SPECIAL SEMINAR - YARDEN KATZ

26/07/2011 - 11:00Add To Calendar 2011-07-26 11:00:00 2011-07-26 11:00:00 סמינר מיוחד - ירדן כץ Seminar  Yarden Katz Chris Burge group, Dept. of Brain and Cognitive Sciences, Dept. of Biology MIT  Title: Analysis and design of RNA sequencing experiments for identifying isoform regulation  JULY 26th  2011 at 11:00 Location: To Be Announced Abstract: Through alternative splicing, most human genes express multiple isoforms that often differ in function. To infer isoform regulation from high-throughput sequencing of cDNA fragments (RNA-seq), we developed the mixture-of-isoforms (MISO) model, a statistical model that estimates expression of alternatively spliced exons and isoforms and assesses confidence in these estimates. Incorporation of mRNA fragment length distribution in paired-end RNA-seq greatly improved estimation of alternative-splicing levels. MISO also detects differentially regulated exons or isoforms. Application of MISO implicated the RNA splicing factor hnRNP H1 in the regulation of alternative cleavage and polyadenylation, a role that was supported by UV cross-linking–immunoprecipitation sequencing (CLIP-seq) analysis in human cells. Our results provide a probabilistic framework for RNA-seq analysis, give functional insights into pre-mRNA processing and yield guidelines for the optimal design of RNA-seq experiments for studies of gene and isoform expression. Katz Y, Wang ET, Airoldi EM, Burge CB. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods, 7(12):1009-15. הפקולטה למדעי החיים webls@mail.biu.ac.il Asia/Jerusalem public

Seminar

 Yarden Katz

Chris Burge group,

Dept. of Brain and Cognitive Sciences,

Dept. of Biology

MIT 

Title: Analysis and design of RNA sequencing experiments for identifying isoform regulation

 JULY 26th  2011 at 11:00

Location: To Be Announced

Abstract:


Through alternative splicing, most human genes express multiple isoforms that often differ in function. To infer isoform regulation from high-throughput sequencing of cDNA fragments (RNA-seq), we developed the mixture-of-isoforms (MISO) model, a statistical model that estimates expression of alternatively spliced exons and isoforms and assesses confidence in these estimates. Incorporation of mRNA fragment length distribution in paired-end RNA-seq greatly improved estimation of alternative-splicing levels. MISO also detects differentially regulated exons or isoforms. Application of MISO implicated the RNA splicing factor hnRNP H1 in the regulation of alternative cleavage and polyadenylation, a role that was supported by UV cross-linking–immunoprecipitation sequencing (CLIP-seq) analysis in human cells. Our results provide a probabilistic framework for RNA-seq analysis, give functional insights into pre-mRNA processing and yield guidelines for the optimal design of RNA-seq experiments for studies of gene and isoform expression.

Katz Y, Wang ET, Airoldi EM, Burge CB. (2010). Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods, 7(12):1009-15.

Last Updated Date : 25/07/2011