Searching journal content for articles similar to Gelfman et al. 23 (5): 789.

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  1. Research: GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium
    • Stefano Gnan,
    • Mélody Matelot,
    • Marion Weiman,
    • Olivier Arnaiz,
    • Frédéric Guérin,
    • Linda Sperling,
    • Mireille Bétermier,
    • Claude Thermes,
    • Chun-Long Chen,
    • and Sandra Duharcourt
    Genome Res. April 2022 32: 699-709; Published in Advance March 9, 2022, doi:10.1101/gr.276125.121
    ...), suggesting a functional role of nucleosome arrays during mRNA maturation. This is in agreement with recent studies showing that intron splicing can occur in a cotranscriptional manner (Brody et al. 2011; Herzel et al. 2017). Some studies have suggested that GC richness at exons, and not nucleosome...
  2. Research: Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons
    • Sahar Gelfman,
    • David Burstein,
    • Osnat Penn,
    • Anna Savchenko,
    • Maayan Amit,
    • Schraga Schwartz,
    • Tal Pupko,
    • and Gil Ast
    Genome Res. January 2012 22: 35-50; Published in Advance October 5, 2011, doi:10.1101/gr.119834.110
    ...Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons Sahar Gelfman 1 , David Burstein 2 , Osnat Penn 2 , Anna Savchenko 1 , Maayan Amit 1 , Schraga Schwartz 1 , 4 , Tal Pupko 2...
  3. Research: Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate
    • Gilad Fuchs,
    • Dror Hollander,
    • Yoav Voichek,
    • Gil Ast,
    • and Moshe Oren
    Genome Res. October 2014 24: 1572-1583; Published in Advance July 21, 2014, doi:10.1101/gr.176487.114
    ...:1572–1583 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/14; www..org another study concluded that H2Bub1 is selectively enriched at exon–intron borders and proposed that this enrichment regulates the splicing of a subset of exons (Jung et al. 2012). In addition to H2Bub1, the gene body of active...
  4. Research: The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages
    • Musa A. Hassan,
    • Vincent Butty,
    • Kirk D.C. Jensen,
    • and Jeroen P.J. Saeij
    Genome Res. March 2014 24: 377-389; Published in Advance November 18, 2013, doi:10.1101/gr.166033.113
    ...splice sites, respectively (Wang et al. 2008), and sequence elements known as intronic/exonic splicing enhancers and silencers (Wang and Burge 2008; Lee et al. 2012). As such, genetic variation at the splice site, in the consensus sequences, or in the intronic/exonic enhancers and repressors may lead...
  5. Research: Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development
    • Sharmistha Pal,
    • Ravi Gupta,
    • Hyunsoo Kim,
    • Priyankara Wickramasinghe,
    • Valérie Baubet,
    • Louise C. Showe,
    • Nadia Dahmane,
    • and Ramana V. Davuluri
    Genome Res. August 2011 21: 1260-1272; Published in Advance June 28, 2011, doi:10.1101/gr.120535.111
    ...transcription or alternative splicing, we categorized alternative first exons (AFE) and alternative last exons (ALE) events as ‘‘transcriptional events’’ and exon skipping (ES), intron retention (IR), alternative 59 splice site (A5SS), and alternative 39 splice site (A3SS) events as ‘‘splicing event.’’ Only...
  6. Research: Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
    • Hagen Tilgner,
    • David G. Knowles,
    • Rory Johnson,
    • Carrie A. Davis,
    • Sudipto Chakrabortty,
    • Sarah Djebali,
    • João Curado,
    • Michael Snyder,
    • Thomas R. Gingeras,
    • and Roderic Guigó
    Genome Res. September 2012 22: 1616-1625; doi:10.1101/gr.134445.111
    ..., compared with 0.3% of exons for which no intron-removal has occurred. The remaining exons exist as a mixture of spliced and fewer unspliced molecules, with a median coSI of 0.75. Thus, most RNAs undergo splicing while being transcribed: “co-transcriptional splicing.” Consistent with co-transcriptional...
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  7. Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
    • Bertille Montibus,
    • James A. Cain,
    • Rocio T. Martinez-Nunez,
    • and Rebecca J. Oakey
    Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
    ...and ∼20% of nested genes span both an intron and an exon (Supplemental Fig. S1B). The remaining overlap with exonic sequences and 3%–5% of nested genes are completely embedded within exons (Supplemental Fig. S1B). In this case, however, nested genes predominantly localized to the last exon of host genes...
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  8. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...as only one allele is expressed. Allele-specific DNA methylation and chromatin composition are two well-established epigenetic systems that control imprinted gene expression (Fournier et al. 2002; Singh et al. 2010; Prendergast et al. 2012).ASE can reflect differential rates of transcription, m...
  9. Research: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
    • Stefan Oberlin,
    • Alexis Sarazin,
    • Clément Chevalier,
    • Olivier Voinnet,
    • and Arturo Marí-Ordóñez
    Genome Res. September 2017 27: 1549-1562; Published in Advance August 7, 2017, doi:10.1101/gr.220723.117
    .../Copia elements based on multiple sequence alignment and the EVD termination site identified by 3′ RACE. By using those predictions together with the newly annotated introns, Ty1/Copia sequences where divided into four bins: (1) Exon 1 encompassing sequences from GAG up to the annotated splice donor site...
  10. Research: Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects
    • Jeremy M. Simon,
    • Kathryn E. Hacker,
    • Darshan Singh,
    • A. Rose Brannon,
    • Joel S. Parker,
    • Matthew Weiser,
    • Thai H. Ho,
    • Pei-Fen Kuan,
    • Eric Jonasch,
    • Terrence S. Furey,
    • Jan F. Prins,
    • Jason D. Lieb,
    • W. Kimryn Rathmell,
    • and Ian J. Davis
    Genome Res. February 2014 24: 241-250; Published in Advance October 24, 2013, doi:10.1101/gr.158253.113
    ..., including intron retention and aberrant splicing, affecting ∼25% of all expressed genes. Furthermore, decreased nucleosome occupancy proximal to misspliced exons was observed in tumors lacking H3K36me3. These results directly link mutations in SETD2 to chromatin accessibility changes and RNA processing...
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