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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
...splicing as well as transcript abundance when interpreting the impact of neuronal activity on the transcriptome.Given the vast complexity of cell types in the brain, direct stimulation of primary neurons in culture provides a powerful means through which to characterize the mechanisms that may contribute...
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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...in a dedicated resource.Gene architecture in eukaryotes facilitates generation of more than one mRNA per gene through a differential combination of exons. The exonic region determination is under regulation of several co- and post-transcriptional mechanisms, in which alternative splicing (AS) plays a central...
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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
..., and translation efficiency. In contrast, ALE-APA results from multiple PASs located in alternative terminal exons, which could lead to the production of truncated protein isoforms (Mariella et al. 2019; Goering et al. 2021). These alternatively polyadenylated mRNAs greatly expand the diversity of transcripts...
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Method: Assessing conservation of alternative splicing with evolutionary splicing graphs
- Diego Javier Zea,
- Sofya Laskina,
- Alexis Baudin,
- Hugues Richard,
- and Elodie Laine
Genome Res. August 2021 31: 1462-1473; Published in Advance June 15, 2021, doi:10.1101/gr.274696.120
...underscore AS functional impact and contribution to protein diversity (Agosto et al. 2019; Marti-Solano et al. 2020).Evolutionary conservation can arguably serve as a reliable indicator of function. Indeed, we expect splice variants selected over millions of years of evolution to comply with physical...
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Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
- Yongkang Long,
- Bin Zhang,
- Shuye Tian,
- Jia Jia Chan,
- Juexiao Zhou,
- Zhongxiao Li,
- Yisheng Li,
- Zheng An,
- Xingyu Liao,
- Yu Wang,
- Shiwei Sun,
- Ying Xu,
- Yvonne Tay,
- Wei Chen,
- and Xin Gao
Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
...rate (FPR) ranges from 30% to 50% (Shah et al. 2021). In addition, these computational methods mainly focus on APA within 3′ UTR. This might be due to the fact that drop of RNA-seq coverage across exon–intron boundaries impacts their detection of splicing-coupled APA, such as intronic polyadenylation...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...on the complexity of the transcriptome of this model eukaryotic species.Nanopore dRNA-seq starts from the 3′-end of the molecule, capturing the full-length poly(A) tail of each RNA. This enables the investigation of poly(A) tail variation among different transcripts and individual mRNA molecules (Workman et al...
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Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
...the SF3B1–mRNA interaction. Thus, although mutated SF3B1 still binds to both sides of the BP in this scenario, the changed SF3B1 protein structure reduces usage of the downstream AG, resulting in widespread splicing defects.DiscussionAlternative splicing plays a critical role in generating transcriptome...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...the characterization of mRNA terminal ends. Although analytical tools have been proposed to correct for some of these challenges when characterizing internal exons (Amarasinghe et al. 2020; Tang et al. 2020; Chen et al. 2023), it remains unclear how these and/or other technical challenges may uniquely impact terminal...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
...more stable, with a half-life of 62 min (vs. 28.6 min for mep-1).These results suggest that mRNA degradation may contribute to the protein dynamics of developmental regulators. In many cases, the regulation of transcription and mRNA decay appear to act in concert to have a coherent impact...
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Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
- Ju Heon Maeng,
- H. Josh Jang,
- Alan Y. Du,
- Shin-Cheng Tzeng,
- and Ting Wang
Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
.... Cells were harvested by trypsin dissociation for long-read CAGE and nanoCAGE library preparation and by scraping for HLA-I pulldown experiment.Library preparation of LRCAGE, LRhex, and nanoCAGETo enrich our RNA samples for reverse transcription with full-length mRNA, we added two additional steps, poly...
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