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Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
- Julie A. Karl,
- Trent M. Prall,
- Hailey E. Bussan,
- Joshua M. Varghese,
- Aparna Pal,
- Roger W. Wiseman,
- and David H. O'Connor
Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
...of human diseases. Although the macaque major histocompatibility complex (MHC) region shares most features with the human leukocyte antigen (HLA) region, macaques have an expanded repertoire of MHC class I genes. Although a chimera of two rhesus macaque MHC haplotypes was first published in 2004...
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Research: Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex
- Claire Vandiedonck,
- Martin S. Taylor,
- Helen E. Lockstone,
- Katharine Plant,
- Jennifer M. Taylor,
- Caroline Durrant,
- John Broxholme,
- Benjamin P. Fairfax,
- and Julian C. Knight
Genome Res. July 2011 21: 1042-1054; Published in Advance May 31, 2011, doi:10.1101/gr.116681.110
...sequence,were found in intergenic regions is also in linewith the 25% recent estimate of ‘‘dark matter transcripts’’ obtained by RNA-seq (Ponting and Belgard 2010) and is, however, of considerable interest, given that theMHC region is the most gene-dense region of the human . Their expression was overall...
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LETTER: Species-Specific Class I Gene Expansions Formed the Telomeric 1 Mb of the Mouse Major Histocompatibility Complex
- Toyoyuki Takada,
- Attila Kumánovics,
- Claire Amadou,
- Masayasu Yoshino,
- Elsy P. Jones,
- Maria Athanasiou,
- Glen A. Evans,
- and Kirsten Fischer Lindahl
Genome Res. April 1, 2003 13: 589-600; doi:10.1101/gr.975303
...Species-Specific Class I Gene Expansions Formed the Telomeric 1 Mb of the Mouse Major Histocompatibility Complex Toyoyuki Takada 1 , 4 , Attila Kumánovics 2 , Claire Amadou 1 , Masayasu Yoshino 1 , Elsy P. Jones 2 , Maria Athanasiou 3...
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Resource: Assembly and analysis of 100 full MHC haplotypes from the Danish population
- Jacob M. Jensen,
- Palle Villesen,
- Rune M. Friborg,
- The Danish Pan-Genome Consortium,
- Thomas Mailund,
- Søren Besenbacher,
- and Mikkel H. Schierup
Genome Res. September 2017 27: 1597-1607; Published in Advance August 3, 2017, doi:10.1101/gr.218891.116
...gene dense part of the class III region, we find long sequence stretches with low recombination rate. We find a high recombination rate in classical loci but also observe a high recombination rate outside classical loci, especially upstream of the Class I region. Jeffreys et al. (2001) determined...
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Research: Extensive variation and low heritability of DNA methylation identified in a twin study
- Kristina Gervin,
- Martin Hammerø,
- Hanne E. Akselsen,
- Rune Moe,
- Heidi Nygård,
- Ingunn Brandt,
- Håkon K. Gjessing,
- Jennifer R. Harris,
- Dag E. Undlien,
- and Robert Lyle
Genome Res. November 2011 21: 1813-1821; Published in Advance September 26, 2011, doi:10.1101/gr.119685.110
...methylation, and the heritable basis of epigenetic differences in the major histocompatibility complex (MHC). The MHC is located on chromosome 6p21.3 and is a particularly polymorphic and gene-dense region, containing genes involved in several aspects of the immune response (Traherne 2008). We focus...
