Cited by 496Genomics and Chromatin DynamicsNuclear Structure and FunctionFungal and yeast genetics research

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

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Rhee, Ho Sung, Pugh, B. Franklin·2012·Nature

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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Authors
Rhee, H. S., & Pugh, B. F.
Affiliations
Pennsylvania State University (US)
Corresponding author
Pugh, B. Franklin
Venue
Nature
Published
2012-01-18
Volume
483
Issue
7389
Pages
295-301
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
OpenAlex
W1974595249
Cited by
496
References
51
Citations by year
2026: 11 · 2025: 11 · 2024: 28 · 2023: 27 · 2022: 27 · 2021: 26 · 2020: 40 · 2019: 22 · 2018: 30 · 2017: 40 · 2016: 54 · 2015: 45 · 2014: 59 · 2013: 56 · 2012: 20
FWCI
23.16
Type
journal article
Language
en
Update notices
erratum (2012-07-04)
Open access
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
Funders
  • Pennsylvania State University
  • National Institutes of Health
  • National Institute of General Medical Sciences (GM059055, R01GM059055)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Keywords
preinitiation complex, transcription initiation, RNA polymerase II, ChIP-exo, Saccharomyces cerevisiae, TATA-less promoter, transcription start site selection, nucleosome-free regions, transcriptional noise, TFIID, transcription factors
MeSH terms
DNA, Fungal, Genes, Fungal, Models, Molecular, Molecular Sequence Data, Nucleosomes, Protein Conformation, RNA Polymerase II, RNA, Fungal, RNA, Messenger, Saccharomyces cerevisiae, Transcription, Genetic, Gene Expression Regulation, Fungal, TATA Box, Genome, Fungal, RNA, Untranslated, Transcription Initiation Site, Transcription Factors, General

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