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

Author

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  • Ho Sung Rhee

    (Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park)

  • B. Franklin Pugh

    (Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park)

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.

Suggested Citation

  • Ho Sung Rhee & B. Franklin Pugh, 2012. "Genome-wide structure and organization of eukaryotic pre-initiation complexes," Nature, Nature, vol. 483(7389), pages 295-301, March.
    • Handle: RePEc:nat:nature:v:483:y:2012:i:7389:d:10.1038_nature10799
    DOI: 10.1038/nature10799
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    Cited by:

    1. Vladislav N. Nikolov & Dhara Malavia & Takashi Kubota, 2022. "SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Jan Zrimec & Xiaozhi Fu & Azam Sheikh Muhammad & Christos Skrekas & Vykintas Jauniskis & Nora K. Speicher & Christoph S. Börlin & Vilhelm Verendel & Morteza Haghir Chehreghani & Devdatt Dubhashi & Ver, 2022. "Controlling gene expression with deep generative design of regulatory DNA," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    3. Brianna J. Klein & Jordan T. Feigerle & Jibo Zhang & Christopher C. Ebmeier & Lixin Fan & Rohit K. Singh & Wesley W. Wang & Lauren R. Schmitt & Thomas Lee & Kirk C. Hansen & Wenshe R. Liu & Yun-Xing W, 2022. "Taf2 mediates DNA binding of Taf14," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    4. Helka Göös & Matias Kinnunen & Kari Salokas & Zenglai Tan & Xiaonan Liu & Leena Yadav & Qin Zhang & Gong-Hong Wei & Markku Varjosalo, 2022. "Human transcription factor protein interaction networks," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    5. Joana Segura & Ofelia Díaz-Ingelmo & Belén Martínez-García & Alba Ayats-Fraile & Christoforos Nikolaou & Joaquim Roca, 2024. "Nucleosomal DNA has topological memory," Nature Communications, Nature, vol. 15(1), pages 1-10, December.

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