Wednesday, 7th February, 2018, 12:00-13.00

Measuring ribosome profiling at isoform level: a step towards unveiling alternative splicing funcional impact

The alternative processing of transcribed genomic loci through alternative transcript initiation, splicing and polyadenylation, is an intermediate step in mRNA maturation, between transcription and translation. These mechanisms produce different mature mRNA transcripts and determine the transcript repertoire of cells. There is evidence showing that the differential production of transcript isoforms, especially through the mechanism of alternative splicing, is crucial in multiple biological processes such as cell differentiation, acquisition of tissue-specific functions, DNA repair, as well as in multiple pathologies, including cancer. This has been exhaustively shown at RNA level but it remains elusive at protein level. Sequencing of ribosome-protected RNA fragments, or ribosome profiling, provides detailed information on the transcripts being translated in the cell. In this work, we have developed a pipeline for the quantification of individual transcript coding sequences (CDSs) from ribosome profiling using both RNA-seq and Ribo-seq data from multiple datasets. Moreover, we investigated at wich extend the isoforms that can be detected with ribosome profiling show further evidence of translation.

Speaker: Marina Reixachs, Computational RNA Biology, GRIB (IMIM/UPF)

Room Aula 473.10 (PRBB, 4th floor)