Publication List

@article{Ruiz-Orera2020b,
title = {Evolution of New Proteins From Translated sORFs in Long Non-Coding RNAs},
author = {Jorge Ruiz-Orera, José Luis Villanueva-Cañas, M.Mar Albà},
year = {2020},
date = {2020-06-01},
journal = {Experimental Cell Research, 391 (1), pp. 111940},
keywords = {de novo gene, lncRNA}
}

@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{Ruiz-Orera2020,
title = {Evolution of New Proteins From Translated sORFs in Long Non-Coding RNAs },
author = {Jorge Ruiz-Orera, José Luis Villanueva-Cañas, M.Mar Albà},
url = {https://www.sciencedirect.com/science/article/abs/pii/S0014482720301452?via%3Dihub},
year = {2020},
date = {2020-03-07},
journal = {Experimental Cell Research},
volume = {391},
number = {1},
pages = {111940},
abstract = {High throughput RNA sequencing techniques have revealed that a large fraction of the genome is transcribed into long non-coding RNAs (lncRNAs). Unlike canonical protein-coding genes, lncRNAs do not contain long open reading frames (ORFs) and tend to be poorly conserved across species. However, many of them contain small ORFs (sORFs) that exhibit translation signatures according to ribosome profiling or proteomics data. These sORFs are a source of putative novel proteins; some of them may confer a selective advantage and be maintained over time, a process known as de novo gene birth. Here we review the mechanisms by which randomly occurring sORFs in lncRNAs can become new functional proteins. },
keywords = {de novo gene, lncRNA, microprotein, ribosome profiling, sORF}
}

@article{Ruiz-Orera2019_2,
title = {Conserved regions in long non-coding RNAs contain abundant translation and protein–RNA interaction signatures},
author = {Jorge Ruiz-Orera, M.Mar Albà},
url = {https://academic.oup.com/nargab/article/1/1/e2/5528612},
year = {2019},
date = {2019-07-05},
journal = {Nucleic Acids Research Genomics and Bioinformatics},
volume = {1},
pages = {e2},
keywords = {lncRNA, micropeptide, protein-RNA interaction, RBP, sORF}
}

@article{Ruiz-Orera2015b,
title = {Origins of de novo genes in human and chimpanzee},
author = {Ruiz-Orera, Jorge, Hernandez-Rodriguez, Jessica, Chiva, Cristina, Sabidó, Eduard, Kondova, Ivanela, Bontrop, Ronald, Marqués-Bonet, Tomàs, Albà, M.Mar},
url = {http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005721},
year = {2015},
date = {2015-12-31},
journal = {Plos Genetics},
volume = {11},
number = {12},
pages = {e1005721},
keywords = {chimpanzee, de novo gene, Evolution, Humans, lncRNA, Promoter, proteomics, ribosome profiling, RNA-Seq, transcription factor binding site, transcriptomics}
}