Spring 2004


Reading List:


Tuesday, March 23

Background Material

 Review article Kadonaga, J.T. (2004) Regulation of RNA Polymerase II Transcription by Sequence-Specific DNA Binding Factors. Cell 116:247-257.



Review article Khorasanizadeh, S. (2004) The Nucleosome: From Genomic Organization to Genomic Regulation. Cell 116:259-272.




Thursday, March 25

Structure of RNA Polymerase II transcription complexes

Cramer, P., Bushnell, D.A., Kornberg, R.D. (2001) Structural Basis of Transcription: RNA Polymerase II at 2.8 Angstrom Resolution. Science 292:1863-1876.  (


Gnatt, A.L., Cramer, P., Fu, J., Bushnell, D.A., Kornberg, R.D. (2001) Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Angstrom Resolution. Science 292:1876-1882.  (


2003 Update Short Commentary Asturias, F.J. and Craighead, J.L. (2003) RNA polymerase II at initiation. Proc. Natl. Acad. Sci. USA 100:6893-6895. (



Tuesday, March 30

Recruitment of Factors to the Initiation Complex

Review article Cosma, M.P. (2002) Ordered Recruitment: Gene-Specific Mechanism of Transcription Activation. Mol. Cell 10:227-236. (


Review article - Boube, M., Joulia, L., Cribbs, D.L., Bourbon, H.-M. (2002) Evidence for a Mediator of RNA Polymerase II Transcriptional Regulation Conserved from Yeast to Man. Cell 110:143-151. (


Kuras, L., Borggrefe, T., Kornberg, R.D. (2003) Association of the Mediator complex with enhancers of active genes. Proc. Natl. Acad. Sci. USA 100:13887-13891. (


Cantin, G.T., Stevens, J.L., Berk, A.J. (2003) Activation domain-mediator interations promote transcription preinitiation complex assembly on promoter DNA. Proc. Natl. Acad. Sci. USA 100:12003-12008. (


Metivier, R., Penot, G., Hubner, M.R., Reid, G., Brand, H., Kos, M., Gannon, F. (2003) Estrogen Receptor-alpha Directs Ordered, Cyclical, and Combinatorial Recruitment of Cofactors on a Natural Target Promoter. Cell 115:751-763. (



Thursday, April 1

Transcription Elongation

Pokholok, D.K., Hannett, N.M., Young, R.A. (2002) Exchange of RNA Polymerase II Initiation and Elongation Factors during Gene Expression In Vivo. Mol. Cell 9:799-809. (


Cheng, C. and Sharp, P.A. (2003) RNA Polymerase II Accumulation in the Promoter-Proximal Region of the Dihydrofolate Reductase and Gamma-Actin Genes. Mol. Cell. Biol. 23:1961-1967. (



Tuesday, April 6

Histone modification histone methylation/transcriptional elongation link

Xiao, T., Hall, H., Kizer, K.O., Shibata, Y., Hall, M.C., Borchers, C.H., Strahl, B.D. (2003) Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev. 17:654-663. (


Ng, H.H., Robert, F., Young, R.A., Struhl, K. (2003) Targeted Recruitment of Set1 Histone Methylase by Elongating Pol II Provides a Localized Mark and Memory of Recent Transcriptional Activity. Mol. Cell 11:709-719. (


Minireview Hampsey, M. and Reinberg, D. (2003) Tails of Intrigue: Phosphorylation of RNA Polymerase II Mediates Histone Methylation. Cell 113:429-432. (



Thursday, April 8

Histone replacement in active chromatin

Ahmad, K. and Henikoff, S. (2002) The Histone Variant H3.3 Marks Active Chromatin by Replication-Independent Nucleosome Assembly. Mol. Cell 9:1191-1200. (

(also, see associated commentary by Smith, M.M. (2003) Histone Variants and Nucleosome Deposition Pathways. Mol. Cell 9:1158-1160. (


Mizuguchi, G., Shen, X., Landry, J., Wu, W.-H., Sen, S., Wu, C. (2004) ATP-Driven Exchange of Histone H2AZ Variant Catalyzed by SWR1 Chromatin Remodeling Complex. Science 303:343-348. (

(also, see associated commentary by Owen-Hughes, T. and Bruno, M. (2004) Breaking the Silence. Science 303:324-325. (