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LETTER: Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex
- Diego Ottaviani,
- Elliott Lever,
- Richard Mitter,
- Tania Jones,
- Tim Forshew,
- Rossitza Christova,
- Eleni M. Tomazou,
- Vardhman K. Rakyan,
- Stephen A. Krawetz,
- Adrian E. Platts,
- Badmavady Segarane,
- Stephan Beck,
- and Denise Sheer
Genome Res. November 2008 18: 1778-1786; Published in Advance October 10, 2008, doi:10.1101/gr.082313.108
...not be permanently attached to the nuclear matrix ( Platts et al. 2006 ; Girod et al. 2007 ; Linnemann et al. 2007 ). Microarray technology now provides an opportunity to map MARs at high resolution across the and address their role in gene expression. The human major histocompatibility complex (MHC) was the first...
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RESEARCH: A 1.1-Mb Transcript Map of the Hereditary Hemochromatosis Locus
- David A. Ruddy,
- Gregory S. Kronmal,
- Vincent K. Lee,
- Gabriel A. Mintier,
- Leah Quintana,
- Rodolfo Domingo, Jr.,
- Nicole C. Meyer,
- Alivelu Irrinki,
- Erin E. McClelland,
- Amy Fullan,
- Felipa A. Mapa,
- Theodore Moore,
- Winston Thomas,
- Deborah B. Loeb,
- Cyrus Harmon,
- Zenta Tsuchihashi,
- Roger K. Wolff,
- Randall C. Schatzman,
- and John N. Feder
Genome Res. May 1, 1997 7: 441-456; doi:10.1101/gr.7.5.441
...responsible for hereditary hemochromatosis (HH), we constructed a 1.1-Mb transcript map of the region of human chromosome 6p that lies 4.5 Mb telomeric to HLA-A . A combination of three gene-finding techniques, direct cDNA selection, exon trapping, and sample sequencing, were used initially for a saturation...
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Method: Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II
- Paul J. Norman,
- Steven J. Norberg,
- Lisbeth A. Guethlein,
- Neda Nemat-Gorgani,
- Thomas Royce,
- Emily E. Wroblewski,
- Tamsen Dunn,
- Tobias Mann,
- Claudia Alicata,
- Jill A. Hollenbach,
- Weihua Chang,
- Melissa Shults Won,
- Kevin L. Gunderson,
- Laurent Abi-Rached,
- Mostafa Ronaghi,
- and Peter Parham
Genome Res. May 2017 27: 813-823; Published in Advance March 30, 2017, doi:10.1101/gr.213538.116
...: 904–907. Chapman SJ, Hill AV. 2012. Human genetic susceptibility to infectious disease. Nat Rev Genet 13: 175–188. Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, et al. 2009. BreakDancer: an algorithm for high-resolution mapping of genomic...
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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
...to common diseases requires the construction of a fully informative polymorphism map. Ideally, every base pair of the would be sequenced in many individuals. Here, we report 4.75 Mb of contiguous sequence for each of two common haplotypes of the major histocompatibility complex (MHC), to which...
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LETTER: Ancient haplotypes of the HLA Class II region
- Christopher K. Raymond,
- Arnold Kas,
- Marcia Paddock,
- Ruolan Qiu,
- Yang Zhou,
- Sandhya Subramanian,
- Jean Chang,
- Anthony Palmieri,
- Eric Haugen,
- Rajinder Kaul,
- and Maynard V. Olson
Genome Res. September 2005 15: 1250-1257; doi:10.1101/gr.3554305
...., Sigurdardottir, S., Barnard, J., Hallbeck, B., Masson, G.A., et al. 2002 . A high-resolution recombination map of the human . Nat. Genet. 31 : 241 -247. ↵ Kotsch, K. and Blasczyk, R. 2000 . The non-coding regions of HLA-DRB uncover inter-lineage recombinations as a mechanism of HLA diversification. In Major...
