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  • 1
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    Major Histocompatibility Complex (MHC) in Health and Disease (2021)
    MDPI - Multidisciplinary Digital Publishing Institute
    Details
    Publication Date: 2024-04-05
    Description: The major histocompatibility complex (MHC) is a highly polymorphic and diverse multigene locus in all jawed vertebrate species that has an integral role in adaptive/innate immune systems, transplantation, and infectious and autoimmune diseases. The MHC supra-locus in mammalian vertebrates is usually partitioned into three distinct regions, known as classes I, II, and III, which, to varying extents, can be found conserved in nonmammalian jawed vertebrates, such as bony fish, amphibians, and bird lineages. The MHC gene region is characterized particularly by the expression of class I and class II glycoproteins that bind peptides derived from intracellular or extracellular antigens to circulating T-cells. While this expressed antigenic specificity remains the predominant interest with respect to MHC function and polymorphism in a population, a broader concept has emerged that examines the MHC as a multifunctional polymorphic controller that facilitates and regulates genome diversity with a much greater array of functions and effects than just MHC-restricted antigen recognition. This volume of 19 reprints presented by various experts and collected from the Special Issue of Cells on “MHC in Health and Disease” covers a broad range of topics on the genomic diversity of the MHC regulatory system in various vertebrate species, including MHC class I, II, and III genes; innate and adaptive immunity; neurology; transplantation; haplotypes; infectious and autoimmune diseases; fecundity; conservation; allelic lineages; and evolution. Taken together, these articles demonstrate the immense complexity and diversity of the MHC structure and function within and between different vertebrate species.
    Keywords: QH301-705.5 ; Q1-390 ; HCP5 ; n/a ; camels ; MHC ; STK19 ; major histocompatibility complex ; human papillomavirus (HPV) ; T-cell receptor ; T1DGC ; bottleneck ; micro-mini-pigs ; life history ; computational analysis ; hepatocellular carcinoma ; phase ; Bactrian camel ; NSDK ; melanoma ; antigen ; autoimmune disease ; RD ; selection ; disease resistance ; autoimmunity ; ancestral haplotype ; Ski complex ; DXO ; high-throughput sequencing ; conservation genetics ; SVA ; lncRNA ; ankylosing spondylitis ; MHC genes ; viral peptides ; competing endogenous RNA (ceRNA) ; astrogliosis ; birds ; long-fragment super haplotype ; SNP ; RLR ; HLA polymorphism ; 5??3? RNA decay ; expression ; 3??5? mRNA turnover ; orthology ; long-read sequencing ; disease association ; dromedary ; polyomavirus ; MHC-II-associated sperm-egg recognition ; experimental medicine ; single nucleotide polymorphism (SNP) ; fish ; SKIV2L ; production trait ; molecular dynamics simulation ; Macaca fascicularis ; human endogenous retrovirus (HERV) ; concerted evolution ; polymorphism ; Old World camels ; MHC polymorphism ; protocol ; nonclassical ; gene duplication ; microglial reaction ; human leukocyte antigen-E ; SKI2W ; quantitative trait loci (QTL) studies ; antiviral immunity ; human immunodeficiency virus (HIV) ; founder effect ; giant panda ; domain movements ; BK virus ; promoter-proximal transcriptional pause ; type 1 diabetes (T1D) ; RP1 ; miR1236 ; KIR ; synaptic covering ; swine leukocyte antigen ; cynomolgus macaque ; HLA ; kidney transplantation ; ?2m knockout mice ; DOM3Z ; interferon ? ; ethnic populations in China ; ecology ; KIR–HLA pairs ; exosomes ; major histocompatibility complex (MHC) ; MHC-I-based mother-fetus recognition ; RNA quality control ; autoimmune diseases ; NELF-E ; haplotype ; genetic drift ; evolution ; nonhuman primate models ; HLA-B27 ; PNS/CNS interface ; risk genes ; pedigree ; MHC-I- and MHC-II-dependent inter-individual recognition ; regulation ; crested ibis ; reproductive performance ; nephropathy ; cancer ; nuclear kinase ; trichohepatoenteric syndrome ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences
    Language: English
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    E-BOOK
  • 2
    Electronic Resource
    Electronic Resource
    Genomic Characterization of the Region Between HLA-B and TNF: Implications for the Evolution of Multicopy Gene Families (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. S147 
    Details
    ISSN: 1432-1432
    Keywords: Key words: HLA-B — TNF — Multicopy gene families
