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LETTER: A microarray analysis of the rice transcriptome and its comparison to Arabidopsis
- Ligeng Ma,
- Chen Chen,
- Xigang Liu,
- Yuling Jiao,
- Ning Su,
- Lin Li,
- Xiangfeng Wang,
- Mengliang Cao,
- Ning Sun,
- Xiuqing Zhang,
- Jingyue Bao,
- Jian Li,
- Soren Pedersen,
- Lars Bolund,
- Hongyu Zhao,
- Longping Yuan,
- Gane Ka-Shu Wong,
- Jun Wang,
- Xing Wang Deng,
- and Jian Wang
Genome Res. September 2005 15: 1274-1283; doi:10.1101/gr.3657405
...DNA sequence for the coexpressed adjacent gene models. The x -axis represents the genomic DNA length along the chromosome, and the y -axis represents the distribution of coexpressed gene models within a specific length of chromosome. A significant fraction of neighboring genes show a coexpression...
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Methods: MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
- Mattia Pelizzola,
- Yasuo Koga,
- Alexander Eckehart Urban,
- Michael Krauthammer,
- Sherman Weissman,
- Ruth Halaban,
- and Annette M. Molinaro
Genome Res. October 2008 18: 1652-1659; Published in Advance September 2, 2008, doi:10.1101/gr.080721.108
...by bisulfite genomic DNA sequencing. Importantly, the model-derived DNA methylation estimates simplify the interpretation of the results both at single-loci and at chromosome-wide levels. Epigenetics can be defined as the study of changes in the regulation of gene activity and expression that are not driven...
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Resource: Dynamic DNA methylation across diverse human cell lines and tissues
- Katherine E. Varley,
- Jason Gertz,
- Kevin M. Bowling,
- Stephanie L. Parker,
- Timothy E. Reddy,
- Florencia Pauli-Behn,
- Marie K. Cross,
- Brian A. Williams,
- John A. Stamatoyannopoulos,
- Gregory E. Crawford,
- Devin M. Absher,
- Barbara J. Wold,
- and Richard M. Myers
Genome Res. March 2013 23: 555-567; Published in Advance January 16, 2013, doi:10.1101/gr.147942.112
...groups observed that the covalent addition of a methyl group to the cytosine base in mammalian genomic DNA at certain loci is associated with differential gene expression of nearby genes (Razin and Riggs 1980; Sutter and Doerfler 1980; van der Ploeg and Flavell 1980). This led to decades of research...
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Methods: Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
- Georg Zeller,
- Richard M. Clark,
- Korbinian Schneeberger,
- Anja Bohlen,
- Detlef Weigel,
- and Gunnar Rätsch
Genome Res. June 2008 18: 918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
...was generated by pooling long-range PCR amplicons of selected regions. For A. thaliana , the entire genomic DNA was subjected to isothermal amplification ( Clark et al. 2007 ). Nevertheless, the framework of our learning algorithm can be adapted to accommodate additional intensity variation resulting from...
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RESOURCE: Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications
- Pierre Hilson,
- Joke Allemeersch,
- Thomas Altmann,
- Sébastien Aubourg,
- Alexandra Avon,
- Jim Beynon,
- Rishikesh P. Bhalerao,
- Frédérique Bitton,
- Michel Caboche,
- Bernard Cannoot,
- Vasil Chardakov,
- Cécile Cognet-Holliger,
- Vincent Colot,
- Mark Crowe,
- Caroline Darimont,
- Steffen Durinck,
- Holger Eickhoff,
- Andéol Falcon de Longevialle,
- Edward E. Farmer,
- Murray Grant,
- Martin T.R. Kuiper,
- Hans Lehrach,
- Céline Léon,
- Antonio Leyva,
- Joakim Lundeberg,
- Claire Lurin,
- Yves Moreau,
- Wilfried Nietfeld,
- Javier Paz-Ares,
- Philippe Reymond,
- Pierre Rouzé,
- Goran Sandberg,
- Maria Dolores Segura,
- Carine Serizet,
- Alexandra Tabrett,
- Ludivine Taconnat,
- Vincent Thareau,
- Paul Van Hummelen,
- Steven Vercruysse,
- Marnik Vuylsteke,
- Magdalena Weingartner,
- Peter J. Weisbeek,
- Valtteri Wirta,
- Floyd R.A. Wittink,
- Marc Zabeau,
- and Ian Small
Genome Res. October 15, 2004 14: 2176-2189; doi:10.1101/gr.2544504
...one AGI gene. All the data presented below on microarray transcript profiling and large-scale cloning relate to the CATMA v1 collection. All functional and structural annotation refers to the TIGR release 5.0 annotation. Synthesis The GSTs were PCR-amplified from genomic DNA. The gene...