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RESOURCE: Complete MHC Haplotype Sequencing for Common Disease Gene Mapping
- C. Andrew Stewart,
- Roger Horton,
- Richard J.N. Allcock,
- Jennifer L. Ashurst,
- Alexey M. Atrazhev,
- Penny Coggill,
- Ian Dunham,
- Simon Forbes,
- Karen Halls,
- Joanna M.M. Howson,
- Sean J. Humphray,
- Sarah Hunt,
- Andrew J. Mungall,
- Kazutoyo Osoegawa,
- Sophie Palmer,
- Anne N. Roberts,
- Jane Rogers,
- Sarah Sims,
- Yu Wang,
- Laurens G. Wilming,
- John F. Elliott,
- Pieter J. de Jong,
- Stephen Sawcer,
- John A. Todd,
- John Trowsdale,
- and Stephan Beck
Genome Res. June 2004 14: 1176-1187; Published in Advance May 12, 2004, doi:10.1101/gr.2188104
...) is a gene-dense region of the human on Chromosome 6p21.31. The complex spans ∼4 Mb and covers &gt;120 expressed genes ( The MHC Sequencing Consortium 1999 ). Forty percent of the expressed loci encode proteins with functions related to immune defense. These include the highly polymorphic class I and class...
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LETTER: Single haplotype analysis demonstrates rapid evolution of the killer immunoglobulin-like receptor (KIR) loci in primates
- Jennifer G. Sambrook,
- Arman Bashirova,
- Sophie Palmer,
- Sarah Sims,
- John Trowsdale,
- Laurent Abi-Rached,
- Peter Parham,
- Mary Carrington,
- and Stephan Beck
Genome Res. January 2005 15: 25-35; doi:10.1101/gr.2381205
...in humans ( Trowsdale 2001 ). They are encoded by large, polymorphic, gene-dense clusters in the Major Histocompatibility Complex (MHC), the Leukocyte Receptor Complex (LRC), and the Natural Killer Complex (NKC) found on chromosomes 6p21.3, 19q13.4, and 12p13.1, respectively. The killer immunoglobulin...
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RESOURCE: A Consensus Linkage Map of the Chicken Genome
- Martien A.M. Groenen,
- Hans H. Cheng,
- Nat Bumstead,
- Bernard F. Benkel,
- W. Elwood Briles,
- Terry Burke,
- Dave W. Burt,
- Lyman B. Crittenden,
- Jerry Dodgson,
- Jossi Hillel,
- Sue Lamont,
- Abel Ponce de Leon,
- Morris Soller,
- Hideaki Takahashi,
- and Alain Vignal
Genome Res. January 1, 2000 10: 137-147; doi:10.1101/gr.10.1.137
...more gene dense then the macrochromosomes, reaching densities comparable to that of the Fugu ( McQueen et al. 1998 ; Clark et al. 1999 ). Second, the level of conserved synteny between chicken and humans appears to be very high ( Burt et al. 1995 ; Hu et al. 1995 ; Klein et al. 1996 ; Jones et al. 1997...
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LETTER: Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas
- Neerja Karnani,
- Christopher Taylor,
- Ankit Malhotra,
- and Anindya Dutta
Genome Res. June 2007 17: 865-876; doi:10.1101/gr.5427007
...-replicating regions are usually gene dense and contain actively transcribed genes. The fine resolution of replication profile possible with the -tiling arrays allowed us to closely examine how such correlations hold up across contiguous stretches of chromosomes. Intriguingly, the TR50 profile of some regions revealed...
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ARTICLE: Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution
- Ross C. Hardison,
- Krishna M. Roskin,
- Shan Yang,
- Mark Diekhans,
- W. James Kent,
- Ryan Weber,
- Laura Elnitski,
- Jia Li,
- Michael O'Connor,
- Diana Kolbe,
- Scott Schwartz,
- Terrence S. Furey,
- Simon Whelan,
- Nick Goldman,
- Arian Smit,
- Webb Miller,
- Francesca Chiaromonte,
- and David Haussler
Genome Res. January 1, 2003 13: 13-26; doi:10.1101/gr.844103
..., and (6) rate of recombination. Features 1 and 2 are measures of nucleotide substitutions at two classes of “neutral” sites, whereas 4 is a measure of recent mutations. Feature 3 is a measure dominated by deletions in mouse, whereas 5 represents insertions in human. It was found that all six vary...

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