Amino Acid Animals Computational Biology Databases de novo gene DNA Evolution Genetic Genome Humans Mice Molecular Molecular Sequence Data Nucleic Acid Proteins Proteins: chemistry Proteins: genetics Repetitive Sequences ribosome profiling RNA-Seq Selection Sequence Analysis Sequence Homology transcriptomics yeast
2007 |
Albà, M Mar, Castresana, Jose On homology searches by protein Blast and the characterization of the age of genes. (Article) BMC evolutionary biology, 7 pp. 53, 2007, ISSN: 1471-2148. (Abstract | Links | BibTeX | Tags: Amino Acid, Animals, Computational Biology, Databases, Evolution, Genes, Humans, Molecular, Phylogeny, Protein, Sequence Analysis, Sequence Homology) @article{Alba2007, title = {On homology searches by protein Blast and the characterization of the age of genes.}, author = {Albà, M Mar and Castresana, Jose}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1855329&tool=pmcentrez&rendertype=abstract}, issn = {1471-2148}, year = {2007}, date = {2007-01-01}, journal = {BMC evolutionary biology}, volume = {7}, pages = {53}, abstract = {It has been shown in a variety of organisms, including mammals, that genes that appeared recently in evolution, for example orphan genes, evolve faster than older genes. Low functional constraints at the time of origin of novel genes may explain these results. However, this observation has been recently attributed to an artifact caused by the inability of Blast to detect the fastest genes in different eukaryotic genomes. Distinguishing between these two possible explanations would be of great importance for any studies dealing with the taxon distribution of proteins and the origin of novel genes.}, keywords = {Amino Acid, Animals, Computational Biology, Databases, Evolution, Genes, Humans, Molecular, Phylogeny, Protein, Sequence Analysis, Sequence Homology} } It has been shown in a variety of organisms, including mammals, that genes that appeared recently in evolution, for example orphan genes, evolve faster than older genes. Low functional constraints at the time of origin of novel genes may explain these results. However, this observation has been recently attributed to an artifact caused by the inability of Blast to detect the fastest genes in different eukaryotic genomes. Distinguishing between these two possible explanations would be of great importance for any studies dealing with the taxon distribution of proteins and the origin of novel genes. |
2004 |
Castresana, Jose, Guigó, Roderic, Albà, M Mar Journal of molecular evolution, 59 (1), pp. 72–9, 2004, ISSN: 0022-2844. (Abstract | Links | BibTeX | Tags: Base Composition, Base Composition: genetics, Chromatin, Chromatin: metabolism, Chromosomes, Computational Biology, Databases, DNA-Binding Proteins, DNA-Binding Proteins: genetics, DNA-Binding Proteins: metabolism, Evolution, Genetic, Genome, human, Humans, Introns, Introns: genetics, Models, Molecular, Multigene Family, Multigene Family: genetics, Pair 19, Pair 19: genetics, Phylogeny, Zinc Fingers, Zinc Fingers: genetics) @article{Castresana2004, title = {Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome.}, author = {Castresana, Jose and Guigó, Roderic and Albà, M Mar}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15383909}, issn = {0022-2844}, year = {2004}, date = {2004-01-01}, journal = {Journal of molecular evolution}, volume = {59}, number = {1}, pages = {72--9}, abstract = {Comparison of the human and mouse genomes has revealed that significant variations in evolutionary rates exist among genomic regions and that a large part of this variation is interchromosomal. We confirm in this work, using a large collection of introns, that human chromosome 19 is the one that shows the highest divergence with respect to mouse. To search for other differences among chromosomes, we examine the distribution of gene functions in human and mouse chromosomes using the Gene Ontology definitions. We found by correspondence analysis that among the strongest clusterings of gene functions in human chromosomes is a group of genes coding for DNA binding proteins in chromosome 19. Interestingly, chromosome 19 also has a very high GC content, a feature that has been proposed to promote an opening of the chromatin, thereby facilitating binding of proteins to the DNA helix. In the mouse genome, however, a similar aggregation of genes coding for DNA binding proteins and high GC content cannot be found. This suggests that the distribution of genes coding for DNA binding proteins and the variations of the chromatin accessibility to these proteins are different in the human and mouse genomes. It is likely that the overall high synonymous and intron rates in chromosome 19 are a by-product of the high GC content of this chromosome.}, keywords = {Base Composition, Base Composition: genetics, Chromatin, Chromatin: metabolism, Chromosomes, Computational Biology, Databases, DNA-Binding Proteins, DNA-Binding Proteins: genetics, DNA-Binding Proteins: metabolism, Evolution, Genetic, Genome, human, Humans, Introns, Introns: genetics, Models, Molecular, Multigene Family, Multigene Family: genetics, Pair 19, Pair 19: genetics, Phylogeny, Zinc Fingers, Zinc Fingers: genetics} } Comparison of the human and mouse genomes has revealed that significant variations in evolutionary rates exist among genomic regions and that a large part of this variation is interchromosomal. We confirm in this work, using a large collection of introns, that human chromosome 19 is the one that shows the highest divergence with respect to mouse. To search for other differences among chromosomes, we examine the distribution of gene functions in human and mouse chromosomes using the Gene Ontology definitions. We found by correspondence analysis that among the strongest clusterings of gene functions in human chromosomes is a group of genes coding for DNA binding proteins in chromosome 19. Interestingly, chromosome 19 also has a very high GC content, a feature that has been proposed to promote an opening of the chromatin, thereby facilitating binding of proteins to the DNA helix. In the mouse genome, however, a similar aggregation of genes coding for DNA binding proteins and high GC content cannot be found. This suggests that the distribution of genes coding for DNA binding proteins and the variations of the chromatin accessibility to these proteins are different in the human and mouse genomes. It is likely that the overall high synonymous and intron rates in chromosome 19 are a by-product of the high GC content of this chromosome. |
