Amino Acid Animals Computational Biology Databases de novo gene DNA Evolution Genetic Genome human Humans Mice Molecular Molecular Sequence Data Proteins Proteins: chemistry Proteins: genetics Repetitive Sequences ribosome profiling RNA-Seq Selection Sequence Analysis Sequence Homology transcriptomics yeast
2019 |
William R. Blevins, Teresa Tavella, Simone G. Moro, Bernat Blasco-Moreno, Adrià Closa-Mosquera, Juana Díez, Lucas B. Carey, M.Mar Albà Scientific Reports, 9 pp. 11005, 2019. (Links | BibTeX | Tags: oxidative stress, proteomics, ribosome profiling, RNA-Seq, translation regulation, yeast) @article{Blevins2019_2, title = {Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker's yeast}, author = {William R. Blevins, Teresa Tavella, Simone G. Moro, Bernat Blasco-Moreno, Adrià Closa-Mosquera, Juana Díez, Lucas B. Carey, M.Mar Albà}, url = {https://www.nature.com/articles/s41598-019-47424-w}, year = {2019}, date = {2019-07-29}, journal = {Scientific Reports}, volume = {9}, pages = {11005}, keywords = {oxidative stress, proteomics, ribosome profiling, RNA-Seq, translation regulation, yeast} } |
William R. Blevins, Lucas B. Carey, M.Mar Albà BMC Research Notes, 12 pp. 250, 2019. (Links | BibTeX | Tags: oxidative stress, RNA-Seq, transcriptomics, yeast) @article{Blevins2019b, title = {Transcriptomics data of 11 species of yeast identically grown in rich media and oxidative stress conditions}, author = {William R. Blevins, Lucas B. Carey, M.Mar Albà}, url = {https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4286-0}, year = {2019}, date = {2019-05-03}, journal = {BMC Research Notes}, volume = {12}, pages = {250}, keywords = {oxidative stress, RNA-Seq, transcriptomics, yeast} } |
William R. Blevins, Jorge Ruiz-Orera, Xavier Messeguer, Bernat Blasco-Moreno, José Luis Villanueva-Cañas, Lorena Espinar, Juana Díez, Lucas B. Carey, M. Mar Albà Frequent birth of de novo genes in the compact yeast genome (Article) bioRxiv, March 13, 2019. (Abstract | Links | BibTeX | Tags: de novo gene, RNA-Seq, Saccharomyces cerevisiae, yeast) @article{Blevins2019, title = {Frequent birth of de novo genes in the compact yeast genome}, author = {William R. Blevins, Jorge Ruiz-Orera, Xavier Messeguer, Bernat Blasco-Moreno, José Luis Villanueva-Cañas, Lorena Espinar, Juana Díez, Lucas B. Carey, M. Mar Albà}, url = {https://doi.org/10.1101/575837 }, year = {2019}, date = {2019-03-13}, journal = {bioRxiv, March 13}, abstract = {Evidence has accumulated that some genes originate directly from previously non-genic sequences, or de novo, rather than by the duplication or fusion of existing genes. However, how de novo genes emerge and eventually become functional is largely unknown. Here we perform the first study on de novo genes that uses transcriptomics data from eleven different yeast species, all grown identically in both rich media and in oxidative stress conditions. The genomes of these species are densely-packed with functional elements, leaving little room for the co-option of genomic sequences into new transcribed loci. Despite this, we find that at least 213 transcripts (~5%) have arisen de novo in the past 20 million years of evolution of baker’s yeast-or approximately 10 new transcripts every million years. Nearly half of the total newly expressed sequences are generated from regions in which both DNA strands are used as templates for transcription, explaining the apparent contradiction between the limited ‘empty’ genomic space and high rate of de novo gene birth. In addition, we find that 40% of these de novo transcripts are actively translated and that at least a fraction of the encoded proteins are likely to be under purifying selection. This study shows that even in very highly compact genomes, de novo transcripts are continuously generated and can give rise to new functional protein-coding genes.}, keywords = {de novo gene, RNA-Seq, Saccharomyces cerevisiae, yeast} } Evidence has accumulated that some genes originate directly from previously non-genic sequences, or de novo, rather than by the duplication or fusion of existing genes. However, how de novo genes emerge and eventually become functional is largely unknown. Here we perform the first study on de novo genes that uses transcriptomics data from eleven different yeast species, all grown identically in both rich media and in oxidative stress conditions. The genomes of these species are densely-packed with functional elements, leaving little room for the co-option of genomic sequences into new transcribed loci. Despite this, we find that at least 213 transcripts (~5%) have arisen de novo in the past 20 million years of evolution of baker’s yeast-or approximately 10 new transcripts every million years. Nearly half of the total newly expressed sequences are generated from regions in which both DNA strands are used as templates for transcription, explaining the apparent contradiction between the limited ‘empty’ genomic space and high rate of de novo gene birth. In addition, we find that 40% of these de novo transcripts are actively translated and that at least a fraction of the encoded proteins are likely to be under purifying selection. This study shows that even in very highly compact genomes, de novo transcripts are continuously generated and can give rise to new functional protein-coding genes. |
