HLA DNA Sequence Variation among Human Populations: Molecular Signatures of Demographic and Selective Events

Molecular differences between HLA alleles vary up to 57 nucleotides within the peptide binding coding region of human Major Histocompatibility Complex (MHC) genes, but it is still unclear whether this variation results from a stochastic process or from selective constraints related to functional differences among HLA molecules. Although HLA alleles are generally treated as equidistant molecular units in population genetic studies, DNA sequence diversity among populations is also crucial to interpret the observed HLA polymorphism. In this study, we used a large dataset of 2,062 DNA sequences defined for the different HLA alleles to analyze nucleotide diversity of seven HLA genes in 23,500 individuals of about 200 populations spread worldwide. We first analyzed the HLA molecular structure and diversity of these populations in relation to geographic variation and we further investigated possible departures from selective neutrality through Tajima's tests and mismatch distributions. All results were compared to those obtained by classical approaches applied to HLA allele frequencies

Genome-Wide Analysis of Heteroduplex DNA in Mismatch Repair–Deficient Yeast Cells Reveals Novel Properties of Meiotic Recombination Pathways

Meiotic DNA double-strand breaks (DSBs) initiate crossover (CO) recombination, which is necessary for accurate chromosome segregation, but DSBs may also repair as non-crossovers (NCOs). Multiple recombination pathways with specific intermediates are expected to lead to COs and NCOs. We revisited the mechanisms of meiotic DSB repair and the regulation of CO formation, by conducting a genome-wide analysis of strand-transfer intermediates associated with recombination events. We performed this analysis in a SK1 × S288C Saccharomyces cerevisiae hybrid lacking the mismatch repair (MMR) protein Msh2, to allow efficient detection of heteroduplex DNAs (hDNAs). First, we observed that the anti-recombinogenic activity of MMR is responsible for a 20% drop in CO number, suggesting that in MMR–proficient cells some DSBs are repaired using the sister chromatid as a template when polymorphisms are present. Second, we observed that a large fraction of NCOs were associated with trans–hDNA tracts constrained to a single chromatid. This unexpected finding is compatible with dissolution of double Holliday junctions (dHJs) during repair, and it suggests the existence of a novel control point for CO formation at the level of the dHJ intermediate, in addition to the previously described control point before the dHJ formation step. Finally, we observed that COs are associated with complex hDNA patterns, confirming that the canonical double-strand break repair model is not sufficient to explain the formation of most COs. We propose that multiple factors contribute to the complexity of recombination intermediates. These factors include repair of nicks and double-stranded gaps, template switches between non-sister and sister chromatids, and HJ branch migration. Finally, the good correlation between the strand transfer properties observed in the absence of and in the presence of Msh2 suggests that the intermediates detected in the absence of Msh2 reflect normal intermediates

Telomeric Trans-Silencing in Drosophila melanogaster: Tissue Specificity, Development and Functional Interactions between Non-Homologous Telomeres

BACKGROUND: The study of P element repression in Drosophila melanogaster led to the discovery of the telomeric Trans-Silencing Effect (TSE), a homology-dependent repression mechanism by which a P-transgene inserted in subtelomeric heterochromatin (Telomeric Associated Sequences, "TAS") has the capacity to repress in trans, in the female germline, a homologous P-lacZ transgene located in euchromatin. TSE can show variegation in ovaries, displays a maternal effect as well as an epigenetic transmission through meiosis and involves heterochromatin and RNA silencing pathways. PRINCIPAL FINDINGS: Here, we analyze phenotypic and genetic properties of TSE. We report that TSE does not occur in the soma at the adult stage, but appears restricted to the female germline. It is detectable during development at the third instar larvae where it presents the same tissue specificity and maternal effect as in adults. Transgenes located in TAS at the telomeres of the main chromosomes can be silencers which in each case show the maternal effect. Silencers located at non-homologous telomeres functionally interact since they stimulate each other via the maternally-transmitted component. All germinally-expressed euchromatic transgenes tested, located on all major chromosomes, were found to be repressed by a telomeric silencer: thus we detected no TSE escaper. The presence of the euchromatic target transgene is not necessary to establish the maternal inheritance of TSE, responsible for its epigenetic behavior. A single telomeric silencer locus can simultaneously repress two P-lacZ targets located on different chromosomal arms. CONCLUSIONS AND SIGNIFICANCE: Therefore TSE appears to be a widespread phenomenon which can involve different telomeres and work across the genome. It can explain the P cytotype establishment by telomeric P elements in natural Drosophila populations

De l'Europe à l'Inde: structure génétique et diversité des populations de part et d'autre de leurs frontières géographiques et culturelles

In this study, we compared HLA-C molecular polymorphism in 39 human populations located from Europe to the Indian subcontinent. This geographic area encompasses more or less the spoken area of the Indo-European linguistic phylum, but some Afro-asiatic and Dravidian speakers were also considered in the comparisons. Our results indicate that geography is one of the main factors acting on population differentiations in Europe. Moreover, we detect a genetic boundary following a north-east / south-west axis cutting through the Alps and the Pyrenees and which separates the western European populations from those located around the Mediterranean basin. On the other hand, we do not find any significant correlation between geography and genetics in the Middle East and the Indian subcontinent. Although geography does not play a major role in these two regions, the factors that could explain the observed genetic diversity are not the same. Indeed, the Middle Eastern populations constitute a genetically homogeneous group, which could reflect a high level of gene flow due to the numerous migrations that took place in that region throughout history. Conversely, the Indian-Pakistani populations are very heterogeneous genetically, particularly the Dravidian speakers. The differentiation of these populations seems to result from rapid genetic drift under the complex influence of social, cultural, linguistic and religious boundaries.Nos résultats nous indiquent que la géographie est l'un des facteurs déterminant les différenciations des populations situées en Europe. De plus, une frontière génétique est repérée le long d'un axe nord-est / sud-ouest à hauteur des Alpes et à travers les Pyrénées, qui met grosso modo en évidence une séparation entre les populations du pourtour méditerranéen et celle d'Europe de l'ouest. En revanche, on ne retrouve pas de corrélation entre géographie et génétique au Proche-Orient ni dans le sous-continent indien. Si la géographie ne semble pas jouer de rôle prépondérant au sein de ces deux groupes, les différenciations génétiques s'expliquent de manière très différente dans ces deux cas. En effet, les populations proche-orientales constituent un groupe génétiquement homogène, ce qui s'expliquerait par un taux élevé de flux génique dû aux migrations dont cette région, située à un carrefour continental, a été le théâtre à travers l'histoire. Au contraire, les populations du groupe indo-pakistanais sont très hétérogènes. La différenciation de ces dernières, dont plusieurs parlent une langue dravidienne, semble avoir été gouvernée par une dérive génétique rapide sous l'influence complexe de barrières culturelles, sociales, linguistiques et/ou religieuses