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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...based on global splicing profiles, using the PSI of exons quantified in all samples. We found that alternatively spliced exons differed in the PCA between KCl and control splicing profiles after 2 and 5 h, but not 30 min, of KCl treatment (Fig. 1E). We then assessed which facet of the data sets drove...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...expression and alternative splicing, thus impacting complex traits and phenotypes (Teng et al. 2024).Our comparative analysis across species revealed both conserved and species-specific aspects of APA regulation. In neuronal and germline cells, APA dynamics were remarkably conserved across evolution, from...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...chromosomes with highly similar gene content, or long-term conservation of the X Chromosome. Differentiating these alternatives phylogenetically would require X and Y Chromosome orthologs, which our species lacks as it is X0. Notably, the 800 Mb grasshopper X Chromosome shares significant gene content...
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Resource: Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish
- Alice S. Naftaly,
- Shana Pau,
- and Michael A. White
Genome Res. August 2021 31: 1486-1497; Published in Advance June 15, 2021, doi:10.1101/gr.274282.120
...it possible to sequence full-length alternative transcripts, accurately characterizing alternative splicing events, alternate transcription start and end sites, and differences in UTR regions. Here, we use Pacific Biosciences (PacBio) long-read RNA-sequencing (Iso-Seq) to examine the transcriptomes of five...
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Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
...system. Alternative splicing events differentially regulated between tissues are more often frame-preserving, are more highly conserved across Caenorhabditis species, and are enriched in specific cis regulatory motifs, when compared with other types of exons. By using this information, we have identified...
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Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
- Étienne Fafard-Couture,
- Pierre-Étienne Jacques,
- and Michelle S. Scott
Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
...RNAs) are structured noncoding RNAs present in multiple copies within eukaryotic s. snoRNAs guide chemical modifications on their target RNA and regulate processes like ribosome assembly and splicing. Most human snoRNAs are embedded within host gene introns, the remainder being independently expressed from intergenic...
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Research: RBFOX splicing factors contribute to a broad but selective recapitulation of peripheral tissue splicing patterns in the thymus
- Kathrin Jansen,
- Noriko Shikama-Dorn,
- Moustafa Attar,
- Stefano Maio,
- Maria Lopopolo,
- David Buck,
- Georg A. Holländer,
- and Stephen N. Sansom
Genome Res. November 2021 31: 2022-2034; Published in Advance October 14, 2021, doi:10.1101/gr.275245.121
...the generation of long “classical” transcripts (with 5′ and 3′ UTRs) but has only a limited impact on alternative splicing in mTEC. Comprehensive assessment of SF expression in mTEC identified a small set of nonpromiscuously expressed SF genes, among which we confirmed RBFOX to be present with AIRE in m...
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Research: Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
- Swati Venkat,
- Arwen A. Tisdale,
- Johann R. Schwarz,
- Abdulrahman A. Alahmari,
- H. Carlo Maurer,
- Kenneth P. Olive,
- Kevin H. Eng,
- and Michael E. Feigin
Genome Res. March 2020 30: 347-360; Published in Advance February 6, 2020, doi:10.1101/gr.257550.119
...through modulation of available regulatory miRNA binding sites.APA-mediated loss of tumor-suppressive miRNA binding sites is associated with poor patient outcomeTo assess global patterns of APA-mediated miRNA binding site loss, we searched for highly conserved miRNA binding sites (conserved across human...
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Method: The dynamic landscape of fission yeast meiosis alternative-splice isoforms
- Zheng Kuang,
- Jef D. Boeke,
- and Stefan Canzar
Genome Res. January 2017 27: 145-156; Published in Advance November 17, 2016, doi:10.1101/gr.208041.116
...the number of reads matching annotated antisense isoforms (Fig. 4E). Therefore, there was potentially a mix of real antisense isoforms and transcriptional noise. Furthermore, we examined the conserved intronic Figure 4. Landscape of alternative splicing events during S. pombe meiosis. (A) Pie chart showing...
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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
...-intron boundary (registered in the RefSeq database), in which normal splicing is disrupted (SS disruption), or (2) a somatic variant located within a newly created SS inferred by an alternative SS usage event (SS creation). To represent the complex relationships, we constructed a bipartite graph showing all...

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