References--eukaryotic transcription

Biochemistry/MCB 568 -- Fall 2006
John W. Little--University of Arizona

Bioc/MCB568 Home Page

 

Reviews:

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.

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

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.

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

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

Lee, T. I. and Young, R. A. Annu.Rev.Genet. 34: 77-137 (2000). "Transcription of eukaryotic protein-coding genes."

Woychik, N.A. and Hampsey, M. Cell 108:453-463 (2002). "The RNA polymerase II machinery: Structure illuminates function."

Orphanides,G. and D.Reinberg. Cell 108: 439-451 (2002). "A unified theory of gene expression."

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.

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

Svejstrup,J.Q. Biochim. Biophys. Acta Gene Struct. Expression 1677: 64-73 (2004). "The RNA polymerase II transcription cycle: cycling through chromatin." A good place to start.

Khorasanizadeh, S. Cell 116: 259-272 (2004). "The nucleosome: From genomic organization to genomic regulation."

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

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.

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.).

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.

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.