2004 Nomenclature for the chicken major histocompatibility (B and Y ) complex

Miller, Marcia M.; Bacon, Larry D.; Hála, K; Hunt, Henry D.; Ewald, Sandra J.; Kaufman, Jim; Zoorob, Rima; Briles, W. E.

doi:10.1007/s00251-004-0682-1

Cited by 117 publications

(113 citation statements)

References 91 publications

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“…While the basic characters of a protein are conserved during evolution, the immunological characters are species specific. Nonhuman hosts have different MHC and TAP molecules (although they share a similar proteasome) (3,23,28,46). Thus, if a specific evolutionary pressure induces epitope removal in HBV, its SIR score should be lower than the ones of nonhuman hepadnaviruses.…”

Section: Resultsmentioning

confidence: 99%

Immune-Induced Evolutionary Selection Focused on a Single Reading Frame in Overlapping Hepatitis B Virus Proteins

Maman

Blancher

Benichou

et al. 2011

J Virol

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Viruses employ various means to evade immune detection. Reduction of CD8؉ T cell epitopes is one of the common strategies used for this purpose. Hepatitis B virus (HBV), a member of the Hepadnaviridae family, has four open reading frames, with about 50% overlap between the genes they encode. We computed the CD8 ؉ T cell epitope density within HBV proteins and the mutations within the epitopes. Our results suggest that HBV accumulates escape mutations that reduce the number of epitopes. These mutations are not equally distributed among genes and reading frames. While the highly expressed core and X proteins are selected to have low epitope density, polymerase, which is expressed at low levels, does not undergo the same selection. In overlapping regions, mutations in one protein-coding sequence also affect the other protein-coding sequence. We show that mutations lead to the removal of epitopes in X and surface proteins even at the expense of the addition of epitopes in polymerase. The total escape mutation rate for overlapping regions is lower than that for nonoverlapping regions. The lower epitope replacement rate for overlapping regions slows the evolutionary escape rate of these regions but leads to the accumulation of mutations more robust in the transfer between hosts, such as mutations preventing proteasomal cleavage into epitopes.

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Section: Resultsmentioning

confidence: 99%

Immune-Induced Evolutionary Selection Focused on a Single Reading Frame in Overlapping Hepatitis B Virus Proteins

Maman

Blancher

Benichou

et al. 2011

J Virol

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“…The BF ⁄ BL region contains two class I genes, BF1 and BF2 genes, which encode typical class I glycoproteins. In peripheral blood cells (PBL), BF2 is expressed up to 10 times as often as BF1 [15,16]. BF has 8 exons and 7 introns.…”

Section: Introductionmentioning

confidence: 99%

Rapid Detection of BF Haplotypes by a Semi‐nested Polymerase Chain Reaction, which Causes Resistance/Susceptibility to Marek’s Disease in Chicken

Jin

Wei

et al. 2010

Scand J Immunol

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A semi‐nested polymerase chain reaction (snPCR) assay was developed for the rapid detection of resistant/susceptible BF haplotypes to Marek’s disease (MD) using the cDNA samples from peripheral blood leucocytes, liver, spleen and heart from Xiayan homozygous chickens: A11, C23, D8 and D12 (resistant to MD), A5 and B21 (susceptible to MD). The snPCR was utilized to span alternative splicing‐out of the sequence encoding the second segment of the cytoplasmic part of the mature BF molecules (exon 7). This alternative exon 7 splice variant was detected in BF*A5 and BF*B21 (susceptible to MD), but not in the MD‐resistant BF*A11, BF*C23, BF*D8 and BF*D12 haplotypes, suggesting a potential role of exon 7 for the detection of resistant/susceptible BF haplotypes to MD.

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“…However, we have also shown that there are two classical class I genes in the MHC of the B12 haplotype (7). These two class I genes, now called BF1 and BF2 (11), are in opposite transcriptional orientation with their promoters outside next to the adjacent genes for DMB2 and C4, and with their polyadenylation sites close to the genes they flank, TAP1 and TAP2 (see Fig. 1).…”

mentioning

confidence: 99%

Different Evolutionary Histories of the Two Classical Class I Genes BF1 and BF2 Illustrate Drift and Selection within the Stable MHC Haplotypes of Chickens

Shaw

Powell

Marston

et al. 2007

The Journal of Immunology

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108

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Compared with the MHC of typical mammals, the chicken MHC (BF/BL region) of the B12 haplotype is smaller, simpler, and rearranged, with two classical class I genes of which only one is highly expressed. In this study, we describe the development of long-distance PCR to amplify some or all of each class I gene separately, allowing us to make the following points. First, six other haplotypes have the same genomic organization as B12, with a poorly expressed (minor) BF1 gene between DMB2 and TAP2 and a well-expressed (major) BF2 gene between TAP2 and C4. Second, the expression of the BF1 gene is crippled in three different ways in these haplotypes: enhancer A deletion (B12, B19), enhancer A divergence and transcription start site deletion (B2, B4, B21), and insertion/rearrangement leading to pseudogenes (B14, B15). Third, the three kinds of alterations in the BF1 gene correspond to dendrograms of the BF1 and poorly expressed class II B (BLB1) genes reflecting mostly neutral changes, while the dendrograms of the BF2 and well-expressed class II (BLB2) genes each have completely different topologies reflecting selection. The common pattern for the poorly expressed genes reflects the fact the BF/BL region undergoes little recombination and allows us to propose a pattern of descent for these chicken MHC haplotypes from a common ancestor. Taken together, these data explain how stable MHC haplotypes predominantly express a single class I molecule, which in turn leads to striking associations of the chicken MHC with resistance to infectious pathogens and response to vaccines.

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2004 Nomenclature for the chicken major histocompatibility (B and Y ) complex

Cited by 117 publications

References 91 publications

Immune-Induced Evolutionary Selection Focused on a Single Reading Frame in Overlapping Hepatitis B Virus Proteins

Immune-Induced Evolutionary Selection Focused on a Single Reading Frame in Overlapping Hepatitis B Virus Proteins

Rapid Detection of BF Haplotypes by a Semi‐nested Polymerase Chain Reaction, which Causes Resistance/Susceptibility to Marek’s Disease in Chicken

Different Evolutionary Histories of the Two Classical Class I Genes BF1 and BF2 Illustrate Drift and Selection within the Stable MHC Haplotypes of Chickens

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