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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
...., and Hardison, R.C. 2003 . Cross-species sequence comparisons: A review of methods and available resources. Genome Res. 13 : 1 -12. ↵ Frazer, K.A., Tao, H., Osoegawa, K., de Jong, P.J., Chen, X., Doherty, M.F., and Cox, D.R. 2004 . Noncoding sequences conserved in a limited number of mammals in the SIM2...
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PERSPECTIVE: Raising the estimate of functional human sequences
- Michael Pheasant and
- John S. Mattick
Genome Res. September 2007 17: 1245-1253; Published in Advance August 9, 2007, doi:10.1101/gr.6406307
....S. ( 2006 ) Conservation of RET regulatory function from human to zebrafish without sequence similarity . Science 312 : 276 – 279 . ↵ Frazer, K.A. , Tao, H. , Osoegawa, K. , de Jong, P.J. , Chen, X. , Doherty, M.F. , Cox, D.R. ( 2004 ) Noncoding sequences conserved in a limited number of mammals in the SIM2...
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ARTICLE: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
- Adam Siepel,
- Gill Bejerano,
- Jakob S. Pedersen,
- Angie S. Hinrichs,
- Minmei Hou,
- Kate Rosenbloom,
- Hiram Clawson,
- John Spieth,
- LaDeana W. Hillier,
- Stephen Richards,
- George M. Weinstock,
- Richard K. Wilson,
- Richard A. Gibbs,
- W. James Kent,
- Webb Miller,
- and David Haussler
Genome Res. August 2005 15: 1034-1050; Published in Advance July 15, 2005, doi:10.1101/gr.3715005
...to be longer and less perfectly conserved, and they overlap genes of somewhat different functional categories. In vertebrates, HCEs are associated with the 3′ UTRs of regulatory genes, stable gene deserts, and megabase-sized regions rich in moderately conserved noncoding sequences. Noncoding HCEs also show...
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LETTER: Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
- Yong Cheng,
- David C. King,
- Louis C. Dore,
- Xinmin Zhang,
- Yuepin Zhou,
- Ying Zhang,
- Christine Dorman,
- Demesew Abebe,
- Swathi A. Kumar,
- Francesca Chiaromonte,
- Webb Miller,
- Roland D. Green,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2008 18: 1896-1905; Published in Advance September 25, 2008, doi:10.1101/gr.083089.108
...is a common approach to predict CRMs from aligned genomic DNA sequences ( Hardison 2000 ; Pennacchio and Rubin 2001 ). Indeed, gain-of-function assays show that almost half of the noncoding sequences conserved across diverse vertebrate lineages (from mammals to fish) ( Pennacchio et al. 2006 ) or almost...
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LETTER: Identification of functional transcription factor binding sites using closely related Saccharomyces species
- Scott W. Doniger,
- Juyoung Huh,
- and Justin C. Fay
Genome Res. May 2005 15: 701-709; Published in Advance April 18, 2005, doi:10.1101/gr.3578205
...in a limited number of mammals in the SIM2 interval are frequently functional. Genome Res. 14 : 367 –372. ↵ Giaever, G., Chu, A.M., Ni, L., Connelly, C., Riles, L., Veronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., Andre, B., et al. 2002 . Functional profiling of the Saccharomyces cerevisiae . Nature 418...
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Chicken Special/Resources: Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
- Ivan Ovcharenko,
- Gabriela G. Loots,
- Belinda M. Giardine,
- Minmei Hou,
- Jian Ma,
- Ross C. Hardison,
- Lisa Stubbs,
- and Webb Miller
Genome Res. January 2005 15: 184-194; Published in Advance December 8, 2004, doi:10.1101/gr.3007205
...the separation of mammals, amphibians, birds, and fish ( Fig. 5 ). View larger version: In this window In a new window Figure 5. Mulan phylogenetic tree ( A ) and sequence conservation profile ( B ) for the GATA3 gene locus from human, rat, mouse, chicken, frog, and three fish s. Each tree branch indicates...
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Methods: Predicting tissue-specific enhancers in the human genome
- Len A. Pennacchio,
- Gabriela G. Loots,
- Marcelo A. Nobrega,
- and Ivan Ovcharenko
Genome Res. February 2007 17: 201-211; Published in Advance January 8, 2007, doi:10.1101/gr.5972507
...the sequence signatures identified by this approach to successfully assign tissue-specific predictions to ∼328,000 human–mouse conserved noncoding elements in the human genome. By overlapping these genome-wide predictions with a data set of enhancers validated in vivo, in transgenic mice, we were able...
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LETTER: Transposon-free regions in mammalian genomes
- Cas Simons,
- Michael Pheasant,
- Igor V. Makunin,
- and John S. Mattick
Genome Res. February 2006 16: 164-172; Published in Advance December 19, 2005, doi:10.1101/gr.4624306
...-913. ↵ Frazer, K.A., Tao, H., Osoegawa, K., de Jong, P.J., Chen, X., Doherty, M.F., and Cox, D.R. 2004 . Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional. Genome Res. 14 : 367 -372. ↵ Greally, J.M. 2002 . Short interspersed transposable...
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LETTER: Experimental validation of predicted mammalian erythroid cis-regulatory modules
- Hao Wang,
- Ying Zhang,
- Yong Cheng,
- Yuepin Zhou,
- David C. King,
- James Taylor,
- Francesca Chiaromonte,
- Jyotsna Kasturi,
- Hanna Petrykowska,
- Brian Gibb,
- Christine Dorman,
- Webb Miller,
- Louis C. Dore,
- John Welch,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2006 16: 1480-1492; Published in Advance October 12, 2006, doi:10.1101/gr.5353806
...for mammalian genes expressed in red blood cells by combining two properties gleaned from aligned, noncoding genome sequences: a positive regulatory potential (RP) score, which detects similarity to patterns in alignments distinctive for regulatory regions, and conservation of a binding site motif...
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LETTER: Organization and Evolution of a Gene-Rich Region of the Mouse Genome: A 12.7-Mb Region Deleted in the Del(13)Svea36H Mouse
- Ann-Marie Mallon,
- Laurens Wilming,
- Joseph Weekes,
- James G.R. Gilbert,
- Jennifer Ashurst,
- Sandrine Peyrefitte,
- Lucy Matthews,
- Matthew Cadman,
- Richard McKeone,
- Chris A. Sellick,
- Ruth Arkell,
- Marc R.M. Botcherby,
- Mark A. Strivens,
- R. Duncan Campbell,
- Simon Gregory,
- Paul Denny,
- John M. Hancock,
- Jane Rogers,
- and Steve D.M. Brown
Genome Res. October 2004 14: 1888-1901; Published in Advance September 13, 2004, doi:10.1101/gr.2478604
...the region with a periodicity of ∼5 Mb. Del36H contains numerous evolutionarily conserved regions (ECRs). Many lie in noncoding regions, are detectable in species as distant as Ciona intestinalis , and therefore are candidate regulatory sequences. This analysis will facilitate functional genomic analysis...

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