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RESOURCE: DupMasker: A tool for annotating primate segmental duplications
- Zhaoshi Jiang,
- Robert Hubley,
- Arian Smit,
- and Evan E. Eichler
Genome Res. August 2008 18: 1362-1368; Published in Advance May 23, 2008, doi:10.1101/gr.078477.108
...chromosomal evolution . Genome Biol. 5 : R23 . ↵ Chen, D.C. , Saarela, J. , Clark, R.A. , Miettinen, T. , Chi, A. , Eichler, E.E. , Peltonen, L. , Palotie, A. ( 2004 ) Segmental duplications flank the multiple sclerosis locus on chromosome 17q . Genome Res. 14 : 1483 – 1492 . ↵ Cheng, Z. , Ventura, M. , She...
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Research: Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments
- Michael I. Robson,
- Jose I. de las Heras,
- Rafal Czapiewski,
- Aishwarya Sivakumar,
- Alastair R.W. Kerr,
- and Eric C. Schirmer
Genome Res. July 2017 27: 1126-1138; Published in Advance April 19, 2017, doi:10.1101/gr.212308.116
...1131 www..org First, we extracted the Rao et al. (2014) subcompartments and separately the 1 kb upstream and downstream flanking DNA. As compartment size varies, individual compartment regions were plotted with lengths equalized. The average log2(Lamin B1/Damonly) ratio from resting Jurkat T cells...
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LETTER: Construction of an ∼700-kb Transcript Map Around the Familial Mediterranean Fever Locus on Human Chromosome 16p13.3
- Michael Centola,
- Xiaoguang Chen,
- Raman Sood,
- Zuoming Deng,
- Ivona Aksentijevich,
- Trevor Blake,
- Darrell O. Ricke,
- Xiang Chen,
- Geryl Wood,
- Nurit Zaks,
- Neil Richards,
- David Krizman,
- Elizabeth Mansfield,
- Sinoula Apostolou,
- Jingmei Liu,
- Neta Shafran,
- Anil Vedula,
- Melanie Hamon,
- Andrea Cercek,
- Tanaz Kahan,
- Deborah Gumucio,
- David F. Callen,
- Robert I. Richards,
- Robert K. Moyzis,
- Norman A. Doggett,
- Francis S. Collins,
- P. Paul Liu,
- Nathan Fischel-Ghodsian,
- and Daniel L. Kastner
Genome Res. November 1, 1998 8: 1172-1191; doi:10.1101/gr.8.11.1172
...is drawn in three levels with resolution increasing on descending levels. Transcripts are not drawn to scale. ( A ) Transcripts identified by direct selection in the flanking intervals are indicated as are the physical map positions of large-insert genomic clones used for analysis. The position of cosmids...
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ARTICLE: Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates
- Hiroshi Kikuta,
- Mary Laplante,
- Pavla Navratilova,
- Anna Z. Komisarczuk,
- Pär G. Engström,
- David Fredman,
- Altuna Akalin,
- Mario Caccamo,
- Ian Sealy,
- Kerstin Howe,
- Julien Ghislain,
- Guillaume Pezeron,
- Philippe Mourrain,
- Staale Ellingsen,
- Andrew C. Oates,
- Christine Thisse,
- Bernard Thisse,
- Isabelle Foucher,
- Birgit Adolf,
- Andrea Geling,
- Boris Lenhard,
- and Thomas S. Becker
Genome Res. May 2007 17: 545-555; Published in Advance March 26, 2007, doi:10.1101/gr.6086307
.... The mammalian syntenic block contains seven known genes, out of which two ( BARHL1 and TSC1 ) have been retained in both copies. Of the four genes between them, three were retained at the barhl1.2 locus only. The fourth one ( GTF3C4 ) was retained only at the barhl1.1 locus, flanked with two HCNE...
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ARTICLE: Construction of a 750-kb bacterial clone contig and restriction map in the region of human chromosome 21 containing the progressive myoclonus epilepsy gene.
