Waterman Lectures
MBB
206 Spring 2009
Transcription
Ext.
42885, mlwaterm@uci.edu, Med Sci I, Rm, B251
Syllabus
for transcription lectures
2008
exam key
Topic
1 Molecular Aspects of Transcription
1°
Paper: Willy PJ, Kobayashi
R, Kadonaga JT. A basal transcription factor that activates or represses
transcription. Science. 2000 Nov 3;290(5493):982-5
Review 1: Struhl K.
Fundamentally different logic of gene regulation in eukaryotes and prokaryotes.
Cell. 1999 Jul 9;98(1):1-4.
Review 2: Levine, M. and R. Tjian. Transcription
Regulation and Animal Diversity. 2003.
Nature Jul. 10 424:147-151.
Supplemental
Info:
Lecture Notes
Powerpoint
presentation
PDF of
presentation
Topic
2 Assembly of Polymerase-Promoter Complexes and Initiation of Transcription
1° Paper: Kanin,
E.I. et al. Chemical inhibition of the TFIIH-associated kinase Cdk7/Kin28 does
not impair global mRNA synthesis.
2007. Proc. Natl. Acad. Sci. 104(14):5812-5817
Review 1: Juven-Gershon
T., J.-Y. Hsu and J.T. Kadonaga. 2006. Perspectives on the RNA polymerase core
promoter. Biochem. Soc. Trans.
34:1047-1050.
Review 2: Wade
JT, Struhl K. The transition from transcriptional initiation to
elongation. Curr Opin Genet Dev. 2008
Feb 16; [Epub ahead of print]
Optional
Resource Reading for Structural Studies: Hahn, S. Structure and Mechanism of the RNA Polymerase II
Transcription Machinery. 2004.
Nat. Struc. Mol. Biol. 11:394.
Optional
Resource Reading for Structural Studies: Lee,
T.I. and R.A. Young. 2000.
Transcription of Eukaryotic Protein-Coding Genes
Powerpoint
Presentation
Notes
PDF of
presentationhttp://jeeves.mmg.uci.edu/mbb206/waterman/mbb206T2.2009.pdf
Topic
3 Promoter Regulation and Transcription Factors
1° Paper: Johnson DS, Mortazavi A, Myers RM, Wold B.
Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007 Jun
8;316(5830):1497-502.
1° Paper: Boyer et al. 2005. Core Transcriptional Regulatory Circuitry
in Human Embryonic Stem Cells.
Cell 122:947-956.
Comment
in: Orkin,
SH. 2005. Chipping away at the embryonic stem
cell network. Cell. 122:828-830.
Review: Kadonaga, J.T.
Regulation of RNA Polymerase II Transcription by Sequence-Specific DNA Binding
Factors. 2004. Cell 116:247-257.
Powerpoint
presentation
PDF of
presentation
Topic
4 Promoter Regulation and Chromatin
1° Paper: Feldman et al.
2006. Nature Cell biology
8:188-194.
Review: Li, B., M.
Carey, and J.L. Workman. 2007. The
role of chromatin during transcription.
Cell 128:707-719
Powerpoint
presentation
PDF of
presentation
Topic
5 Distal Regulatory Regions
1° Paper: Saveliev et al. 2003. DNA triplet repeats mediate
heterochromatin-protein-1-sensitive variegated gene silencing. Nature 422:909-913.
Review 1: Grewal, S.I.S. and D. Moazed. Heterochromatin
and Epigenetic Control of Gene Expression. Science Aug. 8 301:798-802.
Optional
Review: Biggin MD,
Tjian R. Transcriptional regulation in Drosophila: the post-genome
challenge.Funct Integr Genomics. 2001 Mar;1(4):223-34
Optional
Review: Blackwood, E.M.
and J.T. Kadonaga. 2000. Going the Distance: A Current View of Enhancer Action.
Science 281:60-63
Optional
Review: Bell, A.C.,
A.G. West, and G. Felsenfeld. 2001. Insulators and Boundaries: Versatile
Regulatory Elements in the Eukaryotic Genome. Science 291:447-450.
Powerpoint presentation
PDF of
presentation
2008
STEM CELL READING (OPTIONAL)
Primary
Paper: A detailed protocol for
generating iPS cells from mouse fibroblasts
Cautionary
News and Views about iPS stem cells
Letter
to the Editor by iPS scientists about hES cell research