References--eukaryotic transcription

BIOC/MCB 568 -- Fall 2010
John W. Little--University of Arizona

BIOC/MCB568 Home Page

 

Reviews:

RNA polymerase transcription machinery:

Hahn, S. Nature Str. Mol. Biol. 11, 394-403 (2004). "Structure and mechanism of the RNA polymerase II transcription machinery". A good place to start.

Sikorski, T.W. and Buratowski, S. Curr. Op. Cell Biology 21, 344-351 (2009). "The basal initiation machinery: beyond the general transcription factors." Discusses cases in which the classical view of a PIC needs to be expanded or modified.

Thomas, M. C. and Chiang, C. M. Crit Rev.Biochem.Mol.Biol. 41: 105-178 (2006). "The general transcription machinery and general cofactors." A very extensive but up-to-date and clearly written survey of the general transcription machinery (TFIID etc.).

Svejstrup,J.Q. Biochim. Biophys. Acta Gene Struct. Expression 1677: 64-73 (2004). "The RNA polymerase II transcription cycle: cycling through chromatin." Includes discussing the role of chromatin in the transcription cycle.

Smale, S.T. and Kadonaga, J.T. Annu.Rev.Biochem. 72:449-479 (2003). "The RNA polymerase II core promoter". Discusses promoters containing TATA box, Inr, and/or DPE elements, and how these are used.

Green, M.R. Trends in Biochemical Sciences 25, 59-63 (2000). TBP-associated factors (TAFIIs): multiple, selective transcriptional mediators in common complexes.

Nucleosomes and chromatin

Rhodes, D. Nature 389:231-233 (1997). "The nucleosome core all wrapped up." Reviews the crystal structure of the nucleosome core presented in the same issue (Luger et al, see below). Try to read it and look at the paper in the original journal, because the color illustrations help a lot. Link to the PDB file is here.

Ng, H.H. and Bird, A. Trends in Biochemical Sciences 25, 121-126 (2000). Histone deacetylases: silencers for hire.

Peterson, C.L. and Laneil, M. Current Biology 14: R546-R551 (2004). "Histones and histone modifications." A good introduction to this topic.

Reinberg, D. and Sims, R.J. J. Biol. Chem. 281:23297-23301 (2006). "de FACTo nucleosome dynamics". Minireview about FACT and its role indisplacement of H2A and H2B during transcription.

Workman, J.L. Genes Dev. 20:2009-2017 (2006). "Nucleosome displacement in transcription". Review.

Li, B., Carey, M. and Workman, J.L. Cell 128, 707-719 (2007). "The role of chromatin during transcription".

Buratowski, S. Science 322, 1804-1805 (2008). "Gene expression--where to start?". Reviews four articles in the same issue of Science that describe the existence of many short RNA molecules transcribed from near the start point of genes, but which (often) are transcribed in the opposite direction! The meaning of these observations is unclear at present.

 Introduction to regulation (see also References on this topic)

Pugh, B.F. Gene 255, 1-14 (2000). Control of gene expression through regulation of the TATA-binding protein.

Malik, S. and Roeder, R.G. Trends in Biochemical Sciences 25, 277-283 (2000). Transcriptional regulation through Mediator-like coactivators in yeast and metazoan cells.

Kadonaga, J.T. Cell 116: 247-257 (2004). "Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors."

Kornberg, R. Trends Biochem. Sci. 30:235-239 (2005). "Mediator and the mechanism of transcriptional activation."

Papers

Discovery of Mediator:

Thompson, C.M., Koleske, A.J., Chao, D.M. and Young, R.A. Cell 73:1361-1375 (1993). "A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast."

Kim, Y.-J., Björklund, S., Li, Y., Sayre, M.H. and Kornberg, R.D. Cell 77:599-608 (1994). "A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II."

Structure of RNA polymerase II:

Cramer, P., Bushnell, D. A., and Kornberg, R. D. Science 292: 1863-1876 (2001). Structural basis of transcription: RNA polymerase II at 2.8 Ångstrom resolution.

Gnatt, A. L., Cramer, P., Fu, J. H., Bushnell, D. A., and Kornberg, R. D. Science 292: 1876-1882 (2001). Structural basis of transcription: An RNA polymerase II elongation complex at 3.3 Å resolution.

Structures of general transcription factors:

Links to the following structures are on the class Web page (YeastTBP.pdb, TBP&TF2A.pdb, TBP&TF2B.pdb; note that the yeast TBP structure has two molecules of the protein DNA complex; the file "TBP1sub.pdb" shows only one of the two). The papers will serve as guides to the interesting features. Try to look at at least one of the structures.

Kim, J.L., Nikolov, D.B. and Burley, S.K. Nature 365:520-527 (1993). "Co-crystal structure of TBP recognizing the minor groove of a TATA element."

Kim, Y., Geiger, J.H., Hahn, S. and Sigler, P.B. Nature 365:512-520 (1993). "Crystal structure of a yeast TBP/TATA-box complex." PDB file is for this paper, not the previous one.

Nikolov, D.B., Chen, H., Halay, E.D., et al. Nature 377:119-128 (1995). "Crystal structure of a TFIIB-TBP-TATA-element ternary complex".

Geiger, J.H., Sahn, S., Lee, S. and Sigler, P.B. Science 272, 830-836 (1996). Structure of the TFIIA-TBP-DNA complex. Perspective on this here.

Chen, H., Warfield, L. and Hahn, S. Nature Str. Mol. Biol. 14, 696-703 (2007). "The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex". Includes a relatively current structural model for the PIC. Also see a Minireview of this paper.

Structure of the nucleosome:

Luger, K., Mäder, A.W., Richmond, R.K., Sargent, D.F. and Richmond, T.J., Nature 389:251- 260 (1997). "Crystal structure of the nucleosome core particle at 2.8 Å resolution". A tour-de-force. Shows the locations of the histones and the DNA. The histone tails (the sites of acetylation) are mostly not visible, and Rhodes (above) speculates that they may make contacts between different nucleosomes.

Transcription reinitiation:

Yudkovsky, N., Ranish, J.A. and Hahn, S. Nature 408, 225-229 (2000). "A transcription reinitiation intermediate that is stabilized by activator."