Regulation of Gene Expression, MMG 206 Spring 2009
Lectures and Papers for Sandri-Goldin:
Lecture 1: 5'
Capping & 3’ processing
Sandri-Goldin
Lecture 1 Power Point
Papers covered in class:
E. Cho, T. Takagi, C. R. Moore, and S.
Buratowski. 1997. mRNA capping enzyme is recruited to the transcription complex
by phosphorylation of the RNA polymerase II carboxy-terminal domain.
GENES & DEVELOPMENT 11:3319–3326.
S. H. Ahn, .M. Kim, and S. Buratowski.
2004. Phosphorylation of Serine 2 within the RNA Polymerase II C-Terminal Domain
Couples Transcription and 3’ End Processing. Molecular Cell 13, 67–76.
Z. Ni, B.E. Schwartz, J. Werner, J. Suarez,
and J. T. Lis. 2004. Coordination of Transcription, RNA
Processing, and Surveillance by P-TEFb Kinase on Heat Shock Genes. Molecular
Cell 13,55-65.
H. Zhang, J. Y. Lee and B. Tian. 2005. Biased
alternative polyadenylation in human tissues. Genome Biology 6:R100.
Expressed Sequence
Tags (EST)
Lecture 2: Mechanism of splicing; Spliceosome
Assembly
Sandri-Goldin
Lecture 2 Power Point
Papers referenced in class:
Z. Zhou, L. J. Licklider, S. P. Gygi & Robin Reed. 2002. Comprehensive
proteomic analysis of the human
spliceosome NATURE 419:182-188.
R. Das, K. Dufu, B.Romney, M. Feldt, M.
Elenko and R. Reed. 2006. Functional
coupling of RNAP II transcription to spliceosome assembly. Genes & Dev. 2006 20: 1100-1109.
M. J. Hicks, C.-R. Yang, M.V. Kotlajich, and
K. J. Hertel. 2006. Linking Splicing to Pol II Transcription Stabilizes
Pre-mRNAs and Influences Splicing Patterns. PLoS BIOLOGY 4(6): e147.
Review on Spliceosome Composition by Proteomic analysis:
M. S.
Jurica and M. J. Moore. 2003.
Pre-mRNA Splicing: Awash in a Sea of Protein Molecular Cell 12: 5–14.
Lecture 3: Splicing Regulation and SR proteins
Sandri-Goldin
Lecture 3 Power Point
Papers
referenced in lecture 3:
Prasad, J., K. Colwill, T. Pawson,
and J.L. Manley. 1999. The protein kinase Clk/Sty directly modulates SR
protein activity: both hyper- and hypophosphorylation inhibit splicing.
Molecular and Celluar Biology 19:6991-7000.
P.J. Mintz and D.L. Spector. 2000.
Compartmentalization of RNA Processing Factors within Nuclear Speckles. Journal
of Structural Biology 129, 241–251
P.J.
Smith, C. Zhang, J.Wang, S.L. Chew, M.Q. Zhang and A.R. Krainer. 2006. An
increased specificity
score matrix
for the prediction of SF2/ASF-specific exonic splicing enhancers. Human
Molecular Genetics Vol. 15, 2490-2508.
C.Ma1, A.Velazquez-Dones, J.C. Hagopian, G.
Ghosh, X. Fu and J.A. Adams.
2008. Ordered Multi-site Phosphorylation of
the Splicing Factor ASF/SF2 By SRPK1. J. Mol. Biol. 376, 55–68..
R.Das,
J. Yu, Z. Zhang, M.P. Gygi, A.R.. Krainer, S.P. Gygi, and R.Reed. 2007. SR Proteins Function in Coupling
RNAP II Transcription to Pre-mRNA Splicing. Molecular Cell 26, 867–8.
A.
Sapra, M. Anko, I. Grishina, M. Lorenz, M. Pabis, I. Poser, J. Rollins, E.
Weiland, K.M. Neugebauer. 2009. SR protein family members display diverse
activities in the formation of nascent and mature mRNPs in vivo. Molecular Cell
34:179-190.
SR
Protein Reviews:
Gravely, B.
