Publication List

@article{Rado-Trilla2015,
title = {Key role of amino acid repeat expansions in the functional diversification of duplicated transcription factors.},
author = {Radó-Trilla, Núria and Arató, Krisztina and Pegueroles, Cinta and Raya, Alicia and de la Luna, Susana and Albà, M Mar},
url = {http://www.ncbi.nlm.nih.gov/pubmed/25931513},
issn = {1537-1719},
year = {2015},
date = {2015-01-01},
journal = {Molecular biology and evolution},
abstract = {The high regulatory complexity of vertebrates has been related to two closely spaced whole genome duplications (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families originated during the 2R-WGD contain LCRs. The number of gene duplicates with LCRs is 155 out of 550 analyzed (28%), about twice as many as the number of single copy genes with LCRs (15 out of 115, 13%). In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes.},
keywords = {amino acid tandem repeat, Evolution, Gene Duplication, polyalanine, transcription factor, vertebrates}
}

@article{Farre2010,
title = {Heterogeneous patterns of gene-expression diversification in mammalian gene duplicates.},
author = {Farré, Domènec and Albà, M Mar},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19822635},
issn = {1537-1719},
year = {2010},
date = {2010-01-01},
journal = {Molecular biology and evolution},
volume = {27},
number = {2},
pages = {325--35},
abstract = {Gene duplication is a major mechanism for molecular evolutionary innovation. Young gene duplicates typically exhibit elevated rates of protein evolution and, according to a number of recent studies, increased expression divergence. However, the nature of these changes is still poorly understood. To gain novel insights into the functional consequences of gene duplication, we have undertaken an in-depth analysis of a large data set of gene families containing primate- and/or rodent-specific gene duplicates. We have found a clear tendency toward an increase in protein, promoter, and expression divergence with increasing number of duplication events undergone by each gene since the human-mouse split. In addition, gene duplication is significantly associated with a reduction in expression breadth and intensity. Interestingly, it is possible to identify three main groups regarding the evolution of gene expression following gene duplication. The first group, which comprises around 25% of the families, shows patterns compatible with tissue-expression partitioning. The second and largest group, comprising 33-53% of the families, shows broad expression of one of the gene copies and reduced, overlapping, expression of the other copy or copies. This can be attributed, in most cases, to loss of expression in several tissues of one or more gene copies. Finally, a substantial number of families, 19-35%, maintain a very high level of tissue-expression overlap (>0.8) after tens of millions of years of evolution. These families may have been subject to selection for increased gene dosage.},
keywords = {Animals, Evolution, Gene Duplication, Genetic, Humans, Mammals, Mammals: genetics, Models, Molecular}
}

@article{Toll-Riera2009,
title = {Evolution of primate orphan proteins.},
author = {Toll-Riera, Macarena and Castelo, Robert and Bellora, Nicolás and Albà, M Mar},
url = {http://www.ncbi.nlm.nih.gov/pubmed/19614593},
issn = {1470-8752},
year = {2009},
date = {2009-01-01},
journal = {Biochemical Society transactions},
volume = {37},
number = {Pt 4},
pages = {778--82},
abstract = {Genomes contain a large number of genes that do not have recognizable homologues in other species. These genes, found in only one or a few closely related species, are known as orphan genes. Their limited distribution implies that many of them are probably involved in lineage-specific adaptive processes. One important question that has remained elusive to date is how orphan genes originate. It has been proposed that they might have arisen by gene duplication followed by a period of very rapid sequence divergence, which would have erased any traces of similarity to other evolutionarily related genes. However, this explanation does not seem plausible for genes lacking homologues in very closely related species. In the present article, we review recent efforts to identify the mechanisms of formation of primate orphan genes. These studies reveal an unexpected important role of transposable elements in the formation of novel protein-coding genes in the genomes of primates.},
keywords = {Animals, Evolution, Gene Duplication, Genome, Genome: genetics, Molecular, Primates, Primates: genetics, Proteins, Proteins: genetics}
}

@article{Gibbs2004,
title = {Genome sequence of the Brown Norway rat yields insights into mammalian evolution.},
author = {Gibbs, Richard A and Et al.},
url = {http://www.ncbi.nlm.nih.gov/pubmed/15057822},
issn = {1476-4687},
year = {2004},
date = {2004-01-01},
journal = {Nature},
volume = {428},
number = {6982},
pages = {493--521},
abstract = {The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.},
keywords = {Animals, Base Composition, Centromere, Centromere: genetics, Chromosomes, CpG Islands, CpG Islands: genetics, DNA, DNA Transposable Elements, DNA Transposable Elements: genetics, Evolution, Gene Duplication, Genome, Genomics, Humans, Inbred BN, Inbred BN: genetics, Introns, Introns: genetics, Male, Mammalian, Mammalian: genetics, Mice, Mitochondrial, Mitochondrial: genetics, Models, Molecular, Mutagenesis, Nucleic Acid, Nucleic Acid: genetics, Polymorphism, Rats, Regulatory Sequences, Retroelements, Retroelements: genetics, RNA, RNA Splice Sites, RNA Splice Sites: genetics, Sequence Analysis, Single Nucleotide, Single Nucleotide: genetics, Telomere, Telomere: genetics, Untranslated, Untranslated: genetics}
}