

    Minor changes were made to the core promoter consensus sequences.

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Acknowledgements

We thank R. Reja, S. Mahony, P. Albert and Y. Li for bioinformatic assistance, and M. Cousar and K.-Y. Chan-Salis for experimental support. This work was supported by National Institutes of Health grant GM059055.

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Author notes

  1. Bryan J. Venters

    Present address: Present address: Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.,

Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania 16802, USA

    Bryan J. Venters & B. Franklin Pugh

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Contributions

B.J.V. performed the experiments and conducted data analyses. B.J.V. and B.F.P. conceived the experiments, analyses and co-wrote the manuscript.

Corresponding author

Correspondence to B. Franklin Pugh.

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The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Validation of ChIP-exo data and association with ENCODE annotated regions.

a, Pie chart of all 159,117 TFIIB-bound locations in K562 cells parsed into ENCODE-annotated regions. b, Venn overlap among mRNA genes having TBP or TFIIB locations (<500 bp from its TSS) and genes with measured polyadenylated mRNA levels detected by RNA-seq38. Data thresholding may contribute to non-overlapping sets. c, Moving average (100-gene) of mRNA levels versus TFIIB/TBP/Pol II occupancy levels on a median-centred log2 scale.

Extended Data Figure 2 Distribution of TFIIB/TBP/Pol II in CpG islands that overlap mRNA TSSs.

a, Peak-pair distribution for TFIIB, TBP and Pol II at the 5,095 CpG islands that overlap with the mRNA TSSs from Fig. 1b (78% overlap), and with the direction of transcription to the right. Rows are linked, and sorted by CpG island length. CpG island borders are indicated by blue and red bars, respectively. b, Shown is the averaged data from a. c, All 159,117 TFIIB locations were sorted by location, and inter-TFIIB distances calculated (red trace). Data were then sorted by distance, and the standard deviation of adjacent TFIIB occupancy ratios was calculated on a sliding window of 30 values. Peak calling parameters preclude detection of two separate TFIIB locations approximately <40 bp apart. Those that were 40–70 bp apart were correlated, whereas those >70 bp apart were less correlated or uncorrelated.

Extended Data Figure 3 Properties of CPEs associated with RefSeq genes.

a, Average TFIIB and TBP occupancy parsed by the number of mismatches to the TATA consensus. b, Distribution of each candidate CPE relative to each other.

Extended Data Figure 4 CPEs at non-coding loci bound by TFIIB.

a, Bar graph showing the percentage of all 150,754 putative ‘non-coding’ TFIIB binding locations (>500 bp from an annotated RefSeq TSS) that have the indicated number of CPEs. b, Distribution of ChIP-exo peaks on each strand relative to the indicated CPE, for 150,754 putative non-coding TFIIB locations. Opposite strand traces (red) are inverted. c, Distribution of TBP (purple) and Pol II (black) peak-pair midpoints relative to the TATA motif midpoint derived from the 150,754 TFIIB putative non-coding locations. d, TFIIB occupancy versus percentage of locations that code for proteins. All 159,117 TFIIB locations were sorted by occupancy level, and the percentage of locations linked to an annotated RefSeq feature was plotted as a moving average.

Extended Data Figure 5 Enrichment of different RNA fractions at 159,117 TFIIB locations throughout the human genome.

Frequency distribution RNA 5′ ends for poly(A)+(ref. 38) (top) and ENCODE project RNA fractions40 as indicated to the far left. Traces in the left panels are separated by sense (blue) and antisense (red, inverted) orientations relative to the corresponding mRNA TSS, which is directed to the right. Because the TSS orientation is not known for the poly(A)− ncRNA loci, positive and negative strand tags were plotted relative to the TFIIB midpoint. The percentage of putative TFIIB locations that exist within 2 kb of an RNA tag are indicated in the top right corner of each plot.

Extended Data Figure 6 TFIIB core promoter distances.

Candidate CP at varying distances from all 159,117 TFIIB locations, for the indicated spacing variants (not all possible combinations were tested). Digits within spacing variant schematic reflect the base-pair spacing (N) between elements. CPE with high P values (less correlated to the PSPM matrix) have thin lines, whereas low/strong P values (<3 × 10−4) have thick lines.

Extended Data Figure 7 Promoter complexes across cancer cell lines.

a, b, Occupancy levels for TFIIB linked to coding genes (a) and non-coding regions (b) in the indicated cell type were normalized by column. The colour scales represent the range of average-centred, log2-transformed values within each respective column. Detection in all four cell types defines group 1. Groups 2–4 were parsed by k-means clustering. Rows were sorted within groups based on TFIIB occupancy averaged across the four cell types (yellow, black, cyan and grey denote high, medium, low and zero occupancy, respectively). For clarity in b, TFIIB locations that were detected in only one cell line were excluded from clustering. Columns were hierarchically clustered. The MCF7 data set had 20–30% of the coverage of other cell lines (reported in Supplementary Data 3), which probably accounts for an excessive number of zero-occupancy loci (grey).

Extended Data Table 1 Statistics of Illumina sequencing
Full size table

Supplementary information

Supplementary Data 1

This file contains Supplementary Data 1a. (XLSX 23538 kb)

Supplementary Data 2

This file contains Supplementary Data 1b. (XLSX 22234 kb)

Supplementary Data 3

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Supplementary Data 4

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Supplementary Data 5

This file contains Supplementary Data 4. (XLSX 532 kb)

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Venters, B., Pugh, B. Genomic organization of human transcription initiation complexes. Nature 502, 53–58 (2013). https://doi.org/10.1038/nature12535

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