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1.  Genomicus: five genome browsers for comparative genomics in eukaryota 
Nucleic Acids Research  2012;41(D1):D700-D705.
Genomicus (http://www.dyogen.ens.fr/genomicus/) is a database and an online tool that allows easy comparative genomic visualization in >150 eukaryote genomes. It provides a way to explore spatial information related to gene organization within and between genomes and temporal relationships related to gene and genome evolution. For the specific vertebrate phylum, it also provides access to ancestral gene order reconstructions and conserved non-coding elements information. We extended the Genomicus database originally dedicated to vertebrate to four new clades, including plants, non-vertebrate metazoa, protists and fungi. This visualization tool allows evolutionary phylogenomics analysis and exploration. Here, we describe the graphical modules of Genomicus and show how it is capable of revealing differential gene loss and gain, segmental or genome duplications and study the evolution of a locus through homology relationships.
doi:10.1093/nar/gks1156
PMCID: PMC3531091  PMID: 23193262
2.  How much does the amphioxus genome represent the ancestor of chordates? 
One of the main motivations to study amphioxus is its potential for understanding the last common ancestor of chordates, which notably gave rise to the vertebrates. An important feature in this respect is the slow evolutionary rate that seems to have characterized the cephalochordate lineage, making amphioxus an interesting proxy for the chordate ancestor, as well as a key lineage to include in comparative studies. Whereas slow evolution was first noticed at the phenotypic level, it has also been described at the genomic level. Here, we examine whether the amphioxus genome is indeed a good proxy for the genome of the chordate ancestor, with a focus on protein-coding genes. We investigate genome features, such as synteny, gene duplication and gene loss, and contrast the amphioxus genome with those of other deuterostomes that are used in comparative studies, such as Ciona, Oikopleura and urchin.
doi:10.1093/bfgp/els003
PMCID: PMC3310212  PMID: 22373648
deuterostomes; evolutionary rates; gene duplication; gene loss; orthology; synteny
3.  Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes 
Genome Biology  2010;11(5):R51.
Human genes contain a 10 bp repeat of RR dinucleotides focused around the first nucleosome position suggesting a role in transcriptional control.
Background
The position of a nucleosome, both translational along the DNA molecule and rotational between the histone core and the DNA, is controlled by many factors, including the regular occurrence of specific dinucleotides with a period of approximately 10 bp, important for the rotational setting of the DNA around the histone octamer.
Results
We show that such a 10 bp periodic signal of purine-purine dinucleotides occurs in phase with the transcription start site (TSS) of human genes and is centered on the position of the first (+1) nucleosome downstream of the TSS. These data support a direct link between transcription and the rotational setting of the nucleosome. The periodic signal is most prevalent in genes that contain CpG islands that are expressed at low levels in a tissue-specific manner and are involved in the control of transcription.
Conclusions
These results, together with several lines of evidence from the recent literature, support a new model whereby the +1 nucleosome could be more efficiently disassembled from gene promoters by H3K56 acetylation marks if the periodic signal specifies an optimal rotational setting.
doi:10.1186/gb-2010-11-5-r51
PMCID: PMC2898081  PMID: 20462404
4.  Human and Non-Human Primate Genomes Share Hotspots of Positive Selection 
PLoS Genetics  2010;6(2):e1000840.
Among primates, genome-wide analysis of recent positive selection is currently limited to the human species because it requires extensive sampling of genotypic data from many individuals. The extent to which genes positively selected in human also present adaptive changes in other primates therefore remains unknown. This question is important because a gene that has been positively selected independently in the human and in other primate lineages may be less likely to be involved in human specific phenotypic changes such as dietary habits or cognitive abilities. To answer this question, we analysed heterozygous Single Nucleotide Polymorphisms (SNPs) in the genomes of single human, chimpanzee, orangutan, and macaque individuals using a new method aiming to identify selective sweeps genome-wide. We found an unexpectedly high number of orthologous genes exhibiting signatures of a selective sweep simultaneously in several primate species, suggesting the presence of hotspots of positive selection. A similar significant excess is evident when comparing genes positively selected during recent human evolution with genes subjected to positive selection in their coding sequence in other primate lineages and identified using a different test. These findings are further supported by comparing several published human genome scans for positive selection with our findings in non-human primate genomes. We thus provide extensive evidence that the co-occurrence of positive selection in humans and in other primates at the same genetic loci can be measured with only four species, an indication that it may be a widespread phenomenon. The identification of positive selection in humans alongside other primates is a powerful tool to outline those genes that were selected uniquely during recent human evolution.
Author Summary
An advantageous mutation spreads from generation to generation in a population until individuals that carry it, because of their higher reproductive success, completely replace those that do not. This process, commonly known as positive Darwinian selection, requires the selected mutation to induce a new non-neutral heritable phenotypic trait, and this has been shown to occur unexpectedly frequently during recent human evolution. Although the exact advantageous mutation is difficult to identify, it leaves a wider footprint on neighbouring linked neutral variation called a selective sweep. We have developed an empirical method that uses whole-genome shotgun sequences of single individuals to detect selective sweeps. By doing so, we were able to extend to chimpanzee, orangutan, and macaque individuals analyses of recent positive selection that until now were only available for human. Comparisons of genes candidates for positive selection between human and non-human primates then revealed an unexpectedly high number of cases where a selective sweep at a gene in humans is mirrored by independent positive selection at the same gene in multiple other primates. This result has future implications for understanding the nature of biological changes that underlie selective sweeps in humans.
doi:10.1371/journal.pgen.1000840
PMCID: PMC2816677  PMID: 20140238

Results 1-4 (4)