Searching journal content for articles similar to Howard et al. 28 (5): 689.

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  1. Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
    • Daffodil M. Canson,
    • Michael T. Parsons,
    • Gemma Moir-Meyer,
    • Troy Dumenil,
    • Gemma Montalban,
    • Erica Lin,
    • Terri P. McVeigh,
    • Aimee L. Davidson,
    • Shaun M. Bouckaert,
    • Matt Trau,
    • Darren Korbie,
    • and Amanda B. Spurdle
    Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
    ...constructs also incorporated longer flanking intronic sequences, enabling capture of additional splicing signals that could influence splice site recognition.The SeqSplice method was sensitive to detect splice-altering variants irrespective of the produced specific aberrant transcript. Therefore, SeqSplice...
  2. Research: In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors
    • F.X. Reymond Sutandy,
    • Stefanie Ebersberger,
    • Lu Huang,
    • Anke Busch,
    • Maximilian Bach,
    • Hyun-Seo Kang,
    • Jörg Fallmann,
    • Daniel Maticzka,
    • Rolf Backofen,
    • Peter F. Stadler,
    • Kathi Zarnack,
    • Michael Sattler,
    • Stefan Legewie,
    • and Julian König
    Genome Res. May 2018 28: 699-713; Published in Advance April 11, 2018, doi:10.1101/gr.229757.117
    ...are either not regulated or cleared in vivo (Fig. 3C; Supplemental Fig. S3A). The widespread clearance supports the existence of proofreading mechanisms that suppress the recognition of cryptic sites to ensure accurate splicing. In addition, we observe a substantial number of stabilized U2AF2 binding sites...
  3. Research: U2AF1 mutations alter splice site recognition in hematological malignancies
    • Janine O. Ilagan,
    • Aravind Ramakrishnan,
    • Brian Hayes,
    • Michele E. Murphy,
    • Ahmad S. Zebari,
    • Philip Bradley,
    • and Robert K. Bradley
    Genome Res. January 2015 25: 14-26; Published in Advance September 29, 2014, doi:10.1101/gr.181016.114
    ...AG|r (Fig. 1B), which matches the genomic consensus 39 splice site and intron|exon boundary that crosslinks with U2AF1 (Wu et al. 1999). Nevertheless, our understanding of U2AF1:RNA interactions is incomplete. U2AF1’s U2AF homologymotif (UHM) is known tomediate U2AF1: U2AF2 heterodimer formation (Kielkopf...
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  4. Research: Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists
    • Marcin P. Sajek,
    • Danielle Y. Bilodeau,
    • Michael A. Beer,
    • Emma Horton,
    • Yukiko Miyamoto,
    • Katrina B. Velle,
    • Lars Eckmann,
    • Lillian Fritz-Laylin,
    • Olivia S. Rissland,
    • and Neelanjan Mukherjee
    Genome Res. October 2024 34: 1570-1581; Published in Advance September 26, 2024, doi:10.1101/gr.279526.124
    ...found that G. lamblia assemblage A does not use any known auxiliary element (Bilodeau et al. 2022), highlighting the potential diversity of cleavage site recognition within the eukaryotic tree.View larger version: In this window In a new window Figure 1. Characterization of poly(A) signals in diverse...
  5. Research: RNA structure replaces the need for U2AF2 in splicing
    • Chien-Ling Lin,
    • Allison J. Taggart,
    • Kian Huat Lim,
    • Kamil J. Cygan,
    • Luciana Ferraris,
    • Robbert Creton,
    • Yen-Tsung Huang,
    • and William G. Fairbrother
    Genome Res. January 2016 26: 12-23; Published in Advance November 13, 2015, doi:10.1101/gr.181008.114
    ...of (AC)m-(GT)n intron splicing in vivo, morpholino oligo injection was used to block the translation of U2AF2 paralogs in zebrafish embryos. Zebrafish carries two U2af2 homologs, U2af2a and U2af2b. These paralogs share 88% sequence identity; they both encode three RNA-recognition motifs (RRMs), a U2AF...
  6. Research: Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation
    • Jack A. Collora and
    • Ya-Chi Ho
    Genome Res. June 9, 2023 gr.277698.123; Published in Advance June 9, 2023, doi:10.1101/gr.277698.123
    ...aberrant HIV-1-to-host RNA splicing as 13 seen in vivo (Liu et al. 2020). Using four cell line clones as biological replicates enables us to interrogate how 14 different HIV-1 integration sites impact HIV-1-host chromatin interactions. 15 16 17 HIV-1 proviral chromatin accessibility correlates with host...
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  7. Research: Ranking noncanonical 5′ splice site usage by genome-wide RNA-seq analysis and splicing reporter assays
    • Steffen Erkelenz,
    • Stephan Theiss,
    • Wolfgang Kaisers,
    • Johannes Ptok,
    • Lara Walotka,
    • Lisa Müller,
    • Frank Hillebrand,
    • Anna-Lena Brillen,
    • Michael Sladek,
    • and Heiner Schaal
    Genome Res. December 2018 28: 1826-1840; Published in Advance October 24, 2018, doi:10.1101/gr.235861.118
    ...clinical disease manifestation in Fanconi Anemia C patients (Hartmann et al. 2010), underlining the clinical importance of noncanonical splice site recognition.Extensive sequence complementarity between splice junctions in hnRNA molecules and the nucleotide sequence at the 5′ end of U1 snRNA was already...
  8. Method: ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease
    • Riccardo Sangermano,
    • Mubeen Khan,
    • Stéphanie S. Cornelis,
    • Valerie Richelle,
    • Silvia Albert,
    • Alejandro Garanto,
    • Duaa Elmelik,
    • Raheel Qamar,
    • Dorien Lugtenberg,
    • L. Ingeborgh van den Born,
    • Rob W.J. Collin,
    • and Frans P.M. Cremers
    Genome Res. January 2018 28: 100-110; Published in Advance November 21, 2017, doi:10.1101/gr.226621.117
    ...of a strong RHO splice donor and acceptor site, as we observed erroneous exon skipping in MG_ex40 (Fig. 1).Natural skipping of ABCA4 exons 3, 15, and 39/40 was observed by others (Braun et al. 2013) and by us (Supplemental Fig. S2), suggesting that the midigenes mimic the in vivo situation. An accurate...
  9. Method: Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models
    • Dalibor Miklík,
    • Jiří Grim,
    • Daniel Elleder,
    • and Jiří Hejnar
    Genome Res. August 2023 33: 1395-1408; Published in Advance July 18, 2023, doi:10.1101/gr.277694.123
    ...of the preferred nucleotide at one half-site of tDNA can increase the chances of the less preferred nucleotide appearing at the other half-site of tDNA. We thus consider the model in which triggering the strand transfer reaction after tDNA recognition by IN can act asymmetrically.In vitro experiments suggested...
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  10. Research: Base-specific mutational intolerance near splice sites clarifies the role of nonessential splice nucleotides
    • Sidi Zhang,
    • Kaitlin E. Samocha,
    • Manuel A. Rivas,
    • Konrad J. Karczewski,
    • Emma Daly,
    • Ben Schmandt,
    • Benjamin M. Neale,
    • Daniel G. MacArthur,
    • and Mark J. Daly
    Genome Res. July 2018 28: 968-974; Published in Advance June 1, 2018, doi:10.1101/gr.231902.117
    ...databases might be relatively benign owing to the availability of a suitable backup splice site, and thus not additionally punished by the presence of a second mutation.One of the first steps of the splicing process is the recognition of 5′ss by U1 snRNP, which is one of the five snRNPs making up...
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