- N E Stone,
- J B Fan,
- V Willour,
- L A Pennacchio,
- J A Warrington,
- A Hu,
- A de la Chapelle,
- A E Lehesjoki,
- D R Cox,
- and R M Myers
Genome Res. March 1996 6: 218-225; doi:10.1101/gr.6.3.218
...arrows at the top of each map segment). Ichikawa et al. (1993) esti- mated that linking clone markers D21S1458 and D21S1459 flanked a 60-kb NotI fragment, and we calculated the fragment o be -55 kb. The next distal f ragment , f lanked by the markers D21S1459 and D21S1460, was reported as 350 kb from...
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Resource: Analysis of copy number variations among diverse cattle breeds
- George E. Liu,
- Yali Hou,
- Bin Zhu,
- Maria Francesca Cardone,
- Lu Jiang,
- Angelo Cellamare,
- Apratim Mitra,
- Leeson J. Alexander,
- Luiz L. Coutinho,
- Maria Elena Dell'Aquila,
- Lou C. Gasbarre,
- Gianni Lacalandra,
- Robert W. Li,
- Lakshmi K. Matukumalli,
- Dan Nonneman,
- Luciana C. de A. Regitano,
- Tim P.L. Smith,
- Jiuzhou Song,
- Tad S. Sonstegard,
- Curt P. Van Tassell,
- Mario Ventura,
- Evan E. Eichler,
- Tara G. McDaneld,
- and John W. Keele
Genome Res. May 2010 20: 693-703; Published in Advance March 8, 2010, doi:10.1101/gr.105403.110
...3. Colocalization analysis of cattle CNV regions and segmental duplications. Relationships between flanking distances and numbers of cattle CNV regions overlapped with all SDs (A) or 1020 high-confidence SD regions (B). Cattle CNV Genome Research 697 www..org 2006;Marques-Bonet et al. 2009).When...
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Research: Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
- Nanine de Groot,
- Marit van der Wiel,
- Ngoc Giang Le,
- Natasja G. de Groot,
- Jesse Bruijnesteijn,
- and Ronald E. Bontrop
Genome Res. November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124
...haplotypes contain a DRA gene, followed by the presence of a DRB9 segment in close proximity, which consists of exon 2 and its flanking introns. This DR framework is separated from the remaining DRB haplotype by a noncoding stretch that varies in length owing to the presence of different repetitive elements...
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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...: In this window In a new window Figure 1. Long-range PCR enrichment. Primers are designed to flank ROI. PCR can be carried out as single reactions for single targets or with multiple targets in a single PCR reaction. Amplified targets can be optionally size-selected via gel if the target size is known. Amplicons...
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Research: Non-Mendelian inheritance patterns and extreme deviation rates of CGG repeats in autism
- Dale J. Annear,
- Geert Vandeweyer,
- Alba Sanchis-Juan,
- F. Lucy Raymond,
- and R. Frank Kooy
Genome Res. November/December 2022 32: 1967-1980; Published in Advance November 9, 2022, doi:10.1101/gr.277011.122
...expression and subsequently affect phenotype.From an evolutionary perspective, the RANBP2 like and GRIP domain-containing protein (RGPD) genes are a highly interesting family of genes regarding CGG STRs. There are eight segmentally duplicated RGPD genes, originating from RANBP2, located on Chromosome 2...
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Research: A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci
- Elisabeth J. van Bree,
- Rita L.F.P. Guimarães,
- Mischa Lundberg,
- Elena R. Blujdea,
- Jimi L. Rosenkrantz,
- Fred T.G. White,
- Josse Poppinga,
- Paula Ferrer-Raventós,
- Anne-Fleur E. Schneider,
- Isabella Clayton,
- David Haussler,
- Marcel J.T. Reinders,
- Henne Holstege,
- Adam D. Ewing,
- Colette Moses,
- and Frank M.J. Jacobs
Genome Res. April 2022 32: 656-670; Published in Advance March 24, 2022, doi:10.1101/gr.275515.121
...'s disease–associated risk loci and in the BCKDK Parkinson's disease–associated risk locus and assessed multiple aspects of their gene-regulatory influence in a human neuronal context. Together, this study reveals a novel layer of genetic variation in transposable elements that may contribute...
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