Searching journal content for articles similar to GuhaThakurta et al. 12 (5): 701.

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Research: Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity
- Hunter B. Fraser,
- Sasha Levy,
- Arun Chavan,
- Hiral B. Shah,
- J. Christian Perez,
- Yiqi Zhou,
- Mark L. Siegal,
- and Himanshu Sinha
Genome Res. October 2012 22: 1930-1939; Published in Advance May 29, 2012, doi:10.1101/gr.134080.111
...sweeps for multiple cis -regulatory mutations that down-regulate gene expression levels in a pathogenic yeast. To test if these adaptations affect virulence, we created a panel of single-allele knockout strains whose hemizygous state mimics the genes' adaptive down-regulations, and measured...
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Method: Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding
- J. Omar Yáñez-Cuna,
- Huy Q. Dinh,
- Evgeny Z. Kvon,
- Daria Shlyueva,
- and Alexander Stark
Genome Res. October 2012 22: 2018-2030; Published in Advance April 25, 2012, doi:10.1101/gr.132811.111
....] The precise regulation of gene expression plays an important role in development, cell differentiation, and cellular responses to the environment. The spatio-temporal expression of genes is controlled by DNA elements called enhancers (Banerji et al. 1981) or cis-regulatory modules (CRMs) (Kirchhamer et al...
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Research: A novel candidate cis-regulatory motif pair in the promoters of germline and oogenesis genes in C. elegans
- Chaim Linhart,
- Yonit Halperin,
- Amir Darom,
- Shahar Kidron,
- Limor Broday,
- and Ron Shamir
Genome Res. January 2012 22: 76-83; Published in Advance September 19, 2011, doi:10.1101/gr.115626.110
...Caenorhabditis genus. By analyzing several gene expression data sets, our data suggest that this motif pair may function in germline development, oogenesis, and early embryogenesis. Finally, we verify that the motifs are indeed functional cis-regulatory elements using reporter constructs in transgenic C. elegans...
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Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
..., a significant fraction of multiexon genes undergo alternative splicing, with higher frequencies reported across vertebrates (Pan et al. 2008; Wang et al. 2008; Barbosa-Morais et al. 2012; Merkin et al. 2012) in comparison to invertebrate model organisms such as the nematode Caenorhabditis elegans and the fruit...
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LETTER: cis-Regulatory and Protein Evolution in Orthologous and Duplicate Genes
- Cristian I. Castillo-Davis,
- Daniel L. Hartl,
- and Guillaume Achaz
Genome Res. August 2004 14: 1530-1536; Published in Advance July 15, 2004, doi:10.1101/gr.2662504
...relevant cis -regulatory sequence change in homologous genes, and validate it using microarray data and experimentally verified regulatory elements in different eukaryotic species. By comparing the s of Caenorhabditis elegans and C. briggsae , we found that protein and regulatory evolution is weakly...
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Resource: Genome-wide analysis of alternative splicing in Caenorhabditis elegans
- Arun K. Ramani,
- John A. Calarco,
- Qun Pan,
- Sepand Mavandadi,
- Ying Wang,
- Andrew C. Nelson,
- Leo J. Lee,
- Quaid Morris,
- Benjamin J. Blencowe,
- Mei Zhen,
- and Andrew G. Fraser
Genome Res. February 2011 21: 342-348; Published in Advance December 22, 2010, doi:10.1101/gr.114645.110
...on mapping reads to splice sites, identifying novel splice sites, and other computational analyses. Microarray design, hybridization, and analysis Alternative splicing events were identified from alignments of C. elegans mRNA/EST sequences (UniGene Build #26) to C. elegans genomic sequence, essentially...
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Research: Gene regulation and speciation in house mice
- Katya L. Mack,
- Polly Campbell,
- and Michael W. Nachman
Genome Res. April 2016 26: 451-461; Published in Advance February 1, 2016, doi:10.1101/gr.195743.115
...interactions between loci in hybrids (Dobzhansky-Muller incompatibilities) are thought to underlie many examples of post-zygotic reproductive isolation. At the transcriptional level, gene expression is a consequence of the interaction of cis-regulatory elements and trans-acting factors. Cis-regulatory regions...
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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
...should provide information on where (in what cells or tissues) and when (at what stage of development or under what conditions) genes are expressed. They should also indicate in what cellular compartments the corresponding proteins are localized. Caenorhabditis elegans is particularly suited...
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LETTER: Novel transcription regulatory elements in Caenorhabditis elegans muscle genes
- Debraj GuhaThakurta,
- Lawrence A. Schriefer,
- Robert H. Waterston,
- and Gary D. Stormo
Genome Res. December 2004 14: 2457-2468; doi:10.1101/gr.2961104
...98195, USA Abstract We report the identification of three new transcription regulatory elements that are associated with muscle gene expression in the nematode Caenorhabditis elegans . Starting from a subset of well-characterized nematode muscle genes, we identified conserved DNA motifs...
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Research: Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions
- Eric L. Van Nostrand and
- Stuart K. Kim
Genome Res. June 2013 23: 941-953; Published in Advance March 26, 2013, doi:10.1101/gr.152876.112
...Integrative analysis of C. elegans modENCODE ChIP-seq data sets to infer gene regulatory interactions Eric L. Van Nostrand 1 and Stuart K. Kim 2 Department of Genetics and Department of Developmental Biology, Stanford University Medical Center, Stanford...

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