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LETTER: Sequence features in regions of weak and strong linkage disequilibrium
- Albert V. Smith,
- Daryl J. Thomas,
- Heather M. Munro,
- and Gonçalo R. Abecasis
Genome Res. November 2005 15: 1519-1534; doi:10.1101/gr.4421405
..., that the region at ∼50 Mb that exhibits strong disequilibrium in all populations also shows much reduced polymorphism (∼6 × 10–4 vs. ∼6 × 10–4 for the covered by HapMap), very high GC content (∼50% vs. ∼40%), and a high proportion of genic transcripts (∼7% vs. ∼1.2%). When we repeated our analysis, excluding...
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PERSPECTIVE: Genome Function and Nuclear Architecture: From Gene Expression to Nanoscience
- Timothy P. O'Brien,
- Carol J. Bult,
- Christoph Cremer,
- Michael Grunze,
- Barbara B. Knowles,
- Jörg Langowski,
- James McNally,
- Thoru Pederson,
- Joan C. Politz,
- Ana Pombo,
- Günter Schmahl,
- Joachim P. Spatz,
- and Roel van Driel
Genome Res. June 2003 13: 1029-1041; Published in Advance May 12, 2003, doi:10.1101/gr.946403
...for processes such as transcription, replication, and segregation during the cell cycle. These features include centromeric, telomeric, and repetitive DNA as well as promoter proximal elements that control the activity of individual genes and locus control regions, and insulators that regulate the activity...
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RESOURCE: Initial sequence and comparative analysis of the cat genome
- Joan U. Pontius,
- James C. Mullikin,
- Douglas R. Smith,
- Agencourt Sequencing Team,
- Kerstin Lindblad-Toh,
- Sante Gnerre,
- Michele Clamp,
- Jean Chang,
- Robert Stephens,
- Beena Neelam,
- Natalia Volfovsky,
- Alejandro A. Schäffer,
- Richa Agarwala,
- Kristina Narfström,
- William J. Murphy,
- Urs Giger,
- Alfred L. Roca,
- Agostinho Antunes,
- Marilyn Menotti-Raymond,
- Naoya Yuhki,
- Jill Pecon-Slattery,
- Warren E. Johnson,
- Guillaume Bourque,
- Glenn Tesler,
- NISC Comparative Sequencing Program,
- and Stephen J. O’Brien
Genome Res. November 2007 17: 1675-1689; doi:10.1101/gr.6380007
..., or 65% of the 2.5-Gb euchromatin ) than for the higher coverage s. To order and orient the assembly onto the feline chromosomes, we constructed a sequence map using comparative data available from high-coverage dog and human s. The map was built by first aligning the feline sequence to the CanFam2...
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RESEARCH: Clone–Contig and STS Maps of the Hereditary Hemochromatosis Region on Human Chromosome 6p21.3–p22
- Peter Lauer,
- Nicole C. Meyer,
- Cynthia E. Prass,
- Steven M. Starnes,
- Roger K. Wolff,
- and Andreas Gnirke
Genome Res. May 1, 1997 7: 457-470; doi:10.1101/gr.7.5.457
...and spans ∼8 Mb of DNA between the class I region of the major histocompatibility complex on human chromosome 6p21.3 and D6S276 in 6p22. Comparison with published maps revealed a hole in the MIT/Whitehead and CEPH YAC maps that includes the immediate region around the hemochromatosis gene itself...
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RESEARCH: Duplications on Human Chromosome 22 Reveal a Novel Ret Finger Protein-Like Gene Family with Sense and Endogenous Antisense Transcripts
- Eyal Seroussi,
- Darek Kedra,
- Hua-Qin Pan,
- Myriam Peyrard,
- Charles Schwartz,
- Peter Scambler,
- Dian Donnai,
- Bruce A. Roe,
- and Jan P. Dumanski
Genome Res. September 1, 1999 9: 803-814; doi:10.1101/gr.9.9.803
...in regulation of cell differentiation ( Takahashi et al. 1988 ; Cao et al. 1998 ). Ro52 is associated with cytoplasmic ribonucleic particles ( Deutscher et al. 1988 ; Pruijn et al. 1997 ). Both RFP and Ro52 genes map to the human chromosome 6p21 region, in the vicinity of the major histocompatibility complex...

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