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LETTER: Identification and analysis of internal promoters in Caenorhabditis elegans operons
- Peiming Huang,
- Erin D. Pleasance,
- Jason S. Maydan,
- Rebecca Hunt-Newbury,
- Nigel J. O’Neil,
- Allan Mah,
- David L. Baillie,
- Marco A. Marra,
- Donald G. Moerman,
- and Steven J.M. Jones
Genome Res. October 2007 17: 1478-1485; Published in Advance August 21, 2007, doi:10.1101/gr.6824707
.... ( 1995 ) Transcription in archaea: Similarity to that in eucarya . Proc. Natl. Acad. Sci. 92 : 5768 – 5772 . ↵ Lercher, M.J. , Blumenthal, T. , Hurst, L.D. ( 2003 ) Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes . Genome Res. 13 : 238 – 243...
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LETTER: Coexpression of Neighboring Genes in the Genome of Arabidopsis thaliana
- Elizabeth J.B. Williams and
- Dianna J. Bowles
Genome Res. June 2004 14: 1060-1067; doi:10.1101/gr.2131104
...–882. ↵ Lercher, M.J., Urrutia, A.O., and Hurst, L.D. 2002 . Clustering of housekeeping genes provides a unified model of gene order in the human . Nat. Genet. 31 : 180 –183. ↵ Lercher, M.J., Blumenthal, T., and Hurst, L.D. 2003 . Coexpression of neighboring genes in Caenorhabditis elegans is mostly...
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LETTER: Evolutionary dynamics of nematode operons: Easy come, slow go
- Wenfeng Qian and
- Jianzhi Zhang
Genome Res. March 2008 18: 412-421; Published in Advance January 24, 2008, doi:10.1101/gr.7112608
..., but are uncommon in eukaryotes, except nematode worms, where ∼15% of genes reside in over 1100 operons in the model organism Caenorhabditis elegans . It is unclear how operons have become abundant in nematode genomes. The “one-way street” hypothesis asserts that once formed by chance, operons are very difficult...
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RESOURCE: A First Version of the Caenorhabditis elegans Promoterome
- Denis Dupuy,
- Qian-Ru Li,
- Bart Deplancke,
- Mike Boxem,
- Tong Hao,
- Philippe Lamesch,
- Reynaldo Sequerra,
- Stephanie Bosak,
- Lynn Doucette-Stamm,
- Ian A. Hope,
- David E. Hill,
- Albertha J.M. Walhout,
- and Marc Vidal
Genome Res. October 15, 2004 14: 2169-2175; doi:10.1101/gr.2497604
.... Transcriptional regulatory networks in Saccharomyces cerevisiae . Science 298 : 799 -804. ↵ Lercher, M.J., Blumenthal, T., and Hurst, L.D. 2003 . Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res. 13 : 238 -243. ↵ Li, S., Armstrong, C.M., Bertin...
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LETTER: Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans
- Nansheng Chen and
- Lincoln D. Stein
Genome Res. May 2006 16: 606-617; Published in Advance April 10, 2006, doi:10.1101/gr.4515306
...of Caenorhabditis elegans using a public tissue-specific SAGE library data set. We find a strong positive correlation in the expression patterns of neighboring gene pairs that are close together and transcribed in the same direction as well as for neighboring pairs that are located on opposing strands...
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Letter: Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved
- Itai Yanai and
- Craig P. Hunter
Genome Res. December 2009 19: 2214-2220; Published in Advance September 10, 2009, doi:10.1101/gr.093815.109
.... Science 293: 2087–2092. Lercher MJ, Urrutia AO, Hurst LD. 2002. Clustering of housekeeping genes provides a unifiedmodel of gene order in the human .Nat Genet 31: 180–183. Lercher MJ, Blumenthal T, Hurst LD. 2003. Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons...
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LETTER: Genomic clusters, putative pathogen recognition molecules, and antimicrobial genes are induced by infection of C. elegans with M. nematophilum
- Delia O’Rourke,
- Dilair Baban,
- Maria Demidova,
- Richard Mott,
- and Jonathan Hodgkin
Genome Res. August 2006 16: 1005-1016; Published in Advance June 29, 2006, doi:10.1101/gr.50823006
...genes in C. elegans is mostly due to operons and duplicated genes that share common regulatory sequences. This explanation may account for some of the coexpression of the smaller clusters that we observed, though most of the genes concerned are not in operons. However, the large cluster on LGIV...
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Research: Positionally biased gene loss after whole genome duplication: Evidence from human, yeast, and plant
- Takashi Makino and
- Aoife McLysaght
Genome Res. December 2012 22: 2427-2435; Published in Advance July 26, 2012, doi:10.1101/gr.131953.111
...BW, Lander ES. 2004. Proof and evolutionary analysis of ancient duplication in the yeast Saccharomyces cerevisiae.Nature 428: 617–624. Lercher MJ, Blumenthal T, Hurst LD. 2003. Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res 13: 238...
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ARTICLE: Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
- Stephen Richards,
- Yue Liu,
- Brian R. Bettencourt,
- Pavel Hradecky,
- Stan Letovsky,
- Rasmus Nielsen,
- Kevin Thornton,
- Melissa J. Hubisz,
- Rui Chen,
- Richard P. Meisel,
- Olivier Couronne,
- Sujun Hua,
- Mark A. Smith,
- Peili Zhang,
- Jing Liu,
- Harmen J. Bussemaker,
- Marinus F. van Batenburg,
- Sally L. Howells,
- Steven E. Scherer,
- Erica Sodergren,
- Beverly B. Matthews,
- Madeline A. Crosby,
- Andrew J. Schroeder,
- Daniel Ortiz-Barrientos,
- Catharine M. Rives,
- Michael L. Metzker,
- Donna M. Muzny,
- Graham Scott,
- David Steffen,
- David A. Wheeler,
- Kim C. Worley,
- Paul Havlak,
- K. James Durbin,
- Amy Egan,
- Rachel Gill,
- Jennifer Hume,
- Margaret B. Morgan,
- George Miner,
- Cerissa Hamilton,
- Yanmei Huang,
- Lenée Waldron,
- Daniel Verduzco,
- Kerstin P. Clerc-Blankenburg,
- Inna Dubchak,
- Mohamed A.F. Noor,
- Wyatt Anderson,
- Kevin P. White,
- Andrew G. Clark,
- Stephen W. Schaeffer,
- William Gelbart,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. January 2005 15: 1-18; doi:10.1101/gr.3059305
...out of order was also permitted (if it fell within five genes of its expected location). Gene duplications in one species could be perceived as synteny breaks. Gene duplications were not considered in the derivation of synteny blocks. Figure 1 shows the synteny blocks of the chromosomes are short...
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