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LETTER: Long-range comparison of human and mouse Sprr loci to identify conserved noncoding sequences involved in coordinate regulation
- Natalia Martin,
- Satyakam Patel,
- and Julia A. Segre
Genome Res. December 2004 14: 2430-2438; doi:10.1101/gr.2709404
...interval are frequently functional. Genome Res. 14 : 367 -372. ↵ Göttgens, B., Gilbert, J.G., Barton, L.M., Grafham, D., Rogers, J., Bentley, D.R., and Green, A.R. 2001 . Long-range comparison of human and mouse SCL loci: Localized regions of sensitivity to restriction endonucleases correspond precisely...
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LETTER: Conserved Noncoding Sequences in the Grasses
- Dan Choffnes Inada,
- Ali Bashir,
- Chunghau Lee,
- Brian C. Thomas,
- Cynthia Ko,
- Stephen A. Goff,
- and Michael Freeling
Genome Res. September 2003 13: 2030-2041; doi:10.1101/gr.1280703
...for identifying conserved regions in a large set of human–mouse orthologs, they estimated that 26%–56% of mammalian noncoding space is conserved. A Cluster of CNSs in a knotted1 Transcription Factor Gene Intron Corresponds to a Region Where Transposon Insertions Result in Ectopic Expression To address...
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LETTER: Transcriptional Regulation of the Stem Cell Leukemia Gene (SCL) — Comparative Analysis of Five Vertebrate SCL Loci
- Berthold Göttgens,
- Linda M. Barton,
- Michael A. Chapman,
- Angus M. Sinclair,
- Bjarne Knudsen,
- Darren Grafham,
- James G.R. Gilbert,
- Jane Rogers,
- David R. Bentley,
- and Anthony R. Green
Genome Res. May 1, 2002 12: 749-759; doi:10.1101/gr.45502
...elements. Here we show that comparisons of the zebrafish SCL locus with mammalian SCL loci did not identify zebrafish elements homologous with the majority of known murine enhancers (e.g., enhancers corresponding to −4/3, +3, +17, +18, +19 DNase1 hypersensitive sites). In contrast, all known mouse...
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RESOURCE: Analysis of Multiple Genomic Sequence Alignments: A Web Resource, Online Tools, and Lessons Learned From Analysis of Mammalian SCL Loci
- Michael A. Chapman,
- Ian J. Donaldson,
- James Gilbert,
- Darren Grafham,
- Jane Rogers,
- Anthony R. Green,
- and Berthold Göttgens
Genome Res. February 2004 14: 313-318; Published in Advance January 12, 2004, doi:10.1101/gr.1759004
...identifies conserved enhancers. Nat. Biotechnol. 18 : 181 -186. ↵ Göttgens, B., Gilbert, J.G., Barton, L.M., Grafham, D., Rogers, J., Bentley, D.R., and Green, A.R. 2001 . Long-range comparison of human and mouse SCL loci: Localized regions of sensitivity to restriction endonucleases correspond precisely...
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LETTER: A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity
- Aileen M. Smith,
- Maria-Jose Sanchez,
- George A. Follows,
- Sarah Kinston,
- Ian J. Donaldson,
- Anthony R. Green,
- and Berthold Göttgens
Genome Res. September 2008 18: 1422-1432; Published in Advance August 7, 2008, doi:10.1101/gr.077008.108
...of the hypersensitive site was further refined using a restriction endonuclease accessibility assay with a resolution of ∼100 bp ( Gottgens et al. 2001 ) and was found to correspond precisely with the +18 peak of sequence homology ( Fig. 1C ). Chromatin immunoprecipitation (ChIP) analysis of 416B cells demonstrated...
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Methods: Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites
- George A. Follows,
- Pawan Dhami,
- Berthold Göttgens,
- Alexander W. Bruce,
- Peter J. Campbell,
- Shane C. Dillon,
- Aileen M. Smith,
- Christoph Koch,
- Ian J. Donaldson,
- Mike A. Scott,
- Ian Dunham,
- Mary E. Janes,
- David Vetrie,
- and Anthony R. Green
Genome Res. October 2006 16: 1310-1319; Published in Advance September 8, 2006, doi:10.1101/gr.5373606
...with the known α-globin erythroid enhancers ( Yagi et al. 1986 ; Higgs et al. 1990 ; Vyas et al. 1992 ). ADHM identified only one novel hypersensitive site as significantly enriched (+90; P = 0.02; indicated “V” in Fig. 5 ). The tile corresponding to this site contains a 350-bp region of highly conserved DNA...
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ENSEMBL Special: Sockeye: A 3D Environment for Comparative Genomics
- Stephen B. Montgomery,
- Tamara Astakhova,
- Mikhail Bilenky,
- Ewan Birney,
- Tony Fu,
- Maik Hassel,
- Craig Melsopp,
- Marcin Rak,
- A. Gordon Robertson,
- Monica Sleumer,
- Asim S. Siddiqui,
- and Steven J.M. Jones
Genome Res. May 2004 14: 956-962; doi:10.1101/gr.1890304
.... ↵ Gottgens, B., Gilbert, J.G., Barton, L.M., Grafham, D., Rogers, R., Bentley, D.R., and Green, A.R. 2001 . Long-range comparison of human and mouse SCL loci: Localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences. Genome Res. 11 : 87...
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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
..., nonrepetitive genomic sequence that aligns in comparisons between mammalian orders varies over a 10-fold range at different loci ( Endrizzi et al. 1999 ; DeSilva et al. 2002 ). Thus, analysis both of substitutions at apparently neutral sites in coding regions and the extent of aligning DNA in noncoding regions...

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