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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
...tissues (false discovery rate 5%) by using Genotype-Tissue expression (GTex) Project data. Regression models explaining splicing variation by using spl-TRs and other flanking variants suggest that at least some of the spl-TRs directly modulate splicing. In our catalog, two spl-TRs are known loci...
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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
...Ranking noncanonical 5′ splice site usage by -wide RNA-seq analysis and splicing reporter assays Steffen Erkelenz1,4,5, Stephan Theiss2,4, Wolfgang Kaisers3, Johannes Ptok1, Lara Walotka1, Lisa Müller1, Frank Hillebrand1, Anna-Lena Brillen1, Michael Sladek1 and Heiner Schaal1 1Institute of Virology...
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Method: LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq
- Danny A. Bitton,
- Charalampos Rallis,
- Daniel C. Jeffares,
- Graeme C. Smith,
- Yuan Y.C. Chen,
- Sandra Codlin,
- Samuel Marguerat,
- and Jürg Bähler
Genome Res. July 2014 24: 1169-1179; Published in Advance April 7, 2014, doi:10.1101/gr.166819.113
...LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq Danny A. Bitton , Charalampos Rallis , Daniel C. Jeffares , Graeme C. Smith , Yuan Y.C. Chen 1 , Sandra Codlin , Samuel Marguerat 2...
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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
...-rich small nuclear RNA (snRNA). The U1 and U2 snRNAs are responsible for recognizing the 5′ splice site and branchpoint upstream of the 3′ splice site, followed by the U4/U6.U5 tri-snRNP joining the spliceosome before the rearrangements that ultimately lead to the U6 snRNA catalyzing the actual splicing...
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Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
...level using a χ2 contingency test (Supplemental Fig. S4D,E). Hereafter we refer to intron groups with a Euclidean distance >0.379 and χ2 test false discovery rate (FDR) < 0.05 for at least one splicing level as displaying “allele-specific splicing order.”More than half of intron groups displaying allele...
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PERSPECTIVE: Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
- W. Brad Barbazuk,
- Yan Fu,
- and Karen M. McGinnis
Genome Res. September 2008 18: 1381-1392; Published in Advance July 30, 2008, doi:10.1101/gr.053678.106
...Genome-wide analyses of alternative splicing in plants: Opportunities and challenges W. Brad Barbazuk 1 , 3 , 4 , Yan Fu 1 , and Karen M. McGinnis 2 1 Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA; 2...
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Research: Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs
- Marta Melé,
- Kaia Mattioli,
- William Mallard,
- David M. Shechner,
- Chiara Gerhardinger,
- and John L. Rinn
Genome Res. January 2017 27: 27-37; Published in Advance December 7, 2016, doi:10.1101/gr.214205.116
...al. 2015. The human transcriptome across tissues and individuals. Science 348: 660–665. Mercer TR, Clark MB, Andersen SB, Brunck ME, Haerty W, Crawford J, Taft RJ, Nielsen LK, Dinger ME, Mattick JS. 2015. Genome-wide discovery of human splicing branchpoints. Genome Res 25: 290–303. Necsulea A...
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Methods: Genome-wide identification of spliced introns using a tiling microarray
- Zhihong Zhang,
- Jay R. Hesselberth,
- and Stanley Fields
Genome Res. April 2007 17: 503-509; Published in Advance March 9, 2007, doi:10.1101/gr.6049107
...Genome-wide identification of spliced introns using a tiling microarray Zhihong Zhang 1 , 2 , 3 , Jay R. Hesselberth 2 , 3 , and Stanley Fields 1 , 2 , 4 1 Howard Hughes Medical Institute, University of Washington, Seattle, Washington...
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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
...5′ splice site (5′ ss) and branchpoint site (BP). However, there are some examples where the pairing of sites is assisted by intramolecular secondary structure in the intron (Goguel and Rosbash 1993; Libri et al. 1995; Charpentier and Rosbash 1996; Howe and Ares 1997; Spingola et al. 1999...
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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
....DiscussionMany damaging variants responsible for inherited predisposition to cancer alter transcription by introducing or destroying splice sites, leading to premature translation termination. These effects can be caused by variants at or near canonical splice sites, at exonic enhancers, at intronic branchpoints...

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