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The major histocompatibility complex (MHC) contains genes which confer susceptibility to numerous diseases and must be important in primate evolution. In some instances, genes have been mapped to the region between human histocompatibility leukocyte antigen (HLA)-B and tumor necrosis factor (TNF) but precise localization has proven difficult especially since this region is subject to insertions, deletions, and duplications. Utilizing computer similarity searches and coding prediction programs, we have identified several potential coding sequences between HLA-B and TNF. Three of these sequences, PERB11.2, PERB15, and PERB18, are similar to members of multicopy gene families that are located in other regions of the MHC. The identification of numerous fragmented and intact retroelements (L1, Alu, LTR, and THE sequences) flanking the PERB11 and PERB15 genes suggests that these retroelements are involved in the duplication process. The evaluation of candidate genes for disease susceptibility within the MHC is complicated by their similarity to other members of multicopy gene families. The determination of sequence differences within and between species provides a strategy with which to investigate the candidate genes between HLA-B and TNF.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00000064
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  • 3
    Electronic Resource
    Electronic Resource
    The Evolution of MHC Diversity by Segmental Duplication and Transposition of Retroelements (1998)
    Springer
    Journal of molecular evolution 46 (1998), S. 734-734 
    Details
    ISSN: 1432-1432
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006355
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  • 4
    Electronic Resource
    Electronic Resource
    Comparison Between Two Human Endogenous Retrovirus (HERV)-Rich Regions Within the Major Histocompatibility Complex (1999)
    Springer
    Journal of molecular evolution 48 (1999), S. 675-683 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Human endogenous retrovirus — Duplications — Multicopy genes — Major histocompatibility complex
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Sixteen human endogenous retrovirus (HERV) sequences were detected within 656 kb of genomic sequence obtained from the alpha- and beta-block of the class I region of the major histocompatibility complex (MHC). The HERVs were identified and characterized as family members of HERV-16 (11 copies), HERV-L (1 copy), HERV-I (2 copies), HERV-K91 (1 copy), and HARLEQUIN (1 copy) by sequence comparison using CENSOR or Repeat Masker, BLAST searches, and dot plots. The 11 copies of HERV-16 arose as products of duplication of genomic segments containing HLA class I (HLAcI) and PERB11 (MIC) genes inter alia, whereas the other five HERVs arose after duplication probably as a consequence of single insertion events or translocations. HERV-L and HERV-I are located between the duplicated genes PERB11.2 (MICB) and PERB11.1 (MICA), and HLA-B and HLA-C, respectively, whereas HERV-K91 and HARLEQUIN are located telomeric of HLA-C. A highly fragmented copy of HERV-I was also found telomeric of PERB11.4. Structural analysis of open reading frames (ORFs) revealed the absence of intact coding sequence within the putative gag, pol, and env gene regions of all the HERVs with the exception of HERV-K91, which had two large ORFs within the region of the putative protease and pol genes. In addition, the 5′-LTR of HERV-L contained a 2.5-kb element that was AT-rich and large ORFs with putative amino acid sequences rich in tyrosines and isoleucines. HERV-I, HARLEQUIN, and at least four copies of HERV-16 appear to have been receptors for the insertion of other retrotransposons including Alu elements and fragments of L1 and THE1. Examination of flanking sequences suggests that HERV-I and HERV-L had occurred by insertion into ancient L1 fragments. This study has revealed that the alpha- and beta-block region within the MHC is rich in HERV sequences occurring at a much higher ratio (10 to 1) than normally observed in the human genome. These HERV sequences will therefore enhance further studies on disease associations and differences between human haplotypes and primates and their role in the evolution of class I genes in the MHC.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006511
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  • 5
    Electronic Resource
    Electronic Resource
    Coevolution of PERB11 (MIC) and HLA Class I Genes with HERV-16 and Retroelements by Extended Genomic Duplication (1999)
    Springer
    Journal of molecular evolution 49 (1999), S. 84-97 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Coevolution — Segmental duplication — HLA genes — PERB11 (MIC) — Retroelements — HERV-16