2017 |
Willam Blevins, M.Mar Albà, Lucas Carey Comparative transcriptomics and ribo-seq: Looking at de novo gene emergence in Saccharomycotina (Conference) PeerJ preprints 5 (e3030v1), 2017, (The SMBE 2017 Collection). (Abstract | BibTeX | Tags: de novo gene, yeast) @conference{Blevins2017, title = {Comparative transcriptomics and ribo-seq: Looking at de novo gene emergence in Saccharomycotina}, author = {Willam Blevins, M.Mar Albà, Lucas Carey}, year = {2017}, date = {2017-06-20}, journal = {PeerJ Preprints}, volume = {PeerJ preprints 5}, number = {e3030v1}, abstract = { In de novo gene emergence, a segment of non-coding DNA undergoes a series of changes which enables transcription, potentially leading to a new protein that could eventually acquire a novel function. Due to their recent origins, young de novo genes have no homology with other genes. Furthermore, de novo genes may not initially be under the same selective constraints as other genes. Dozens of de novo genes have recently been identified in many diverse species; however, the mechanisms leading to their appearance are not yet well understood. To study this phenomenon, we have performed deep RNA sequencing (RNA-seq) on 11 species of yeast from the phylum of Ascomycota in both rich media and oxidative stress conditions. Furthermore, we performed ribosome profiling (Ribo-seq) experiments in both conditions with S. cerevisiae. These data have been used to classify the conservation of genes at different depths in the yeast phylogeny. Hundreds of genes in each species were novel (unannotated), and many were identified as putative de novo genes; these candidates were then tested for signals of translation using our Ribo-seq data. We show that putative de novo genes have different properties relative to phylogenetically conserved genes. This comparative phylotranscriptomic analysis advances our understanding of de novo gene origins. }, note = {The SMBE 2017 Collection}, keywords = {de novo gene, yeast} } In de novo gene emergence, a segment of non-coding DNA undergoes a series of changes which enables transcription, potentially leading to a new protein that could eventually acquire a novel function. Due to their recent origins, young de novo genes have no homology with other genes. Furthermore, de novo genes may not initially be under the same selective constraints as other genes. Dozens of de novo genes have recently been identified in many diverse species; however, the mechanisms leading to their appearance are not yet well understood. To study this phenomenon, we have performed deep RNA sequencing (RNA-seq) on 11 species of yeast from the phylum of Ascomycota in both rich media and oxidative stress conditions. Furthermore, we performed ribosome profiling (Ribo-seq) experiments in both conditions with S. cerevisiae. These data have been used to classify the conservation of genes at different depths in the yeast phylogeny. Hundreds of genes in each species were novel (unannotated), and many were identified as putative de novo genes; these candidates were then tested for signals of translation using our Ribo-seq data. We show that putative de novo genes have different properties relative to phylogenetically conserved genes. This comparative phylotranscriptomic analysis advances our understanding of de novo gene origins. |
2015 |
van Dijk, David, Dhar, Riddhiman, Missarova, Alsu M, Espinar, Lorena, Blevins, William R, Lehner, Ben, Carey, Lucas B Nature Communications, 6 pp. 7972, 2015, ISBN: 10.1038/ncomms8972. (Links | BibTeX | Tags: RNA polymerase error rate, transcriptomics, yeast) @article{vanD2015, title = {Slow-growing cells within isogenic populations have increased RNA polymerase error rates and DNA damage}, author = {van Dijk, David, Dhar, Riddhiman, Missarova, Alsu M, Espinar, Lorena, Blevins, William R, Lehner, Ben, Carey, Lucas B}, url = {http://www.nature.com/ncomms/2015/150813/ncomms8972/full/ncomms8972.html}, isbn = {10.1038/ncomms8972}, year = {2015}, date = {2015-08-13}, journal = {Nature Communications}, volume = {6}, pages = {7972}, keywords = {RNA polymerase error rate, transcriptomics, yeast} } |
