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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...is associated with gene regulation. Although previous studies reported several tandem repeats regulating gene splicing in cis (spl-TRs), no large-scale study has been conducted. In this study, we established a -wide catalog of 9537 spl-TRs with a total of 58,290 significant TR–splicing associations across 49...
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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
...), individual genes have different expression levels. In order to compare splice site usage across genes, detected exon junction reads need to be separately normalized within each gene by the expression level of this particular gene in the studied cell type.To obtain estimates for gene expression, we determined...
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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
..., particularly for variants that induce new or cryptic splice site usage. Here, we present SeqSplice, a high-throughput RNA splicing methodology utilizing barcoded minigene constructs together with a bespoke bioinformatics pipeline for identifying and quantifying the impacts for splice-altering variants. Seq...
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Resource: Genome-wide discovery of human splicing branchpoints
- Tim R. Mercer,
- Michael B. Clark,
- Stacey B. Andersen,
- Marion E. Brunck,
- Wilfried Haerty,
- Joanna Crawford,
- Ryan J. Taft,
- Lars K. Nielsen,
- Marcel E. Dinger,
- and John S. Mattick
Genome Res. February 2015 25: 290-303; Published in Advance January 5, 2015, doi:10.1101/gr.182899.114
...-PCR amplification followed by Sanger sequencing was also performed to independently confirm the location of 10 branchpoint nucleotides (Supplemental Fig. 3F). Branchpoint features This first large-scale experimental annotation of branchpoints afforded an opportunity for the global analysis of branchpoint features...
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Research: RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing
- Heidi Dvinge,
- Jamie Guenthoer,
- Peggy L. Porter,
- and Robert K. Bradley
Genome Res. October 2019 29: 1591-1604; Published in Advance August 21, 2019, doi:10.1101/gr.246678.118
...enable these RNAs to regulate alternative splicing. However, it is unknown whether such variation occurs in healthy cells. Only 100–200 nt in length, snRNAs are not detected by most large-scale assays routinely used in functional genomics (e.g., microarrays and most RNA-seq protocols), unless those...
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Research: Pathogenicity and selective constraint on variation near splice sites
- Jenny Lord,
- Giuseppe Gallone,
- Patrick J. Short,
- Jeremy F. McRae,
- Holly Ironfield,
- Elizabeth H. Wynn,
- Sebastian S. Gerety,
- Liu He,
- Bronwyn Kerr,
- Diana S. Johnson,
- Emma McCann,
- Esther Kinning,
- Frances Flinter,
- I. Karen Temple,
- Jill Clayton-Smith,
- Meriel McEntagart,
- Sally Ann Lynch,
- Shelagh Joss,
- Sofia Douzgou,
- Tabib Dabir,
- Virginia Clowes,
- Vivienne P.M. McConnell,
- Wayne Lam,
- Caroline F. Wright,
- David R. FitzPatrick,
- Helen V. Firth,
- Jeffrey C. Barrett,
- Matthew E. Hurles,
- and on behalf of the Deciphering Developmental Disorders study
Genome Res. February 2019 29: 159-170; Published in Advance December 26, 2018, doi:10.1101/gr.238444.118
...), their utility for other splice relevant regions is less clear (Tang et al. 2016). In the clinical setting, often multiple algorithms and expert judgment are used to predict pathogenicity, whereas for large-scale research projects, the classification of variants is often binary, with CSS mutations typically...
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Method: Quantifying full-length circular RNAs in cancer
- Ken Hung-On Yu,
- Christina Huan Shi,
- Bo Wang,
- Savio Ho-Chit Chow,
- Grace Tin-Yun Chung,
- Raymond Wai-Ming Lung,
- Ke-En Tan,
- Yat-Yuen Lim,
- Anna Chi-Man Tsang,
- Kwok-Wai Lo,
- and Kevin Y. Yip
Genome Res. December 2021 31: 2340-2353; Published in Advance October 18, 2021, doi:10.1101/gr.275348.121
...in quantifying the expression levels of full-length circRNA isoforms. Because large-scale experimental data of full-length circRNA expression levels based on short-read RNA-seq data alone are not available, we first performed this evaluation using two sets of simulated data (Supplemental Methods). We benchmarked...
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Research: A comprehensive characterization of cis-acting splicing-associated variants in human cancer
- Yuichi Shiraishi,
- Keisuke Kataoka,
- Kenichi Chiba,
- Ai Okada,
- Yasunori Kogure,
- Hiroko Tanaka,
- Seishi Ogawa,
- and Satoru Miyano
Genome Res. August 2018 28: 1111-1125; Published in Advance July 16, 2018, doi:10.1101/gr.231951.117
...1, GATA3, and CDKN2A, which offers genetic clues for understanding their functional properties. Collectively, our findings delineate a comprehensive portrait of SAVs, novel insights into transcriptional de-regulation in cancer.Comprehensive genomic characterization of multiple cancer types in large-scale...
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Resource: Regulation of alternative splicing in Drosophila by 56 RNA binding proteins
- Angela N. Brooks,
- Michael O. Duff,
- Gemma May,
- Li Yang,
- Mohan Bolisetty,
- Jane Landolin,
- Ken Wan,
- Jeremy Sandler,
- Benjamin W. Booth,
- Susan E. Celniker,
- Brenton R. Graveley,
- and Steven E. Brenner
Genome Res. November 2015 25: 1771-1780; Published in Advance August 20, 2015, doi:10.1101/gr.192518.115
...with each other, not antagonistically. We also identified a cross-regulatory network where splicing regulators affected the splicing of pre-mRNAs encoding other splicing regulators. This large-scale study substantially enhances our understanding of recent models of splicing regulation and provides...
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Research: Evolution of splicing regulatory networks in Drosophila
- C. Joel McManus,
- Joseph D. Coolon,
- Jodi Eipper-Mains,
- Patricia J. Wittkopp,
- and Brenton R. Graveley
Genome Res. May 2014 24: 786-796; Published in Advance February 10, 2014, doi:10.1101/gr.161521.113
...skipping may reflect a higher complexity of SE regulatory networks. The relative contributions of cisand trans-regulatory differences to splicing divergence are still debated. While large-scale studies have reported different conclusions regarding the role of cis-regulatory changes in SE regulation (Irimia...

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