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Research: Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes
- Konstantinos Kritsas,
- Samuel E. Wuest,
- Daniel Hupalo,
- Andrew D. Kern,
- Thomas Wicker,
- and Ueli Grossniklaus
Genome Res. December 2012 22: 2455-2466; Published in Advance September 17, 2012, doi:10.1101/gr.129346.111
...elements 5. E. coli contamination 6. Encoding a protein motif 7. In intron–exon junctions 2456 Genome Research www..org Kritsas et al. and Vitis. High levels of conservation were also found within the less complete of papaya, where 20 ULEs have identities ranging from 84% to 100%. Only nine of 36 ULEs were...
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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
...genes, but matching publicly available mRNA or spliced EST sequences (“other mRNA” in Fig. 3 ) show 9.2% coverage by conserved elements (a 2.1-fold enrichment), and regions not in known genes or other mRNAs, but transcribed according to data from the Affymetrix/NCI Human Transcriptome project (“other...
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Research: An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
- Ignacio Maeso,
- Manuel Irimia,
- Juan J. Tena,
- Esther González-Pérez,
- David Tran,
- Vydianathan Ravi,
- Byrappa Venkatesh,
- Sonsoles Campuzano,
- José Luis Gómez-Skarmeta,
- and Jordi Garcia-Fernàndez
Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111
.... milii contigs were searched at the NCBI genomic BLASTwebpage for unfinished eukaryotic s (http://www.ncbi.nlm.nih.gov/sutils/genom_ table.cgi?organism=eukaryotes). Manually curated Sowah mRNA sequences from selected metazoan species are included as Supplemental Data S2. All other final gene annotations...
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Research: Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila
- Marcin von Grotthuss,
- Michael Ashburner,
- and José M. Ranz
Genome Res. August 2010 20: 1084-1096; Published in Advance July 2, 2010, doi:10.1101/gr.103713.109
...arbitrarily set a threshold value of 21 IGAs as the minimum size for an HCB to be considered (‘‘ultraconserved genomic regions’’ hereafter). We scrutinized 21 ultraconserved regions from Muller’s elements B–E (;1% of the total number of orthologous landmarks), plus the largest one on Muller’s element A...
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12 Drosophila Genomes/Letter: Genomic regulatory blocks underlie extensive microsynteny conservation in insects
- Pär G. Engström,
- Shannan J. Ho Sui,
- Øyvind Drivenes,
- Thomas S. Becker,
- and Boris Lenhard
Genome Res. December 2007 17: 1898-1908; Published in Advance November 7, 2007, doi:10.1101/gr.6669607
...Abstract Insect genomes contain larger blocks of conserved gene order (microsynteny) than would be expected under a random breakage model of chromosome evolution. We present evidence that microsynteny has been retained to keep large arrays of highly conserved noncoding elements (HCNEs) intact...
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REVIEW: Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping
- Albertha J.M. Walhout
Genome Res. December 2006 16: 1445-1454; Published in Advance October 19, 2006, doi:10.1101/gr.5321506
...by directly interacting with their target mRNAs. Arrow, transcription start site; purple box, microRNA gene; green line, 3′ UTR of target microRNA (purple line); yellow circle, RNA binding protein. Upstream regulation of miRNA expression (by the pink TF binding to the light blue element) is indicated...

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