Searching journal content for articles similar to Castellino 7 (10): 943.

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  1. Research: Extreme HOT regions are CpG-dense promoters in C. elegans and humans
    • Ron A.-J. Chen,
    • Przemyslaw Stempor,
    • Thomas A. Down,
    • Eva Zeiser,
    • Sky K. Feuer,
    • and Julie Ahringer
    Genome Res. July 2014 24: 1138-1146; Published in Advance March 20, 2014, doi:10.1101/gr.161992.113
    ...Extreme HOT regions are CpG-dense promoters in C. elegans and humans Ron A.-J. Chen , Przemyslaw Stempor , Thomas A. Down , Eva Zeiser , Sky K. Feuer and Julie Ahringer 1 The Gurdon Institute and Department of Genetics...
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  2. Resource: The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures
    • Ron A.-J. Chen,
    • Thomas A. Down,
    • Przemyslaw Stempor,
    • Q. Brent Chen,
    • Thea A. Egelhofer,
    • LaDeana W. Hillier,
    • Tess E. Jeffers,
    • and Julie Ahringer
    Genome Res. August 2013 23: 1339-1347; Published in Advance April 2, 2013, doi:10.1101/gr.153668.112
    ...The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures Ron A.-J. Chen 1 , 5 , Thomas A. Down 1 , 5 , Przemyslaw Stempor 1 , Q. Brent Chen 2 , Thea A. Egelhofer 3 , La...
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  3. Research: A functional methylome map of ulcerative colitis
    • Robert Häsler,
    • Zhe Feng,
    • Liselotte Bäckdahl,
    • Martina E. Spehlmann,
    • Andre Franke,
    • Andrew Teschendorff,
    • Vardhman K. Rakyan,
    • Thomas A. Down,
    • Gareth A. Wilson,
    • Andrew Feber,
    • Stephan Beck,
    • Stefan Schreiber,
    • and Philip Rosenstiel
    Genome Res. November 2012 22: 2130-2137; Published in Advance July 23, 2012, doi:10.1101/gr.138347.112
    .... Down 4 , Gareth A. Wilson 2 , Andrew Feber 2 , Stephan Beck 2 , 6 , Stefan Schreiber 1 , 6 , 7 and Philip Rosenstiel 1 , 6 , 7 1 Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, 24105...
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  4. Research: The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome
    • M. Reza Sailani,
    • Periklis Makrythanasis,
    • Armand Valsesia,
    • Federico A. Santoni,
    • Samuel Deutsch,
    • Konstantin Popadin,
    • Christelle Borel,
    • Eugenia Migliavacca,
    • Andrew J. Sharp,
    • Genevieve Duriaux Sail,
    • Emilie Falconnet,
    • Kelly Rabionet,
    • Clara Serra-Juhé,
    • Stefano Vicari,
    • Daniela Laux,
    • Yann Grattau,
    • Guy Dembour,
    • Andre Megarbane,
    • Renaud Touraine,
    • Samantha Stora,
    • Sofia Kitsiou,
    • Helena Fryssira,
    • Chariklia Chatzisevastou-Loukidou,
    • Emmanouel Kanavakis,
    • Giuseppe Merla,
    • Damien Bonnet,
    • Luis A. Pérez-Jurado,
    • Xavier Estivill,
    • Jean M. Delabar,
    • and Stylianos E. Antonarakis
    Genome Res. September 2013 23: 1410-1421; Published in Advance June 19, 2013, doi:10.1101/gr.147991.112
    ...beadchips, we genotyped rs7282991 and rs2183593 on chromosome 21 by pyrosequencing for 96 DS samples that were also genotyped by Illumina BeadChips. We found 100% concordance for the genotypes called by both methods. To check for trisomic SNPs that violate Hardy-Weinberg equilibrium (HWE) in Down syndrome...