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The recent availability of genomic sequence information for the class I region of the MHC has provided an opportunity to examine the genomic organization of HLA class I (HLAcI) and PERB11/MIC genes with a view to explaining their evolution from the perspective of extended genomic duplications rather than by simple gene duplications and/or gene conversion events. Analysis of genomic sequence from two regions of the MHC (the alpha- and beta-blocks) revealed that at least 6 PERB11 and 14 HLAcI genes, pseudogenes, and gene fragments are contained within extended duplicated segments. Each segment was searched for the presence of shared (paralogous) retroelements by RepeatMasker in order to use them as markers of evolution, genetic rearrangements, and evidence of segmental duplications. Shared Alu elements and other retroelements allowed the duplicated segments to be classified into five distinct groups (A to E) that could be further distilled down to an ancient preduplication segment containing a HLA and PERB11 gene, an endogenous retrovirus (HERV-16), and distinctive retroelements. The breakpoints within and between the different HLAcI segments were found mainly within the PERB11 and HLA genes, HERV-16, and other retroelements, suggesting that the latter have played a major role in duplication and indel events leading to the present organization of PERB11 and HLAcI genes. On the basis of the features contained within the segments, a coevolutionary model premised on tandem duplication of single and multipartite genomic segments is proposed. The model is used to explain the origins and genomic organization of retroelements, HERV-16, DNA transposons, PERB11, and HLAcI genes as distinct segmental combinations within the alpha- and beta-blocks of the human MHC.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006537
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  • 6
    Electronic Resource
    Electronic Resource
    The Evolution of MHC Diversity by Segmental Duplication and Transposition of Retroelements (1997)
    Springer
    Journal of molecular evolution 45 (1997), S. 599-609 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Retroelements — Segmental duplication — MHC — Diversity — Alu
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Sequence analysis of a 237 kb genomic fragment from the central region of the MHC has revealed that the HLA-B and HLA-C genes are contained within duplicated segments peri-B (53 kb) and peri-C (48 kb), respectively, and separated by an intervening sequence (IF) of 30 kb. The peri-B and peri-C segments share at least 90% sequence homology except when interrupted by insertions/deletions including Alu, L1, an endogenous retrovirus, and pseudogenes. The sequences of peri-B, IF, and peri-C were searched for the presence of Alu elements to use as markers of evolution, chromosomal rearrangements, and polymorphism. Of 29 Alu elements, 14 were identified in peri-B, 11 in peri-C, and 4 in IF. The Alu elements in peri-B and peri-C clustered phylogenetically into two clades which were classified as ``preduplication'' and ``postduplication'' clades. Four Alu J elements that are shared by peri-B and peri-C and are flanked by homologous sequences in their paralogous locations, respectively, clustered into a ``preduplication'' clade. By contrast, the majority of Alu elements, which are unique to either peri-B or peri-C, clustered into a postduplication clade together with the Alu consensus subfamily members ranging from platyrrhine-specific (Spqxcg) to catarrhine-specific Alu sequences (Y). The insertion of platyrrhine-specific Alu elements in postduplication locations of peri-B and peri-C implies that these two segments are the products of a duplication which occurred in primates prior to the divergence of the New World primate from the human lineage (35–44 mya). Examination of the paralogous Alu integration sites revealed that 9 of 14 postduplication Alu sequences have produced microsatellites of different length and sequence within the Alu 3′-poly A tail. The present analysis supports the hypothesis that HLA-B and HLA-C genes are products of an extended segmental duplication between 44 and 81 million years ago (mya), and that subsequent diversification of both genomic segments occurred because of the mobility and mutation of retroelements such as Alu repeats.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006264
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  • 7
    Electronic Resource
    Electronic Resource
    The central region of the major histocompatibility complex contains a sequence with similarity to the pol gene of Moloney retroviruses (1996)
    Springer
    Immunogenetics 44 (1996), S. 157-158 
    Details
    ISSN: 1432-1211
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002510050105
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  • 8
    Electronic Resource
    Electronic Resource
    Using Alu J Elements as Molecular Clocks to Trace the Evolutionary Relationships Between Duplicated HLA Class I Genomic Segments (2000)
