Publication List

@article{Reixachs-Solé2020,
title = {Ribosome Profiling at Isoform Level Reveals Evolutionary Conserved Impacts of Differential Splicing on the Proteome},
author = {Marina Reixachs-Solé, Jorge Ruiz-Orera, M.Mar Albà, Eduardo Eyras},
url = {https://www.nature.com/articles/s41467-020-15634-w},
isbn = { 10.1038/s41467-020-15634-w },
year = {2020},
date = {2020-04-14},
journal = {Nature Communications},
volume = {11},
number = {1},
pages = {1768},
abstract = {The differential production of transcript isoforms from gene loci is a key cellular mechanism. Yet, its impact in protein production remains an open question. Here, we describe ORQAS (ORF quantification pipeline for alternative splicing), a pipeline for the translation quantification of individual transcript isoforms using ribosome-protected mRNA fragments (ribosome profiling). We find evidence of translation for 40-50% of the expressed isoforms in human and mouse, with 53% of the expressed genes having more than one translated isoform in human, and 33% in mouse. Differential splicing analysis revealed that about 40% of the splicing changes at RNA level are concordant with changes in translation. Furthermore, orthologous cassette exons between human and mouse preserve the directionality of the change, and are enriched in microexons in a comparison between glia and glioma. ORQAS leverages ribosome profiling to uncover a widespread and evolutionarily conserved impact of differential splicing on translation, particularly of microexon-containing isoforms. },
keywords = {cancer, de novo gene, isoform, lncRNA, microexon, sORF}
}

@article{Reixachs-Sole2019,
title = {Ribosome profiling at isoform level reveals an evolutionary conserved impact of differential splicing on the proteome},
author = {Marina Reixachs-Sole, Jorge Ruiz-Orera, M.Mar Albà, Eduardo Eyras},
url = {https://doi.org/10.1101/582031 },
year = {2019},
date = {2019-03-19},
journal = {bioRxiv, March 19},
abstract = {The differential production of transcript isoforms from gene loci is a key mechanism in multiple biological processes and pathologies. Although this has been exhaustively shown at RNA level, it remains elusive at protein level. Here, we describe a new pipeline ORQAS (ORF quantification pipeline for alternative splicing) for the translation quantification of individual transcript isoforms using ribosome-protected mRNA fragments (Ribosome profiling). We found evidence of translation for 40-50% of the expressed transcript isoforms in human and 50% in mouse, with 53% of the expressed genes having more than one translated isoform in human, and 33% in mouse. Differential analysis revealed that about 40% of the splicing changes measured at RNA level in human were concordant with changes in translation; and that 21.7% of changes measured at RNA level, and 17.8% at translation level, were conserved between human and mouse. Furthermore, orthologous cassette exons preserving the directionality of the change were found enriched in microexons in a comparison between glia and glioma in both, and were conserved between human and mouse.. In summary, we established a moderate but widespread impact of differential splicing in the translation of isoforms and found evidence of an impact on the translation of microexons as a consequence of differential splicing. ORQAS is available at https://github.com/comprna/orqas .},
keywords = {human, isoform, mouse, nervous system, ribosome profiling}
}