Fruitfly ncRNA journal club

Time

2-4pm.

Venue

321 Stanley Hall.

Dates

• 01 Nov 2007 - RB: RNAz
• 08 Nov 2007 - YB: Celniker & Rubin, IH: zipcodes
• 15 Nov 2007 - MS: Evofold (fly section)
• 22 Nov 2007 - Thanksgiving holiday (no meeting)
• 29 Nov 2007 - Postponed (lab move)
• 06 Dec 2007 - Postponed
• 13 Dec 2007 - IH: RNA regulons
• 10 Jan 2008 - RB: Global analysis of localization
• 31 Jan 2008 - RNA binding proteins

Papers

Alternate between "bio" and "informatics" papers?

Bio reviews:

• ncRNA section (p102-103) of this paper (fly genome review):
  • Celniker SE, Rubin GM.  The Drosophila melanogaster genome.  Annu Rev Genomics Hum Genet. 2003;4:89-117.

• RNA localization (see also Fly Zipcodes, Nanos Biology)
  • 2005 meeting review (genome-wide screen for localization!): Jansen RP, Kiebler M.  Intracellular RNA sorting, transport and localization.  Nat Struct Mol Biol. 2005 Oct;12(10):826-9.
  • 2005 review: St Johnston D.  Moving messages: the intracellular localization of mRNAs.  Nat Rev Mol Cell Biol. 2005 May;6(5):363-75.
  • K10: Bullock SL, Ish-Horowicz D.  Conserved signals and machinery for RNA transport in Drosophila oogenesis and embryogenesis.  Nature. 2001 Dec 6;414(6864):611-6.
  • review: Lipshitz HD, Smibert CA.  Mechanisms of RNA localization and translational regulation.  Curr Opin Genet Dev. 2000 Oct;10(5):476-88.
  • nanos/review: Gavis ER.  Expeditions to the pole: RNA localization in Xenopus and Drosophila.  Trends Cell Biol. 1997 Dec;7(12):485-92.

• "RNA regulons"
  • Keene JD.  RNA regulons: coordination of post-transcriptional events.  Nat Rev Genet. 2007 Jul;8(7):533-43.

• RNA binding proteins
  • Gamberi C, Johnstone O, Lasko P.  Drosophila RNA binding proteins.  Int Rev Cytol. 2006;248:43-139.

Sequence analysis screens:

• Computational RNomics of Drosophilids (Rna Z)

• Drosophila ncRNA section of this paper (Evo Fold):
  • Siepel A et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.  Genome Res. 2005 Aug;15(8):1034-50. Epub 2005 Jul 15.

• AAA papers (to appear, preprints available)

• Eric Lai
  • Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC.  Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs.  Genome Res. 2007 Nov 7;.

Functional genomics screens:

• Pavel Tomancak's genome-wide localization assays:
  • Lecuyer E, Yoshida H, Parthasarathy N, Alm C, Babak T, Cerovina T, Hughes TR, Tomancak P, Krause HM.  Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.  Cell. 2007 Oct 5;131(1):174-87.