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  • 1
    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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  • 2
    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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  • 3
    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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  • 4
    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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  • 5
    Electronic Resource
    Electronic Resource
    The Major Histocompatability Complex (MHC) Contains Conserved Polymorphic Genomic Sequences That Are Shuffled by Recombination to Form Ethnic-Specific Haplotypes (1997)
    Springer
    Journal of molecular evolution 45 (1997), S. 17 -23 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Polymorphism — Recombination — Ancestral haplotypes — Major histocompatibility complex —Homo sapiens
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The major histocompatibility complex (MHC) consists of polymorphic frozen blocks (PFBs) that are linked to form megabase haplotypes. These blocks consist of polymorphic sequences and define regions where recombination appears to be inhibited. We have been able to show, using a highly polymorphic sequence centromeric of HLA-B (within the beta block), that PFBs are conserved and contain specific insertions/deletions and substitutions that are the same for individuals with the same MHC haplotype but that differ between at least most different haplotypes. A sequence comparison between ethnic-specific haplotypes shows that these sequences have remained stable and predate the formation of these haplotypes. To determine whether the same conserved block has been involved in the generation of multiple haplotypes, we compared the block typing profiles of different ethnic specific haplotypes. Block typing profiles have previously been shown to be identical in individuals with the same MHC haplotype but, generally, to differ between different haplotypes. It was found that some PFBs are common to more than one haplotype, implying a common ancestry. Subsequently, haplotypes have been generated by the shuffling and exchange of these PFBs. The regions between these PFBs appear to permit the recombination sites and therefore could be expected to exhibit either low polymorphism or a localized ``hotspot.''
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006194
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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
    Genomics of the major histocompatibility complex: haplotypes, duplication, retroviruses and disease (1999)
    Oxford, UK : Blackwell Publishing Ltd
    Immunological reviews 167 (1999), S. 0 
    Details
    ISSN: 1600-065X
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Medicine
    Notes: Summary: The genomic region encompassing the Major Histocompatibility Complex (MHC) contains polymorphic frozen blocks which have developed by local imperfect sequential duplication associated with insertion and deletion (indels), In the alpha block surrounding HLA-A, there are ten duplication units or beads on the 62,1 ancestral haplotype. Each bead contains or contained sequences representing Class 1, PERB11 (MHC Class I chain related (MIC)) and human endogenous retrovirus (HERV) 16, Here we consider explanations for co-occurrence of genomic polymorphism, duplication and HERVs and we ask how these features encode susceptibility to numerous and very diverse diseases. Ancestral haplotypes differ in their copy number and indels in addition to their coding regions. Disease susceptibility could be a function of all of these differences. We propose a model of the evolution of the human MHC. Population-specific integration of retroviral sequences could explain rapid diversification through duplication and differential disease susceptibility. If HERV sequences can be protective, there are exciting prospects for manipulation. In the mean-while, it will be necessary to understand the function of MHC genes such as PEKB11 (MIC) and many others discovered by genomic sequencing.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1600-065X.1999.tb01399.x
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  • 9
    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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  • 10
    Electronic Resource
    Electronic Resource
    Coevolution of HLA-B and PERB11.1 (MICA): Significance of Independent Triplet Expansion Within the Transmembrane Region of PERB11.1 (MICA) (2000)
    Springer
    Journal of molecular evolution 50 (2000), S. 359-365 
    Details
    ISSN: 1432-1432
    Keywords: Key words: PERB11.1 — MICA — Nomenclature — Putative lineage — Polymorphism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Several highly polymorphic sequences are present in the beta block of the MHC, especially HLA-B, HLA-C, PERB11.1 (MICA), and PERB11.2 (MICB). It is now apparent that the polymorphism of PERB11.1 is of the same order as that of HLA-A, -B, and -C and it has been suggested that PERB11 could explain some of the disease associations previously attributed to HLA-B. Phylogenetic analysis of PERB11 α-domain sequences demonstrates relationships with HLA-B cross-reactive serogroups. In contrast, the transmembrane polymorphisms do not appear to be associated with either PERB11 or HLA-B. These data indicate that PERB11 and HLA-B have evolved in concert from their common ancestors and that the transmembrane polymorphisms have arisen independently and more recently. MHC disease associations will need to be reviewed in the light of mechanisms such as receptor binding and signaling.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002399910039
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