Journal Article

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

Pugh, B. Franklin, Rhee, Ho Sung

2012

Overview

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. Ultra-high-resolution mapping of the eukaryotic transcription machinery across the yeast genome reveals several unifying principles of pre-initiation complexes at coding and non-coding genes. Mapping eukaryotic pre-initiation complexes Assembly of the RNA polymerase II pre-initiation complex (PIC) is a crucial early step in gene transcription. Here, a high-resolution technique termed ChIP-exo is used to map precisely the binding and composition of PICs across the yeast genome. The findings include the presence of two divergently oriented PICs at promoters, and a broader role for TATA-like elements than was previously appreciated. This allows new insights into the mechanism of transcription.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/208/212 / 631/337/572 / 631/45/535 / Binding sites / Biological and medical sciences / Deoxyribonucleic acid / DNA / DNA, Fungal - genetics / DNA, Fungal - metabolism / Eukaryotes / Fundamental and applied biological sciences. Psychology / Gene Expression Regulation, Fungal / Genes, Fungal - genetics / Genetic regulation / Genetic research / Genetic transcription / Genome, Fungal - genetics / Genome-wide association studies / Genomes / Humanities and Social Sciences / Kinases / Methods / Models, Molecular / Molecular and cellular biology / Molecular genetics / Molecular Sequence Data / multidisciplinary / Nucleosomes - genetics / Nucleosomes - metabolism / Properties / Protein Conformation / RNA polymerase / RNA Polymerase II - chemistry / RNA Polymerase II - metabolism / RNA, Fungal - genetics / RNA, Messenger - biosynthesis / RNA, Messenger - genetics / RNA, Untranslated - genetics / Saccharomyces cerevisiae - chemistry / Saccharomyces cerevisiae - enzymology / Saccharomyces cerevisiae - genetics / Saccharomyces cerevisiae - metabolism / Science / Science (multidisciplinary) / Site selection / TATA Box - genetics / Transcription Factors, General - chemistry / Transcription Factors, General - deficiency / Transcription Factors, General - metabolism / Transcription Initiation Site / Transcription, Genetic - genetics / Transcription. Transcription factor. Splicing. Rna processing