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

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.

Figure 1. Genome-wide structural organization of PICs

a, Raw ChIP-exo tag distribution for GTFs and pol II around the RPS14B gene. Filled plots represent unfiltered 5′ ends of sequencing tags on the sense (darker fill) and antisense strand (lighter fill). b, Average GTF and pol II occupancy around the TATA box of 676 annotated mRNA genes. Plots are as in panel a. c, Relationship of four TFIIB crosslinking points to crystallographic-based models of the PIC. Upper panel is expanded from panel b for TFIIB. The middle and lower panels show modeled “open” and “closed” TBP/TFIIB/Pol II/promoter DNA complexes, respectively.

Figure 2. Identification of TATA-like elements at TATA-less genes

The left panel shows TFIIB occupancy around individual TFIIB-enriched TATA elements of mRNA genes (rows, n=3,945), sorted by occupancy level. Occupancy on the sense (blue) and antisense (red) strands is shown with respect to TSS orientation. The right panel shows a color chart representation of the DNA sequence located between ±20 bp from the TATA element midpoint and ordered as shown in the left panel.

Figure 3. PIC organization in relation to TFIID and the +1 nucleosome

a, GTFs occupancy around the nearest nucleosome position (essentially “+1”) to an mRNA PIC, which were sorted by the distance between the two. Unfiltered tags on each strand were shifted in the 3′ direction by a fixed distance (~8 bp depending on each GTF, 73 bp for nucleosomes), so as to better reflect the points of crosslinking. TAF1-depleted and TAF1-enriched genes were determined as being distinct clusters when GTF occupancies of all genes were clustered by k-means (see Fig. 5a). For all graphs of this type, image resolution is less than the number of rows, resulting in some averaging and thus the appearance of less variance across adjacent rows. See Supplementary Data 2 for underlying values, which can be visualized in Treeview. “RP” indicates ribosomal protein genes. The right panel shows transcription frequency. The nucleosome borders are denoted by vertical dashed black lines. b, Same as panel a, but showing an overlay of TATA elements, TFIIB, and TSS. c, Model of PIC organization at TATA box-containing and TATA-less/TFIID-dependent genes.

Figure 4. Genomic view of PICs in relation to genes

a, GTF occupancy around transcript and ORF start sites, sorted by gene length. See Supplementary Data 3-5 for underlying values. Transcript or ORF ends are indicated by black dashed and solid lines, respectively. The right panel shows transcription frequency. b, GTF distribution around the 3′ ends of mRNA genes, sorted by intergenic length, and sectioned by convergent vs tandem gene-pairs. Occupancy at eight reported looped genes^, is shown in Supplementary Fig. 5. c, GTF distribution around the TSS of mRNA genes, sorted by intergenic length, and sectioned by inverted vs tandem gene-pairs.

Figure 5. Distribution of ncRNA PICs

a, GTF occupancy levels at PICs for mRNA, ncRNA, and orphans, sectioned by k-means clustering. Occupancy levels of each GTF were median normalized, log₂ transformed, then sorted by row median. The small M1 group represents a terminating polymerase originating from upstream. b, Distribution of ncRNA PICs relative to mRNA genes. mRNA genes were filtered to retain only those having a nearby ncRNA-associated PIC (defined as having >10% of the genome-wide TFIIB average). Plotted are the locations of TATA elements associated with the mRNA (gray), sense-directed ncRNA (blue), and antisense-directed ncRNA (red). Additional plot details are as described in Fig. 4.