    Springer
    Journal of molecular evolution 50 (2000), S. 510-519 
    Details
    ISSN: 1432-1432
    Keywords: Key words: HLA class I region — Genomic organization — Duplications — Alu J retroelements
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The class I region of the major histocompatibility complex contains two subgenomic blocks (250–350 kb each), known as the alpha and beta blocks. These blocks contain members of multicopy gene families including HLA class I, HERV-16 (previously called P5 sequences), and PERB11 (MIC). We have previously shown that each block consists of imperfect duplicated segments (duplicons) containing linked members of different gene families, retroelements and transposons that have coevolved as part of two separate evolutionary events. Another region provisionally designated here as the kappa block is located between the alpha and the beta blocks and contains HLA-E, -30, and -92, HERV-16 (P5.3), and PERB11.3 (MICC) within about 250 kb of sequence. Using Alu elements to trace the evolutionary relationships between different class I duplicons, we have found that (a) the kappa block contains paralogous (duplicated) Alu J sequences and other retroelement patterns more in common with the beta than the alpha block; (b) the retroelement pattern associated with the HLA-E duplicon is different from all other HLA class I duplicons, indicating a more complex evolution; (c) the HLA-92 duplicon, although substantially shorter, is closely related in sequence to the HLA-B and -C duplicons; (d) two of the six paralogous Alu J elements within the HLA-B and -C duplicons are associated with the HLA-X duplicon, confirming their evolutionary relationships within the beta block; and (e) the paralogous Alu J elements within the alpha block are distinctly different from those identified within the beta and kappa blocks. The sequence conservation and location of duplicated (paralogous) Alu J elements in the MHC class I region show that the beta and kappa blocks have evolved separately from the alpha block beginning at a time before or during the evolution of Alu J elements in primates.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002390010054
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  • 9
    Electronic Resource
    Electronic Resource
    Duplication and Diversification of the Apolipoprotein CI (APOCI) Genomic Segment in Association with Retroelements (2000)
    Springer
    Journal of molecular evolution 50 (2000), S. 391-396 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Apolipoprotein CI — Hepatic control region — Duplication — Alu — Retroelements — Diversity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. We have previously shown that several multicopy gene families within the major histocompatibility complex (MHC) arose from a process of segmental duplication. It has also been observed that retroelements play a role in generating diversity within these duplicated segments. The objective of this study was to compare the genomic organization of a gene duplication within another multicopy gene family outside the MHC. Using new continuous genomic sequence encompassing the APOE-CII gene cluster, we show that APOCI and its pseudogene, APOCI′, are contained within large duplicated segments which include sequences from the hepatic control region (HCR). Flanking Alu sequences are observed at both ends of the duplicated unit, suggesting a possible role in the integration of these segments. As observed previously within the MHC, the major differences between the segments are the insertion of sequences (approximately 200–1000 bp in length), consisting predominantly of Alu sequences. Ancestral retroelements also contribute to the generation of sequence diversity between the segments, especially within the 3′ poly(A) tract of Alu sequences. The exonic and regulatory sequences of the APOCI and HCR loci show limited sequence diversity, with exon 3 being an exception. Finally, the typing of pre- and postduplication Alus from both segments indicates an estimated time of duplication of approximately 37 million years ago (mya), some time prior to the separation of Old and New World monkeys.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002399910042
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  • 10
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    Mapping of susceptibility and protective loci for acute GVHD in unrelated HLA-matched bone marrow transplantation donors and recipients using 155 microsatellite markers on chromosome 22 (2007)
    Springer
    Details
    Publication Date: 2007-01-03
    Print ISSN: 0093-7711
    Electronic ISSN: 1432-1211
    Topics: Biology , Medicine
    Published by Springer
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