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63 results for “MHC genes”
Red Queen processes drive positive selection on Major Histocompatibility Complex (MHC) genes
<p>The dataset for the manuscript "Red Queen processes drive positive selection on Major Histocompatibility Complex (MHC) genes" submitted to PLOS Computational Biology. The dataset is packed in ZIP archive 'MHC_PosSel_dataset.zip' and contain the results of the simulation model.</p>
The genomic architecture of the passerine MHC region: high repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes
<p><span>The Major Histocompatibility Complex (MHC) is of central importance to the immune system, and an optimal MHC diversity is believed to maximize pathogen elimination. Birds show substantial variation in MHC diversity, ranging from few genes in most bird orders to very many genes in passerines. Our understanding of the evolutionary trajectories of the MHC in passerines is hampered by lack of data on genomic organization. Therefore, we assemble and annotate the MHC genomic region of the great reed warbler (<em>Acrocephalus arundinaceus</em>), using long-read sequencing and optical mapping. The MHC region is large (>5.5Mb), characterized by structural changes compared to hitherto investigated bird orders and shows higher repeat content</span><span> than the genome average. These features were supported by analyses in three additional passerines. MHC genes in passerines are found in two different chromosomal arrangements, either as single copy MHC genes located among non-MHC genes, or as tandemly duplicated tightly linked MHC genes. Some single copy MHC genes are old and putative orthologs among species. In contrast tandemly duplicated MHC genes are monophyletic within species and have evolved by simultaneous gene duplication of several MHC genes. Structural differences in the MHC genomic region among bird orders seem substantial compared to mammals and have possibly been fuelled by clade-specific immune system adaptations. Our study provides methodological guidance in characterizing complex genomic regions, constitutes a resource for MHC research in birds, and calls for a revision of the general belief that avian MHC has a conserved gene order and small size compared to mammals.</span></p>
Data from: Neutral and selective processes shape MHC gene diversity and expression in stocked brook charr populations (Salvelinus fontinalis)
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Data from: Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda
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Data from: Extreme MHC class I diversity in the sedge warbler (Acrocephalus schoenobaenus); selection patterns and allelic divergence suggest that different genes have different functions
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Data from: Cryptic haplotype-specific gamete selection yields offspring with optimal MHC immune genes
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The genomic architecture of the passerine MHC region: high repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes
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Data from: Gene duplication and divergence produce divergent MHC genotypes without disassortative mating
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Data from: Diversity of MHC DQB and DRB genes in the endangered Australian sea lion (Neophoca cinerea)
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Data from: Positive selection in coding regions and motif duplication in regulatory regions of bottlenose dolphin MHC class II genes
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Data from: Disentangling the roles of natural selection and genetic drift in shaping variation at MHC immunity genes
The major histocompatibility complex (MHC) forms an integral component of the vertebrate immune response, and, due to strong selection pressures, is one of the most polymorphic regions of the entire genome. Despite over 15 years of research, empirical studies offer highly contradictory explanations of the relative roles of opposing evolutionary forces, selection and genetic drift, acting on MHC genes during population bottlenecks. Here, we take a meta-analytical approach to quantify the results of studies into the effects of bottlenecks on MHC polymorphism. We show that the consequences of selection acting on MHC loci prior to a bottleneck event, combined with drift during the bottleneck, will result in overall loss of MHC polymorphism that is approximately 15% greater than loss of neutral genetic diversity. These results are counter to general expectations that selection should maintain MHC polymorphism, but do agree with the results of recent simulation models and at least two empirical studies. Notably, our results suggest that negative frequency-dependent selection could be more important than overdominance for maintaining high MHC polymorphism in pre-bottlenecked populations.
Data from: Expression and phylogenetic analyses reveal paralogous lineages of putatively classical and non-classical MHC-I genes in three sparrow species (Passer)
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Data from: Disentangling the roles of natural selection and genetic drift in shaping variation at MHC immunity genes
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Data from: Selective pressures on MHC class II genes in the guppy (Poecilia reticulata) as inferred by hierarchical analysis of population structure.
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Data from: Pervasive introgression of MHC genes in newt hybrid zones
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The aging kidney is characterized by tubuloinflammaging, a phenotype associated with MHC-II gene expression
GEO Series GSE233718. Mus musculus. 17 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profiles of OT-1 T cells co-cultured with MHC-I Negative Tumors and Antigen Loaded Macrophages
GEO Series GSE220960. Mus musculus. 9 samples. Type: Expression profiling by array.
Multi-omic analysis identifies erythroid cells as the major population in mouse placentas expressing genes for antigen presentation in MHC class II, chemokines, and antibacterial immune response
GEO Series GSE289175. Mus musculus. 18 samples. Type: Expression profiling by array; Other.
Epigenetic regulations in the IFNγ signalling pathway: IFNγ-mediated MHC class I upregulation on tumour cells is associated with DNA demethylation of antigen-presenting machinery genes [RVPC3_DAC]
GEO Series GSE53465. Mus musculus. 6 samples. Type: Expression profiling by array.
NLRC5 specifically transactivates MHC class I and related genes through a distinctive SXY module
GEO Series GSE59092. Mus musculus. 9 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
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