Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region.

Frontiers in Genetics
J K KulskiTakashi Shiina

Abstract

The major histocompatibility complex (MHC) on chromosome 6p21 is one of the most single-nucleotide polymorphism (SNP)-dense regions of the human genome and a prime model for the study and understanding of conserved sequence polymorphisms and structural diversity of ancestral haplotypes/conserved extended haplotypes. This study aimed to follow up on a previous analysis of the MHC class I region by using the same set of 95 MHC haplotype sequences downloaded from a publicly available BioProject database at the National Center for Biotechnology Information to identify and characterize the polymorphic human leukocyte antigen (HLA)-class II genes, the MTCO3P1 pseudogene alleles, the indels of transposable elements as haplotypic lineage markers, and SNP-density crossover (XO) loci at haplotype junctions in DNA sequence alignments of different haplotypes across the extended class II region (∼1 Mb) from the telomeric PRRT1 gene in class III to the COL11A2 gene at the centromeric end of class II. We identified 42 haplotypic indels (20 Alu, 7 SVA, 13 LTR or MERs, and 2 indels composed of a mosaic of different transposable elements) linked to particular HLA-class II alleles. Comparative sequence analyses of 136 haplotype pairs revealed 98 ...Continue Reading

References

Aug 1, 1992·Human Immunology·M A Degli-EspostiR L Dawkins
Jan 29, 1986·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·W F BodmerJ Bodmer
Jan 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·Z L AwdehC A Alper
Jan 1, 1983·Immunological Reviews·R L DawkinsP J Zilko
Dec 1, 1993·Current Opinion in Genetics & Development·G A Dover
Feb 20, 1996·Proceedings of the National Academy of Sciences of the United States of America·A F Smit, A D Riggs
Jan 1, 1996·Progress in Nucleic Acid Research and Molecular Biology·C W Schmid
Dec 31, 1997·The Journal of Biological Chemistry·S BiM Reitman
Feb 21, 1998·Journal of Molecular Evolution·J K KulskiR L Dawkins
Apr 16, 1998·Trends in Genetics : TIG·G AnderssonL Rask
Jul 24, 1998·Frontiers in Bioscience : a Journal and Virtual Library·G Andersson
Apr 26, 2000·Genome Research·S SchwartzW Miller
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Feb 22, 2001·Science·J C VenterX Zhu
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Oct 5, 2001·Nature Genetics·M J DalyE S Lander
May 25, 2002·Science·Stacey B GabrielDavid Altshuler
Sep 26, 2002·American Journal of Human Genetics·Michael CullenMary Carrington
Feb 28, 2003·Biology of Reproduction·Ivan BiècheMichel Vidaud
Jun 12, 2003·Proceedings of the National Academy of Sciences of the United States of America·Tatsuya AnzaiHidetoshi Inoko
Apr 7, 2004·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Alec J JeffreysAdam J Webb
May 22, 2004·Nature Reviews. Genetics·Liisa KauppiScott Keeney
Jul 8, 2005·Human Molecular Genetics·Gen TamiyaHidetoshi Inoko
May 16, 2006·Human Immunology·Chester A AlperEdmond J Yunis

❮ Previous
Next ❯

Software Mentioned

Sequencher
MultiPipMaker
Preview
Fasta
Dfam
Ensembl
Coffee
clustalW
RepeatMasker
Excel

Related Concepts

Related Feeds

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.

Related Papers

European Journal of Immunogenetics : Official Journal of the British Society for Histocompatibility and Immunogenetics
J Trowsdale, R D Campbell
© 2021 Meta ULC. All rights reserved