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Vancouver Bioinformatics User Group (VanBUG) » archive for December, 2011

 François Major

PIMS-sponsored speaker

Download Seminar Poster PDF

Talk Title:
Simulating and Predicting the MicroTargetome

Date/Time:
Thursday, December 8th, 2011, 6:00 pm

Affiliation:
Institut de Recherche en Immunologie et en Cancérologie and Département d’Informatique et de Recherche Opérationnelle, Université de Montréal

URL:
François Major

Abstract:
Protein output determines cell types and states. In animals, microRNAs (miRNAs) are key actors in controlling protein output. Mature miRNAs are about 22-nucleotide long. They are loaded in RNA-induced silencing complexes (RISCs), which bind to miRNA complementary sites in messenger RNAs (mRNAs) to repress their translation. Besides, recent studies indicate that various non-coding RNAs control protein output by competitive attraction of miRNAs. I will present an algorithm to predict the microTargetome, i.e. the RISC/mRNA matching, which considers all competing endogenous RNAs (ceRNAs). The model uses a free-energy of hybridization, and an algorithm that mimics miRNA competition and cooperation. Using this algorithm, we simulated the overexpression of single miRNAs in a specific cell line, and derived a series of biological consequences related to such a protein expression control system. MiRNA, ceRNA, and mRNA levels vary in different cell types and states, including cancer cells. Understanding and predicting microTargetome changes could thus bring insights into the role of RNA in cell differentiation, as well as in cancer development and progression.

Please note:
Trainees are invited to meet with the VanBUG speaker for open discussion of both science and career paths. This takes place 4:30-5:30pm in either the Boardroom or Lunchroom on the ground floor of the BCCRC

Recommended Readings
MC-Fold and MC-Sym pipeline
Designing artificial RNAs
E2F/mir-20a autoregulatory feedback loop

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Introductory Speaker:
Fong Chun Chan, MSc candidate, Gascoyne Lab, BC Cancer Research Centre

Title:
Detection of Differentially Expressed Alternative Transcripts using Conventional Microarrays