The Basal Transcriptional Machinery

Chapter

Abstract

The identification and characterization of TSS regions, also called core promoter regions, is a pre-requisite for the understanding how Pol II transcription is controlled. Pol II is the core of the basal transcriptional machinery, which contains a large number of general transcription factors, many of them are summarized as the TFIID complex. Via another multi-protein complex of co-activators, termed Mediator, the basal transcriptional machinery is connected with activating and repressing cell- and site-specific transcription factors binding to genomic regions that are distal to the TSS region.

Whole genome sequencing and associated new technologies indicated that i) most human promoter regions do not contain a TATA box, ii) the TSS of many genes is not a single defined nucleotide and iii) most genes have multiple promoter regions. Alternative TSS usage generates diversity and complexity in the human transcriptome and the resulting proteome. A comprehensive survey of promoter regions is a major step towards understanding transcriptional control networks.

In this chapter, we will discuss how the basal transcriptional machinery assembles on the core promoter. We will understand the TATA box as the prototype of a site-specific transcription factor-binding site. The association of TBP with this site will introduce the principles of specific recognition of DNA and protein complex formation on it. We will learn that a number of alternative binding sites for general transcription factors allow the assembly of more or less the same multi-protein complex on the core promoter. Finally, we will recognize the Mediator as an evolutionarily conserved, multi-protein complex that interacts with a large variation of transcription factors and in parallel coordinates the action of co-activators and co-repressors, some of which are chromatin modifiers.

Keywords

RNA polymerase II Transcription factor TBP TATA box Core promoter Transcription start site Basal transcriptional machinery TFIID Sequence logo Position weight matrix TAF Transcription factor binding site RNA-seq Mediator complex 

Further Reading

  1. Cheung ACM, Cramer P (2012) A movie of RNA polymerase II transcription. Cell 149:1431–1437PubMedCrossRefGoogle Scholar
  2. Lenhard B, Sandelin A, Carninci P (2012) Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet 13:233–245PubMedGoogle Scholar
  3. Malik S, Roeder RG (2010) The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nat Rev Genet 11:761–772PubMedCrossRefGoogle Scholar
  4. Papai G, Weil GP, Schultz P (2011) New insights into the function of transcription factor TFIID from recent structural studies. Curr Opin Genet Dev 21:219–224PubMedCrossRefGoogle Scholar
  5. Raab JR, Kamakaka RT (2010) Insulators and promoters: closer than we think. Nat Rev Genet 11:439–446PubMedCrossRefGoogle Scholar
  6. Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DA (2007) Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet 8:424–436PubMedCrossRefGoogle Scholar
  7. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63PubMedCrossRefGoogle Scholar
  8. Wasserman WW, Sandelin A (2004) Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 5:276–287PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  1. 1.Institute of Biomedicine, School of MedicineUniversity of Eastern FinlandKuopioFinland
  2. 2.Institute of Biopharmacy School of PharmacyUniversity of Eastern FinlandKuopioFinland

Personalised recommendations