Category Archives: ribosome profiling
Our group is participating in the SMBE Satellite Meeting on de novo gene birth
Cova Vara and Chris Papadopoulos have presented their research in this week’s Symposium on de novo genes celebrated in Texas A&M University (College Station, Nov 6-9 2023). The research aims to explore the evolution of new genes in populations and … Continue reading
Filed under de novo gene evolution, mammal, micropeptide, ribosome profiling, RNA-Seq, transcriptomics, yeast
The functions of human de novo originated proteins start to be revealed
Proteins restricted to a given species or lineage are mysterious. Many of them have emerged de novo from ancestral non-coding genomic regions rather than from pre-existing genes. A new study by Vakirlis et al. shows that a large portion of … Continue reading
Our group goes to ECCB 2022
We had a great time at the European Conference in Computational Biology celebrated in Sitges in September 2022. Mar gave a keynote talk on The emerging small proteome, and Marta, Lili and José Carlos presented their PhD research in the … Continue reading
Filed under lncRNA, ribosome profiling, transcriptomics, yeast
ERC Advanced Grant NovoGenePop
Our ERC Advanced Grant NovoGenePop has just started! This means we can already recruits scientists and start to gather data. The project will investigate how new genes arise in closely related species and populations. This will involve the development of … Continue reading
Filed under de novo gene evolution, ribosome profiling, RNA-Seq, transcriptomics, yeast
mRNA molecules one at a time
Fascinated by the potential of long read technologies to make a difference in our knowldege of the transcriptome, two years ago we started generating Nanopore dRNA data for different yeast species, including the yeast S. pombe. This organism is ideal … Continue reading
Filed under ribosome profiling, transcriptomics, yeast
Large scale annotation of small proteins by ribosome profiling
We participate in a a new world-wide initiative for the large-scale annotation of small ORF translation events detected by ribosome profiling in the human genome. The initiative, led by researchers at Ensembl, Max Delbrück Center and Broad Institute, among others, … Continue reading
Filed under de novo gene evolution, lncRNA, micropeptide, ribosome profiling
Protein translation from uORFs: roles in stress
The current view of an mRNA is that of a central coding sequence (CDS) flanked by 5′ and 3′ untranslated regions (UTRs). But often UTRs contain open reading frames which, as revealed by ribosome profiling, can also be translated. The … Continue reading
Filed under ribosome profiling, yeast
Thousands of small ORFs are translated, what are they doing?
The high throughput sequencing of ribosome-protected RNA fragments, or ribosome profiling (Ribo-Seq), has uncovered the translation of thousands of novel small ORFs (< 100 amino acids) that were not annotated. These ORFs had remained hidden from annotation pipelines because of … Continue reading
Filed under de novo gene evolution, proteomics, ribosome profiling, science
Using ribosome profiling to improve our understanding of gene regulation
To measure changes in the expression of the genes we normally compare mRNA abundances using high throughput RNA sequencing data (RNA-Seq), as a proxy for the changes in the encoded proteins. However, it is well known that the correlation between … Continue reading
