Searching journal content for articles similar to Coutinho et al. 21 (8): 1349.

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  1. Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
    • Daniela M. Riley,
    • Randa Elsayed,
    • Mark D. Walsh,
    • Simaran Johal,
    • Ying Lin,
    • Harry Walton,
    • Till Bretschneider,
    • Sascha Ott,
    • and Andrew C. Nelson
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
    ..., for conserved genes to mediate consistent phenotypic outcomes, there must also be consistent regulation of such genes by cis-regulatory modules (CRMs). CRMs consist of clusters of transcription factor binding sites (TFBSs) that regulate the expression of target genes through collective or competitive binding...
  2. Resource: Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq
    • Margaret C.W. Ho,
    • Porfirio Quintero-Cadena,
    • and Paul W. Sternberg
    Genome Res. December 2017 27: 2108-2119; Published in Advance October 26, 2017, doi:10.1101/gr.223735.117
    ...,890 TF footprints, as well as 15,841 putative CRMs in the L1 arrest larvae containing 32,685 TF footprints.Prior research in metazoans has described many types of cis-regulatory modules (CRMs) such as enhancers, repressors, and insulators that can be located far from target genes (for review, see Noonan...
  3. Research: Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions
    • Marina Naval-Sánchez,
    • Delphine Potier,
    • Lotte Haagen,
    • Máximo Sánchez,
    • Sebastian Munck,
    • Bram Van de Sande,
    • Fernando Casares,
    • Valerie Christiaens,
    • and Stein Aerts
    Genome Res. January 2013 23: 74-88; Published in Advance October 15, 2012, doi:10.1101/gr.140426.112
    ..., with the aim to gain further knowledge of the transcriptional program underlying eye development, and to identify new eye enhancers. The master regulators of Drosophila eye development frame the conserved retinal determination gene network (RDGN), with five highly conserved TFs, namely, eyeless (ey; PAX6...
  4. Methods: Conserved introns reveal novel transcripts in Drosophila melanogaster
    • Michael Hiller,
    • Sven Findeiß,
    • Sandro Lein,
    • Manja Marz,
    • Claudia Nickel,
    • Dominic Rose,
    • Christine Schulz,
    • Rolf Backofen,
    • Sonja J. Prohaska,
    • Gunter Reuter,
    • and Peter F. Stadler
    Genome Res. July 2009 19: 1289-1300; Published in Advance May 20, 2009, doi:10.1101/gr.090050.108
    ...Conserved introns reveal novel transcripts in Drosophila melanogaster Michael Hiller 1 , 2 , 9 , Sven Findeiß 3 , 4 , Sandro Lein 5 , Manja Marz 3 , Claudia Nickel 5 , Dominic Rose 3 , Christine Schulz 6...
  5. Letter: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
    • Andrew L. Hufton,
    • Susanne Mathia,
    • Helene Braun,
    • Udo Georgi,
    • Hans Lehrach,
    • Martin Vingron,
    • Albert J. Poustka,
    • and Georgia Panopoulou
    Genome Res. November 2009 19: 2036-2051; Published in Advance August 24, 2009, doi:10.1101/gr.093237.109
    ...). To determine which PCNEs have enhancer activity, we compare the number of GFP expressing embryos observed when injected with each PCNE to the number observed in injections with the GFP vector alone, and assess the significance of any difference with a conservative statistical test (Williams-corrected G...
  6. ARTICLE: The Genexpress Index: a resource for gene discovery and the genic map of the human genome.
    • R Houlgatte,
    • R Mariage-Samson,
    • S Duprat,
    • A Tessier,
    • S Bentolila,
    • B Lamy,
    • and C Auffray
    Genome Res. October 1995 5: 272-304; doi:10.1101/gr.5.3.272
    .... and Myers. R.M. 1994 . Assessing mapping progress in the human project. Science 265 : 2031 – 2032 . Davies, R.W., Roberts, A.B. Morris, A.J. Griffith, G.W. Jerecic, J. Ghandi, S. Kaiser, K. and Savioz. A. 1994 . Enhanced access to rare brain cDNAs by prescreening libraries: 207 new mouse brain ESTs...
  7. Research: Identification of FMR1-regulated molecular networks in human neurodevelopment
    • Meng Li,
    • Junha Shin,
    • Ryan D. Risgaard,
    • Molly J. Parries,
    • Jianyi Wang,
    • Deborah Chasman,
    • Shuang Liu,
    • Sushmita Roy,
    • Anita Bhattacharyya,
    • and Xinyu Zhao
    Genome Res. March 2020 30: 361-374; Published in Advance March 16, 2020, doi:10.1101/gr.251405.119
    ...as absence of the neuroepithelial marker PAX6 (Supplemental Fig. S1C,D). Off-target CRISPR mutations at the top five predicted sites in the FMR1-FLAG hPSC lines were examined by Sanger sequencing, and no off-target mutations were detected (Supplemental Fig. S1E).View larger version: In this window In a new...
  8. Research: Noncoding origins of anthropoid traits and a new null model of transposon functionalization
    • Ricardo C.H. del Rosario,
    • Nirmala Arul Rayan,
    • and Shyam Prabhakar
    Genome Res. September 2014 24: 1469-1484; Published in Advance July 20, 2014, doi:10.1101/gr.168963.113
    ...functional in the neural retina and dorsal spinal cord, which are again involved in neurogenesis. In order to uncover the target gene of ASC192, we used the 3C assay, which probes for physical interactions between the enhancer and flanking regions (Hag#3;ege et al. 2007). Human brain tissue is inaccessible...
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  9. Resource: The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
    • Stefan Schoenfelder,
    • Mayra Furlan-Magaril,
    • Borbala Mifsud,
    • Filipe Tavares-Cadete,
    • Robert Sugar,
    • Biola-Maria Javierre,
    • Takashi Nagano,
    • Yulia Katsman,
    • Moorthy Sakthidevi,
    • Steven W. Wingett,
    • Emilia Dimitrova,
    • Andrew Dimond,
    • Lucas B. Edelman,
    • Sarah Elderkin,
    • Kristina Tabbada,
    • Elodie Darbo,
    • Simon Andrews,
    • Bram Herman,
    • Andy Higgs,
    • Emily LeProust,
    • Cameron S. Osborne,
    • Jennifer A. Mitchell,
    • Nicholas M. Luscombe,
    • and Peter Fraser
    Genome Res. April 2015 25: 582-597; Published in Advance March 9, 2015, doi:10.1101/gr.185272.114
    ...control (Bulger andGroudine 2011). For example, developmental enhancers can be located at considerable genomic distances from the gene promoters they regulate, often bypassing several promoters located in the intervening DNA sequence to interact with their target genes (Carvajal et al. 2001; Carter et al...
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  10. Research: Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting
    • Phil Arnold,
    • Anne Schöler,
    • Mikhail Pachkov,
    • Piotr J. Balwierz,
    • Helle Jørgensen,
    • Michael B. Stadler,
    • Erik van Nimwegen,
    • and Dirk Schübeler
    Genome Res. January 2013 23: 60-73; Published in Advance September 10, 2012, doi:10.1101/gr.142661.112
    ...by the Polycomb repressive complex 2 (PRC2). The protein enhancer of zeste homolog 2 (EZH2) catalyzes the methylation of H3K27 as part of PRC2 (Czermin et al. 2002;Muller et al. 2002) and it is required for differentiation and reprogramming (O’Carroll et al. 2001; Pereira et al. 2010). Target genes include...
    OPEN ACCESS ARTICLE
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