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Genome-wide structure and organization of eukaryotic pre-initiation complexes

Nature volume 483, pages 295–301 (2012)Cite this article

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An Erratum to this article was published on 04 July 2012

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Abstract

Transcription and regulation of genes originate from transcription pre-initiation complexes (PICs). Their structural and positional organization across eukaryotic genomes is unknown. Here we applied lambda exonuclease to chromatin immunoprecipitates (termed ChIP-exo) to examine the precise location of 6,045 PICs in Saccharomyces. PICs, including RNA polymerase II and protein complexes TFIIA, TFIIB, TFIID (or TBP), TFIIE, TFIIF, TFIIH and TFIIK were positioned within promoters and excluded from coding regions. Exonuclease patterns were in agreement with crystallographic models of the PIC, and were sufficiently precise to identify TATA-like elements at so-called TATA-less promoters. These PICs and their transcription start sites were positionally constrained at TFIID-engaged downstream +1 nucleosomes. At TATA-box-containing promoters, which are depleted of TFIID, a +1 nucleosome was positioned to be in competition with the PIC, which may allow greater latitude in start-site selection. Our genomic localization of messenger RNA and non-coding RNA PICs reveals that two PICs, in inverted orientation, may occupy the flanking borders of nucleosome-free regions. Their unambiguous detection may help distinguish bona fide genes from transcriptional noise.

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Figure 1: Genome-wide structural organization of PICs.
Figure 2: Identification of TATA-like elements at TATA-less genes.
Figure 3: PIC organization in relation to TFIID and the +1 nucleosome.
Figure 4: Genomic view of PICs in relation to genes.
Figure 5: Distribution of ncRNA PICs.

Accession codes

Primary accessions

Sequence Read Archive

Data deposits

Sequencing data have been deposited at theNCBI Sequence Read Archive under accession number SRA046523.

Change history

  • 20 February 2012

    Supplementary Data file 1 contained some errors and was replaced.

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Acknowledgements

We thank I. Albert and Y. Li for bioinformatic support, and members of the Pugh laboratory and the Penn State Center for Eukaryotic Gene Regulation for valuable discussions. Sequencing was performed at the Penn State Genomics Core Facility. This work was supported by National Institutes of Health grant GM059055.

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Authors and Affiliations

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

    Ho Sung Rhee & B. Franklin Pugh

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  1. Ho Sung Rhee
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Contributions

H.S.R. performed the experiments and conducted data analyses. H.S.R. and B.F.P. conceived the experiments, analyses, and co-wrote the manuscript.

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Correspondence to B. Franklin Pugh.

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Supplementary information

Supplementary Information

The file contains Supplementary Figures 1-10 with legends and additional references. (PDF 4841 kb)

Supplementary Data 1-3

This zipped file contains Supplementary Data sets 1-3 as follows: (1) a list of the top 6,045 PICs, their associated gene, type of RNA produced, TSS and TATA location, occupancy levels of individual GTFs, and TATA and TAF classification; (2) underlying numerical values associated with Fig. 3a, GTF occupancy around the nearest nucleosome. Text file conversion can be visualized with Treeview software; (3) underlying numerical values associated with Fig. 4a, GTF occupancy around transcript and ORF start sites sorted by gene length. Text file conversion can be visualized with Treeview software. Supplementary Data file 1 contained some errors and was replaced on 20 February 2012. (ZIP 13219 kb)

Supplementary Data 4-7

This zipped file contains Supplementary Data 4-7 as follows: (4) underlying numerical values associated with Fig. 4b, GTF distribution around the 3’ ends of genes sorted by intergenic length. Text file conversion can be visualized with Treeview software; (5) underlying numerical values associated with Fig. 4c, GTF distribution around the TSS, and sorted by intergenic length. Text file conversion can be visualized with Treeview software (Excel, 36 MB); (6 ) underlying numerical values associated with Supplementary Fig. 8, GTF occupancy around individual +1 nucleosomes of ncRNA and orphan PICs. Text file conversion can be visualized with Treeview software (Excel, 5 MB); (7) underlying numerical values associated with Supplementary Fig. 9, GTFs occupancy around the TSS of SUTs and CUTs. Text file conversion can be visualized with Treeview software. (ZIP 18667 kb)

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Rhee, H., Pugh, B. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature 483, 295–301 (2012). https://doi.org/10.1038/nature10799

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