  5. Research: Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains
    • Vardhman K. Rakyan,
    • Thomas A. Down,
    • Siarhei Maslau,
    • Toby Andrew,
    • Tsun-Po Yang,
    • Huriya Beyan,
    • Pamela Whittaker,
    • Owen T. McCann,
    • Sarah Finer,
    • Ana M. Valdes,
    • R. David Leslie,
    • Panogiotis Deloukas,
    • and Timothy D. Spector
    Genome Res. April 2010 20: 434-439; Published in Advance March 10, 2010, doi:10.1101/gr.103101.109
    ...Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains Vardhman K. Rakyan 1 , 5 , 7 , Thomas A. Down 2 , 5 , Siarhei Maslau 2 , Toby Andrew 3 , Tsun-Po Yang 4 , Huriya Beyan 1...
  6. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...immunoprecipitation (ChIP) in 1984 followed by ChIP-qPCR and ChIP-seq, which allowed scientists to probe the full palette of DNA molecules bound by proteins of interest. A ChIP experiment begins by using formaldehyde to chemically cross-link DNA and protein molecules (Das et al. 2004). Nuclei are isolated...
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  7. Letter: Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level
    • Alexander W. Bruce,
    • Andrés J. López-Contreras,
    • Paul Flicek,
    • Thomas A. Down,
    • Pawandeep Dhami,
    • Shane C. Dillon,
    • Christoph M. Koch,
    • Cordelia F. Langford,
    • Ian Dunham,
    • Robert M. Andrews,
    • and David Vetrie
    Genome Res. June 2009 19: 994-1005; Published in Advance April 28, 2009, doi:10.1101/gr.089086.108
    ...line. siRNA-mediated knockdown of REST in combination with ChIP-chip was used to investigate clearance of REST binding sites in K562 cells. Computationally, we used a two-state hidden Markov model (“NESSIE”; Koch et al. 2007 ) to define REST binding sites in our datasets and “NestedMICA” ( Down...
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  8. Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
    • Manuela Baquero Pérez,
    • Gertjan Laenen,
    • Isabelle Loïodice,
    • Mickaël Garnier,
    • Ugo Szachnowski,
    • Antonin Morillon,
    • Myriam Ruault,
    • and Angela Taddei
    Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
    ...down, 3% of coding genes remain active. Furthermore, RNA polymerase II (RNAPII) accumulates at one-third of gene promoters. The corresponding genes are highly enriched among those showing a high level of transcription and high frequency of expression in individual cells, shortly after cells are refed...
  9. Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
    • Kangli Wang,
    • Weikun Xia,
    • Yingli Gu,
    • Songpeng Zu,
    • Qian Yang,
    • Maria Luisa Amaral,
    • Yaozhi Wang,
    • Allen Wang,
    • Xiang-Dong Fu,
    • William C. Mobley,
    • and Bing Ren
    Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
    .... S8D). In addition, motif enrichment analysis of up- and down-regulated 235 DACs identified by the pseudo-bulk method in dopaminergic neurons revealed an enrichment 236 for motif families such as ZF, HTH, and FOX, including CTCF, RFX, and FOXA1 (Supplemental 237 Fig. S8E,F). Foxa1 is a member...
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  10. RESOURCE: An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
    • Vardhman K. Rakyan,
    • Thomas A. Down,
    • Natalie P. Thorne,
    • Paul Flicek,
    • Eugene Kulesha,
    • Stefan Gräf,
    • Eleni M. Tomazou,
    • Liselotte Bäckdahl,
    • Nathan Johnson,
    • Marlis Herberth,
    • Kevin L. Howe,
    • David K. Jackson,
    • Marcos M. Miretti,
    • Heike Fiegler,
    • John C. Marioni,
    • Ewan Birney,
    • Tim J.P. Hubbard,
    • Nigel P. Carter,
    • Simon Tavaré,
    • and Stephan Beck
    Genome Res. September 2008 18: 1518-1529; Published in Advance June 24, 2008, doi:10.1101/gr.077479.108
    ...An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs) Vardhman K. Rakyan 1 , 9 , 10 , Thomas A. Down 2 , 9 , Natalie P. Thorne 3 , 9 , Paul Flicek 4 , 9...
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