The Punctilious RNA Polymerase II Core Promoter

Overview

Journal Genes Dev

Specialty Molecular Biology

Date 2017 Aug 16

PMID 28808065

Citations 78

Authors

Long Vo Ngoc

Yuan-Liang Wang

George A Kassavetis

James T Kadonaga

Affiliations

Soon will be listed here.

Abstract

The signals that direct the initiation of transcription ultimately converge at the core promoter, which is the gateway to transcription. Here we provide an overview of the RNA polymerase II core promoter in bilateria (bilaterally symmetric animals). The core promoter is diverse in terms of its composition and function yet is also punctilious, as it acts with strict rules and precision. We additionally describe an expanded view of the core promoter that comprises the classical DNA sequence motifs, sequence-specific DNA-binding transcription factors, chromatin signals, and DNA structure. This model may eventually lead to a more unified conceptual understanding of the core promoter.

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References

Vermeulen M, Mulder K, Denissov S, Pijnappel W, Van Schaik F, Varier R . Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell. 2007; 131(1):58-69. DOI: 10.1016/j.cell.2007.08.016. View

Gazdag E, Rajkovic A, Torres-Padilla M, Tora L . Analysis of TATA-binding protein 2 (TBP2) and TBP expression suggests different roles for the two proteins in regulation of gene expression during oogenesis and early mouse development. Reproduction. 2007; 134(1):51-62. DOI: 10.1530/REP-06-0337. View

LaGrange T, Kapanidis A, Tang H, Reinberg D, Ebright R . New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes Dev. 1998; 12(1):34-44. PMC: 316406. DOI: 10.1101/gad.12.1.34. View

Dang X, Singh A, Spetman B, Nolan K, Isaacs J, Dennis J . Label-Free Relative Quantitation of Isobaric and Isomeric Human Histone H2A and H2B Variants by Fourier Transform Ion Cyclotron Resonance Top-Down MS/MS. J Proteome Res. 2016; 15(9):3196-203. PMC: 6261780. DOI: 10.1021/acs.jproteome.6b00414. View

Emami K, Navarre W, Smale S . Core promoter specificities of the Sp1 and VP16 transcriptional activation domains. Mol Cell Biol. 1995; 15(11):5906-16. PMC: 230842. DOI: 10.1128/MCB.15.11.5906. View

Zhou H, Grubisic I, Zheng K, He Y, Wang P, Kaplan T . Taf7l cooperates with Trf2 to regulate spermiogenesis. Proc Natl Acad Sci U S A. 2013; 110(42):16886-91. PMC: 3801064. DOI: 10.1073/pnas.1317034110. View

Deato M, Tjian R . Switching of the core transcription machinery during myogenesis. Genes Dev. 2007; 21(17):2137-49. PMC: 1950853. DOI: 10.1101/gad.1583407. View

Lewis B, Kim T, Orkin S . A downstream element in the human beta-globin promoter: evidence of extended sequence-specific transcription factor IID contacts. Proc Natl Acad Sci U S A. 2000; 97(13):7172-7. PMC: 16518. DOI: 10.1073/pnas.120181197. View

Crowley T, Hoey T, Liu J, Jan Y, Jan L, Tjian R . A new factor related to TATA-binding protein has highly restricted expression patterns in Drosophila. Nature. 1993; 361(6412):557-61. DOI: 10.1038/361557a0. View

10.

Louder R, He Y, Lopez-Blanco J, Fang J, Chacon P, Nogales E . Structure of promoter-bound TFIID and model of human pre-initiation complex assembly. Nature. 2016; 531(7596):604-9. PMC: 4856295. DOI: 10.1038/nature17394. View

11.

Cianfrocco M, Kassavetis G, Grob P, Fang J, Juven-Gershon T, Kadonaga J . Human TFIID binds to core promoter DNA in a reorganized structural state. Cell. 2013; 152(1-2):120-31. PMC: 3552382. DOI: 10.1016/j.cell.2012.12.005. View

12.

Kopytova D, Krasnov A, Kopantceva M, Nabirochkina E, Nikolenko J, Maksimenko O . Two isoforms of Drosophila TRF2 are involved in embryonic development, premeiotic chromatin condensation, and proper differentiation of germ cells of both sexes. Mol Cell Biol. 2006; 26(20):7492-505. PMC: 1636870. DOI: 10.1128/MCB.00349-06. View

13.

Zehavi Y, Kuznetsov O, Ovadia-Shochat A, Juven-Gershon T . Core promoter functions in the regulation of gene expression of Drosophila dorsal target genes. J Biol Chem. 2014; 289(17):11993-12004. PMC: 4002106. DOI: 10.1074/jbc.M114.550251. View

14.

Jacobson R, Ladurner A, King D, Tjian R . Structure and function of a human TAFII250 double bromodomain module. Science. 2000; 288(5470):1422-5. DOI: 10.1126/science.288.5470.1422. View

15.

Dantonel J, Wurtz J, Poch O, Moras D, Tora L . The TBP-like factor: an alternative transcription factor in metazoa?. Trends Biochem Sci. 1999; 24(9):335-9. DOI: 10.1016/s0968-0004(99)01436-x. View

16.

Lam M, Cho H, Lesch H, Gosselin D, Heinz S, Tanaka-Oishi Y . Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature. 2013; 498(7455):511-5. PMC: 3839578. DOI: 10.1038/nature12209. View

17.

Duttke S, Doolittle R, Wang Y, Kadonaga J . TRF2 and the evolution of the bilateria. Genes Dev. 2014; 28(19):2071-6. PMC: 4180970. DOI: 10.1101/gad.250563.114. View

18.

Xu M, Sharma P, Pan S, Malik S, Roeder R, Martinez E . Core promoter-selective function of HMGA1 and Mediator in Initiator-dependent transcription. Genes Dev. 2011; 25(23):2513-24. PMC: 3243061. DOI: 10.1101/gad.177360.111. View

19.

Core L, Martins A, Danko C, Waters C, Siepel A, Lis J . Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet. 2014; 46(12):1311-20. PMC: 4254663. DOI: 10.1038/ng.3142. View

20.

Danino Y, Even D, Ideses D, Juven-Gershon T . The core promoter: At the heart of gene expression. Biochim Biophys Acta. 2015; 1849(8):1116-31. DOI: 10.1016/j.bbagrm.2015.04.003. View