2000. Sorting out the complexity of SR protein functions. RNA 6:1197-1211.
Hertel,
K.J. and B. Gravely. 2005. RS domains contact the pre-mRNA throughout
spliceosome assembly. Trends Biochem. Sci. 30:115-118.
Lecture
4 Alternative Splicing:
Sandri-Goldin
Lecture 4
Recommended
Reviews of Alternative Splicing that you may find helpful and papers that I
covered in class.
K.
Lynch. Consequences of regulated pre-mRNA splicing in the immune system. 2004.
Nature Reviews-Immunology 4:931.
A.J. Matlin,
F. Clark and C.W.J. Smith. 2005. Understanding alternative splicing: towards a
cellular code. Nature Reviews-Molecular Cellular Biology 6:386.
R.
Klinck, A. Bramard, L. Inkel, G. Dufresne-Martin, J.Gervais-Bird, R. Madden,
E.R. Paquet, C. Koh, J.P. Venables, P. Prinos, M. Jilaveanu-Pelmus, R.
Wellinger, C. Rancourt, B. Chabot and S. Elela. 2008. Multiple Alternative
Splicing Markers for Ovarian Cancer. Cancer Res. 68: 657-63.
Feng
Y, Valley MT, Lazar J, Yang AL, Bronson RT, Firestein S, Coetzee WA, Manley JL.
2009. SRp38
regulates alternative splicing and is required for Ca(2+) handling in the
embryonic heart. Dev Cell. 2009 Apr;16(4):528-38.
Study
Guide:
EXAMS
on Post-transcriptional Regulation, from 2004-2008:
MBB 206 Exam 2, May,
2004, answer key
MBB 206 Exam 2, May
2005
MBB 206 Exam 2, May 2006
MBB 206 Exam 2, June 2007, &
answer key
MBB 206 Exam 2, May, 2008 &
answer key
MMG 206 Exam 2, May 2009 & answer
key
Lecture
5: RNA Editing in mammalian cells:
Sandri-Goldin
Lecture 5
E. BRATT and M. OHMAN.
Coordination of editing and splicing of glutamate receptor pre-mRNA. RNA 2003, 9:309–318.
J. OHLSON, J. S. PEDERSEN, D. HAUSSLER, and M.
O HMAN. 2007. Editing modifies the GABAA receptor subunit a3. RNA 13:698–703.
Whitney
et al. Calcium-permeable AMPA receptors containing Q/R-unedited GluR2 direct
human neural progenitor cell differentiation to neurons. 2008. FASEB Journal
doi. 10.1096/fj.07-104661.
Y.
Kawahara,
A. Grimberg, S. Teegarden, C. Mombereau,
S. Liu,
T.L. Bale, J.A. Blendy, and K. Nishikura1.
2008. Dysregulated Editing of Serotonin 2C Receptor mRNAs
Results in Energy Dissipation and Loss of Fat Mass. The
Journal of Neuroscience, November 26, 2008 • 28(48):12834
–12844
Reviews
on RNA Editing
Keegan,
L.P., A. Gallo and M.A. O'Connell. 2001. The many roles of an RNA editor.
Nature Genetics Reviews 2:869-880.
R. A. Reenan. The RNA world meets
behavior: A to I pre-mRNA editing in animals. TRENDS in Genetics Vol.17
February 2001.
Lecture 6: mRNA
Export:
Sandri-Goldin
Lecture 6
Papers covered in class:
M. Luo, Z. Zhou, K. Magni, C.
Christoforides, J. Rappsilber, M. Mann and R. Reed. 2001. Pre-mRNA splicing and
mRNA export linked by direct interactions between UAP56 and Aly/REF. 2001. Nature 413:644-647.
P.
Valencia, A.P. Dias and R. Reed. 2008. Splicing promotes rapid and efficient
mRNA export in mammalian cells. PNAS
105:3386-3391.
H.
Cheng, K. Dufu, C. Lee, J.L Hsu and R. Reed. 2006. Human mRNA export machinery
recruited to 5' end of mRNA. Cell
127:1389-1400.