CB 399: RNAi Screening: From Design to Data Analysis Spring 2013

RNAi Screening: From Design to Data Analysis
Nanocourse Director: Norbert Perrimon

Lecturers: Steve Elledge, Stephanie Mohr, Jen Smith, Norbert Perrimon and Caroline Shamu
Curriculum Fellow: Dr. Leah Brault, lbrault@genetics.med.harvard.edu

Tissue culture cells have provided a powerful system for studying many fundamental problems in signal transduction, cell differentiation and physiology. However, functional studies in cultured cells were hampered in the past by the lack of a powerful method for perturbing gene activities. A turning point came with the discovery of RNA interference and its rapid rise from small scale to genome-scale screening. Today, the most commonly used approaches are based on long dsRNA for Drosophila cells, and either synthetic siRNAs or vector-expressed short hairpin RNAs (shRNAs) for mammalian cells. Driven by genome-sequence data, RNAi is now widely used in high-throughput (HT) screens in both basic and applied biology. It is a powerful method for addressing many cell biological questions, and its amenability for use in modifier screens in addition to direct loss of function screening has made it particularly useful for the analysis of signal transductions pathways. RNAi has also become a method of choice for key steps in the development of therapeutic agents, from target discovery and validation to the analysis of the mechanisms of action of small molecules. This nanocourse will focus on both the technology and applications of RNAi screens.


First Session: Wednesday, March 13, 2013 12:00 - 3:30 PM
Location: TMEC Building, Room 250
Second Session: Wednesday, March 27, 2013 12:00 - 2:30 PM
Location: TMEC Building, Room 447


Instructions for Registered Students

The second meeting of this course will be on Wednesday, March 27th from 12:00 – 2:30 p.m. Please arrive on time for this session!  In preparation for this session, selected publications posted below will be required for you to read.  The required readings are:

Mohr, S., Bakal, C. and Perrimon N. (2010) Genomic screening with RNAi: Results and Challenges. Annual Reviews in Biochemistry. 79. 37-64. PMID: 20367032.

Joyce EF, Williams BR, Xie T, Wu CT. (2012) Identification of Genes That Promote or Antagonize Somatic Homolog Pairing Using a High-Throughput FISH-Based Screen. PLoS Genet. 8(5):e1002667 PubMed ID: 22589731

Brass AL, Huang I-C, Benita Y, John SP, Krishnan MN, Feeley EM, Ryan BJ, Weyer JL, van der Weyden L, Fikrig E, Adams DJ, Xavier RJ, Farzan M, Elledge SJ.  (2009)  The IFITM Proteins Mediate Cellular Resistance to Influenza A H1N1 Virus, West Nile Virus, and Dengue Virus. Cell 139:1243-1254.  PubMed ID: 20064371

Adamson B, Smogorzewska A, Sigoillot FD, King RW, Elledge SJ. (2012) A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Nat Cell Biol. 2012 Feb 19;14(3):318-28. doi: 10.1038/ncb2426. PubMed PMID: 22344029; PubMed Central


All students are required to submit a 1-page description of an RNAi screen which addresses a specific biological question. (“Specific” is to be taken literally…studying “cell death”, “cell viability” or “effects on antennae” are too broad.  Be exact in your question!)  In your answer you should describe the primary screening assay, at least one secondary assay, appropriate controls, data analysis and validation strategies. Note that you are permitted to describe an assay that is related to your thesis work but you should not recycle a previous assignment or specific aims from your thesis proposal. These assignments will be the basis for discussion on the 27th, so work hard on them. You should also be ready to ask questions and give constructive feedback to fellow students on Wednesday.

This assignment must be submitted to the curriculum fellow (lbrault@genetics.med.harvard.edu) by Monday, March 25th at 12:00 p.m. (noon).


DROP DEADLINE: Wednesday, March 6, 2013