Study topics for Etgar seminarion

Alternative splicing. The topic covers types of alternative splicing, regulating mechanisms, functional importance, and connection to human diseases.
Roy Shen, Ariella Klutstein, Yonathan Guttel

B. Hartmann, J. Valcarcel (2009). Decrypting the genome's alternative messages. Current Opinion in Cell Biology, advanced publication.
J. Tazi, N. Bakkour, S. Stamm (2009). Alternative splicing and disease. Biochim Biophys Acta, 1792:14-26.
G.S. Wang, T.A. Cooper (2007). Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet, 8:749-761.
M. Eriksson et al. (2003). Recurrent de novo point mutations in lamin A cause Hutchinson–Gilford progeria syndrome. Nature, 423:293-298.

Mirtrons. The topic covers the role and biogenesis of microRNAs, how mirtrons are different in their biogenesis, and phylogenetic span of mirtrons.

J.G. Ruby, C.H. Jan, D.P. Bartel (2007). Intronic microRNA precursors that bypass Drosha processing. Nature 448:83-87.

Nonsense-mediated decay (NMD). The topic covers the mechanism of intron-dependent NMD, and its relations with the length and location of the introns.

Y.F. Chang, J.S. Imam, M.F. Wilkinson (2007). The nonsense-mediated decay RNA surveillance pathway. Annual Review of Biochemistry 76:51-74.

Export. The topic covers the mechanism of export of the mRNA from the nucleous to the cytoplasm, how it is linked to splicing, and how it helps in regulating the expression level of genes.
Adi Biton, Inbal Caspi

R. Reed, E. Hurt (2002). A conserved mRNA export machinery coupled to pre-mRNA splicing. Cell 108:523-531.
M.-J. Luo, R. Reed (1999). Splicing is required for rapid and efficient mRNA export in metazoans. PNAS 96:14937-14942.
P. Valencia, A.P. Dias, R. Reed (2008). Splicing promotes rapid and efficient mRNA export in mammalian cells. PNAS 105:3386-3391.
R. Reed, H. Cheng (2005). TREX, SR proteins and export of mRNA. Current Opinion in Cell Biology 17:269-273.

AS-NMD regulation. The topic studies how a coupling between alternative splicing and NMD can form another mechanism to control genes' expression level.
Roni Harel, Yael Gabai

N.J. McGlincy, C.W. Smith (2008). Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense? Trends in Biochemistry Science 33:385-393.
R.T. Hillman, R.E. Green, S.E. Brenner (2004). An unappreciated role for RNA surveillance. Genome Biol 5:R8.
J. Wittmann, E.M. Hol, H.M. Jack (2006). hUPF2 silencing identifies physiologic substrates of mammalian nonsense-mediated mRNA decay. Mol Cell Biol 26:1272-1287.
Q. Pan et al. (2006). Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. Genes Dev 20:153-158.

First introns. The topic covers the differences between first (5'-most) introns and other introns, and its functional implications.

K.R. Bradnam, I. Korf (2008). Longer first introns are a general property of eukaryotic gene structure. PLoS ONE 3:e3093.