Searching journal content for articles similar to Friedman et al. 18 (10): 1643.

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  1. Research: Reactivation of transposable elements following hybridization in fission yeast
    • Sergio Tusso,
    • Fang Suo,
    • Yue Liang,
    • Li-Lin Du,
    • and Jochen B.W. Wolf
    Genome Res. February 2022 32: 324-336; Published in Advance December 14, 2021, doi:10.1101/gr.276056.121
    ...present in both ancestral backgrounds. However, the functional significance of this insertion is not clear and warrants future experimental exploration.Overall, this study offers a comprehensive characterization of the global diversity of transposable elements in S. pombe. Phylogenetic and population...
  2. Methods: A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data—A case study using E2F1
    • Victor X. Jin,
    • Alina Rabinovich,
    • Sharon L. Squazzo,
    • Roland Green,
    • and Peggy J. Farnham
    Genome Res. December 2006 16: 1585-1595; Published in Advance October 19, 2006, doi:10.1101/gr.5520206
    ...mechanisms in different species. The other improvement expands the analysis beyond the search for a single motif to the identification of cis -regulatory modules (CRMs) and is based on the concept that the biochemical specificity of transcription is generated by combinatorial interactions between...
  3. Method: Quantitative evaluation of all hexamers as exonic splicing elements
    • Shengdong Ke,
    • Shulian Shang,
    • Sergey M. Kalachikov,
    • Irina Morozova,
    • Lin Yu,
    • James J. Russo,
    • Jingyue Ju,
    • and Lawrence A. Chasin
    Genome Res. August 2011 21: 1360-1374; Published in Advance June 9, 2011, doi:10.1101/gr.119628.110
    ...Quantitative evaluation of all hexamers as exonic splicing elements Shengdong Ke 1 , Shulian Shang 1 , 4 , Sergey M. Kalachikov 2 , 3 , Irina Morozova 2 , 3 , Lin Yu 2 , 3 , James J. Russo 2 , 3 , Jingyue Ju 2 , 3...
  4. Letter: Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts
    • Jeremy R. Sanford,
    • Xin Wang,
    • Matthew Mort,
    • Natalia VanDuyn,
    • David N. Cooper,
    • Sean D. Mooney,
    • Howard J. Edenberg,
    • and Yunlong Liu
    Genome Res. March 2009 19: 381-394; Published in Advance December 30, 2008, doi:10.1101/gr.082503.108
    ...) together. Inclusion of an exon into the mature mRNA is regulated by cis -acting RNA elements known as exonic or intronic splicing enhancers and silencers (ESE, ISE, and ESS, ISS, respectively) that function to recruit trans -acting RNA-binding proteins. In the cytoplasm, these same RNA elements are decoded...
  5. Research: NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors
    • Joseph D. Fleming,
    • Giulio Pavesi,
    • Paolo Benatti,
    • Carol Imbriano,
    • Roberto Mantovani,
    • and Kevin Struhl
    Genome Res. August 2013 23: 1195-1209; Published in Advance April 17, 2013, doi:10.1101/gr.148080.112
    ...immunoprecipitation (ChIP), formaldehyde-assisted isolation of regulatory elements (FAIRE), and DNase I hypersensitivity techniques coupled to massively parallel DNA sequencing, such classification of functional genomic regions has been done in several cell lines in the context of ENCODE (The ENCODE Project...
  6. LETTER: Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches
    • Victor X. Jin,
    • Henriette O’Geen,
    • Sushma Iyengar,
    • Roland Green,
    • and Peggy J. Farnham
    Genome Res. June 2007 17: 807-817; doi:10.1101/gr.6006107
    ...identification and experimental confirmation of a common set of OCT4 and SRY targets demonstrate that our ChIPMotifs and ChIPModules approaches can work in concert to efficiently mine ChIP-chip data, allowing the development of de novo motifs and the identification of new cis -regulatory modules. Importantly...
    OPEN ACCESS ARTICLE
  7. Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
    • Yuan Lu,
    • Edward Rice,
    • Kang Du,
    • Susanne Kneitz,
    • Magali Naville,
    • Corentin Dechaud,
    • Jean-Nicolas Volff,
    • Mikki Boswell,
    • William Boswell,
    • LaDeana Hillier,
    • Chad Tomlinson,
    • Kremitzki Milin,
    • Ronald B. Walter,
    • Manfred Schartl,
    • and Wesley C. Warren
    Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
    ...) and their interspecies hybrids (Lu et al. 2015). Differences between species appeared mainly owing to cis-regulatory elements, whereas changes in trans-regulatory elements and/or the interaction of both cis- and trans-effects were also shown to play important roles (Lu et al. 2018). However, -wide structural...
  8. Resource: Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis
    • Chirag Nepal,
    • Yavor Hadzhiev,
    • Christopher Previti,
    • Vanja Haberle,
    • Nan Li,
    • Hazuki Takahashi,
    • Ana Maria M. Suzuki,
    • Ying Sheng,
    • Rehab F. Abdelhamid,
    • Santosh Anand,
    • Jochen Gehrig,
    • Altuna Akalin,
    • Christel E.M. Kockx,
    • Antoine A.J. van der Sloot,
    • Wilfred F.J. van IJcken,
    • Olivier Armant,
    • Sepand Rastegar,
    • Craig Watson,
    • Uwe Strähle,
    • Elia Stupka,
    • Piero Carninci,
    • Boris Lenhard,
    • and Ferenc Müller
    Genome Res. November 2013 23: 1938-1950; Published in Advance September 3, 2013, doi:10.1101/gr.153692.112
    ...to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in different physiological and developmental contexts. Here, we provide a first and comprehensive description of the core promoter repertoire...
  9. Method: ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs
    • Piotr J. Balwierz,
    • Mikhail Pachkov,
    • Phil Arnold,
    • Andreas J. Gruber,
    • Mihaela Zavolan,
    • and Erik van Nimwegen
    Genome Res. May 2014 24: 869-884; Published in Advance February 10, 2014, doi:10.1101/gr.169508.113
    ...regulators ab initio. We also present a number of novel predictions including regulatory interactions in innate immunity, a master regulator of mucociliary differentiation, TFs consistently disregulated in cancer, and TFs that mediate specific chromatin modifications. Footnotes ↵ 1...
    OPEN ACCESS ARTICLE
  10. Method: New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes
    • Brian J. Parker,
    • Ida Moltke,
    • Adam Roth,
    • Stefan Washietl,
    • Jiayu Wen,
    • Manolis Kellis,
    • Ronald Breaker,
    • and Jakob Skou Pedersen
    Genome Res. November 2011 21: 1929-1943; Published in Advance October 12, 2011, doi:10.1101/gr.112516.110
    ...) and since one of these families is in glutamate receptor genes, already known to harbor several exonic sites, these hairpins are also candidate intronic editing sites, which may change the function of splicing enhancers or other cis-regulatory elements. Alternatively, they may be involved in regulation...
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