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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
...Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs Qiuhan Wen1,2, Zhen Wang1, Qi Bao1, Tianli Ding1, Haihan Zhang3, Jianbo Li4, Zhuang Liu5, Jieping Huang2 and Guoqiang Yi1,6,7 1Shenzhen Branch, Guangdong Laboratory of Lingnan...
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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
.... Finally, applying APAIQ on 421 RNA-seq samples from liver cancer patients, we identified >540 tumor-associated APA events and experimentally validated two intronic polyadenylation candidates, demonstrating its capacity to unveil cancer-related APA with a large-scale RNA-seq data set.In eukaryotes...
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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...and AI Institute, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding author: ajbattle@jhu.eduAbstractGene coexpression networks (GCNs) describe relationships among genes that maintain cellular identity and homeostasis. However, typical RNA-seq experiments often lack sufficient sample...
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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...Evaluation of strategies for evidence-driven annotation using long-read RNA-seq Alejandro Paniagua1,2,6, Cristina Agustín-García1,6, Francisco J. Pardo-Palacios1, Thomas Brown3,4, Maite De Maria5, Nancy D. Denslow5, Camila J. Mazzoni3,4 and Ana Conesa1 1Institute for Integrative Systems Biology...
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Method: TransMeta simultaneously assembles multisample RNA-seq reads
- Ting Yu,
- Xiaoyu Zhao,
- and Guojun Li
Genome Res. July 2022 32: 1398-1407; Published in Advance July 20, 2022, doi:10.1101/gr.276434.121
...analyzes multiple RNA-seq samples and outputs a set of meta-annotations, as well as a set of transcripts for each sample. PsiCLASS uses statistical methods to build the global subexon graphs and generates the assembly by dynamic programming optimization and voting algorithms. Although it achieves higher...
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Method: Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression
- Yipeng Gao,
- Lei Li,
- Christopher I. Amos,
- and Wei Li
Genome Res. October 2021 31: 1856-1866; Published in Advance May 25, 2021, doi:10.1101/gr.271346.120
...developed dynamic analysis of alternative polyadenylation from scRNA-seq (scDaPars), a bioinformatics algorithm for quantifying and recovering APA usage at the single-cell and single-gene resolution using standard scRNA-seq data. Because APA is reported to be regulated in a cell-state- or cell...
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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
..., the poly(A) signal is an AAUAAA hexamer, but we recently found that the deeply branching eukaryote Giardia lamblia uses a distinct hexamer (AGURAA) and lacks any known auxiliary elements. Our discovery prompted us to explore the evolutionary dynamics of poly(A) signals and auxiliary elements...
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Research: Compartment-specific and ELAVL1-coordinated regulation of intronic polyadenylation isoforms by doxorubicin
- Alina Chakraborty,
- Mandy Cadix,
- Sébastien Relier,
- Nicolò Taricco,
- Tina Alaeitabar,
- Alexandre Devaux,
- Céline M. Labbé,
- Sylvain Martineau,
- Amélie Heneman-Masurel,
- Pierre Gestraud,
- Alberto Inga,
- Nicolas Servant,
- Stéphan Vagner,
- and Martin Dutertre
Genome Res. July 2022 32: 1271-1284; Published in Advance July 20, 2022, doi:10.1101/gr.276192.121
...). To investigate more extensively IPA isoform regulation by Doxo in whole-cells transcriptome, we used the 3′-seq technique, which is more efficient than exon-arrays and RNA-seq for this type of event, and consists in targeted sequencing of the 3′ end of polyadenylated transcripts upstream of the poly(A) tail...
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Method: BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
- Lars Gabriel,
- Tomáš Brůna,
- Katharina J. Hoff,
- Matthis Ebel,
- Alexandre Lomsadze,
- Mark Borodovsky,
- and Mario Stanke
Genome Res. May 2024 34: 769-777; Published in Advance June 12, 2024, doi:10.1101/gr.278090.123
...extrinsic and intrinsic evidence. Extrinsic evidence is extracted from transcripts and cross-species homologous proteins. RNA-seq reads offer direct evidence on introns and, if assembled, on a gene structure. Protein sequences from related s can be used to identify regions of a that encode proteins...
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Research: Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments
- John T. Chamberlin,
- Younghee Lee,
- Gabor T. Marth,
- and Aaron R. Quinlan
Genome Res. February 2024 34: 179-188; Published in Advance February 14, 2024, doi:10.1101/gr.278253.123
...window Figure 1. Conceptual depictions of key technical aspects of sc/snucRNA-seq. (A) Nuclei contain less total RNA but are enriched for pre-mRNA compared with cells. All pre-mRNAs in the nucleus are also in the cell, but most mRNAs are outside the nucleus. (B) Pre-mRNA tends to generate intronic reads...
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