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PERSPECTIVE: The Arabidopsis genome: A foundation for plant research
- Michael Bevan and
- Sean Walsh
Genome Res. December 2005 15: 1632-1642; doi:10.1101/gr.3723405
...tags (GSTs) has also been created ( Hilson et al. 2004 ) in the CATMA (Complete Arabidopsis Transcriptome Analysis) project ( http://www.catma.org/ ). These are PCR-amplified regions of genomic DNA between 150 and 300 bp long that provide gene-specific probes to ∼21,000 Arabidopsis genes. These have...
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Research: Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer
- Jung H. Kim,
- Saravana M. Dhanasekaran,
- John R. Prensner,
- Xuhong Cao,
- Daniel Robinson,
- Shanker Kalyana-Sundaram,
- Christina Huang,
- Sunita Shankar,
- Xiaojun Jing,
- Matthew Iyer,
- Ming Hu,
- Lee Sam,
- Catherine Grasso,
- Christopher A. Maher,
- Nallasivam Palanisamy,
- Rohit Mehra,
- Hal D. Kominsky,
- Javed Siddiqui,
- Jindan Yu,
- Zhaohui S. Qin,
- and Arul M. Chinnaiyan
Genome Res. July 2011 21: 1028-1041; doi:10.1101/gr.119347.110
...2009), and accumulation of promoter DNA methylation is associated with gene silencing (Jones and Baylin 2007). Previously, DNA methylation studies in prostate cancer have usedmethodologies of variable scale, focusing on either a few promoters (Li et al. 2005) or several thousand genomic regions with a...
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Resource: A spatial and temporal map of C. elegans gene expression
- W. Clay Spencer,
- Georg Zeller,
- Joseph D. Watson,
- Stefan R. Henz,
- Kathie L. Watkins,
- Rebecca D. McWhirter,
- Sarah Petersen,
- Vipin T. Sreedharan,
- Christian Widmer,
- Jeanyoung Jo,
- Valerie Reinke,
- Lisa Petrella,
- Susan Strome,
- Stephen E. Von Stetina,
- Menachem Katz,
- Shai Shaham,
- Gunnar Rätsch,
- and David M. Miller III
Genome Res. February 2011 21: 325-341; Published in Advance December 22, 2010, doi:10.1101/gr.114595.110
...). Figure 3. mSTAD detects TARs corresponding to protein-coding genes and to novel transcribed regions. (A) Novel TARs detected in larval L2 intestine. Enlarged region shows location of primers and predicted RT-PCR amplicon from two TARs, L2-int-1 and L2-int-2. (B) RT-PCR detects novel TARs expressed...
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Letter: The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer
- Agustin F. Fernandez,
- Cecilia Rosales,
- Pilar Lopez-Nieva,
- Osvaldo Graña,
- Esteban Ballestar,
- Santiago Ropero,
- Jesus Espada,
- Sonia A. Melo,
- Amaia Lujambio,
- Mario F. Fraga,
- Irene Pino,
- Biola Javierre,
- Francisco J. Carmona,
- Francesco Acquadro,
- Renske D.M. Steenbergen,
- Peter J.F. Snijders,
- Chris J. Meijer,
- Pascal Pineau,
- Anne Dejean,
- Belen Lloveras,
- Gabriel Capella,
- Josep Quer,
- Maria Buti,
- Juan-Ignacio Esteban,
- Helena Allende,
- Francisco Rodriguez-Frias,
- Xavier Castellsague,
- Janos Minarovits,
- Jordi Ponce,
- Daniela Capello,
- Gianluca Gaidano,
- Juan Cruz Cigudosa,
- Gonzalo Gomez-Lopez,
- David G. Pisano,
- Alfonso Valencia,
- Miguel Angel Piris,
- Francesc X. Bosch,
- Ellen Cahir-McFarland,
- Elliott Kieff,
- and Manel Esteller
Genome Res. March 2009 19: 438-451; Published in Advance February 10, 2009, doi:10.1101/gr.083550.108
...of the clustering. The HBV DNA methylomes may be examined at http://ubio.bioinfo.cnio.es/Methylyzer/main/index.html . Examples of the bisulfite genomic sequencing of multiple clones are shown in Figure 3B . Most importantly, the presence of DNA methylation at the HBVgp4 and HBVgp2 genes, which, respectively, code...
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Research: Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
- Ozren Bogdanović,
- Steven W. Long,
- Simon J. van Heeringen,
- Arie B. Brinkman,
- Jose Luis Gómez-Skarmeta,
- Hendrik G. Stunnenberg,
- Peter L. Jones,
- and Gert Jan C. Veenstra
Genome Res. August 2011 21: 1313-1327; Published in Advance June 2, 2011, doi:10.1101/gr.114843.110
..., their genomic distribution was determined relative to gene position (Supplemental Fig. S3). No differences were observed in the overall distribution of DNA methylation between the developmental stages or salt elutions. Approximately 50% of the peaks are located in gene-distant regions (>5000 bp upstream...

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