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Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
- Wenyu Zhang,
- Anja Guenther,
- Yuanxiao Gao,
- Kristian Ullrich,
- Bruno Huettel,
- Aftab Ahmad,
- Lei Duan,
- Kaizong Wei,
- and Diethard Tautz
Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
...: wyzhang@nwpu.edu.cn, tautz@evolbio.mpg.deAbstractThe ability to generate multiple RNA transcript isoforms from the same gene is a general phenomenon in eukaryotes. However, the complexity and diversity of alternative isoforms in natural populations remain largely unexplored. Using a newly developed full-length...
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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
..., J, and C gene segments may affect the antibody repertoire of a given individual, representing the potential of future precision medicine based on individual variation (Kidd et al. 2016; Kenter et al. 2021; Peres et al. 2023).In the work presented here, we generated full-length single-cell antibody...
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Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
...of complex RNA isoforms (Steijger et al. 2013). In contrast, long-read RNA sequencing provides full-length reads that span entire transcripts, enabling precise characterization of intricate isoforms and annotation-agnostic detection of novel structures. The primary shortcoming of long-read sequencing is its...
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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
...of which were common. The numbers of down-regulated genes were larger, with 136 from the BSJ list and 214 from the full-length list, 89 of which were common. This trend of reduced circRNA expression in NPC is consistent with similar observations in prostate cancer and colorectal cancer (Bachmayr-Heyda et...
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Method: Marker-free characterization of full-length transcriptomes of single live circulating tumor cells
- Sarita Poonia,
- Anurag Goel,
- Smriti Chawla,
- Namrata Bhattacharya,
- Priyadarshini Rai,
- Yi Fang Lee,
- Yoon Sim Yap,
- Jay West,
- Ali Asgar Bhagat,
- Juhi Tayal,
- Anurag Mehta,
- Gaurav Ahuja,
- Angshul Majumdar,
- Naveen Ramalingam,
- and Debarka Sengupta
Genome Res. January 2023 33: 80-95; Published in Advance November 22, 2022, doi:10.1101/gr.276600.122
...a single matrix, obtained by integrating individual scRNA-seq data sets based on common genes, whereas Integrative Seurat uses canonical correlation analysis (CCA)/reciprocal principal component analysis (RPCA)–based approaches for integration of multiple studies (Supplemental Note 1). Vanilla Seurat...
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Method: Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing
- Charles Cole,
- Ashley Byrne,
- Matthew Adams,
- Roger Volden,
- and Christopher Vollmers
Genome Res. April 2020 30: 589-601; Published in Advance April 20, 2020, doi:10.1101/gr.257188.119
...in some isoforms expressed by these genes (Sotillo et al. 2015; Byrne et al. 2017; Fischer et al. 2017). Determining isoform-level transcriptomes of healthy and cancerous immune cells might inform treatment decisions and future development.Second, full-length cDNA sequencing could be used to accurately...
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Resource: The full-length transcriptome of C. elegans using direct RNA sequencing
- Nathan P. Roach,
- Norah Sadowski,
- Amelia F. Alessi,
- Winston Timp,
- James Taylor,
- and John K. Kim
Genome Res. February 2020 30: 299-312; Published in Advance February 5, 2020, doi:10.1101/gr.251314.119
...nanopore-based direct RNA sequencing to characterize the developmental polyadenylated transcriptome of C. elegans. Taking advantage of long reads spanning the full length of mRNA transcripts, we provide support for 23,865 splice isoforms across 14,611 genes, without the need for computational...
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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
...splicing events by using the mapping tracks of full-length RNA transcripts, which allowed us to identify 57,000 novel isoforms that are absent in the current annotation. We detected putative stage-specific expression of isoforms that was independent of the stage-specific expression of genes. Finally, we...
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Method: Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
- Adrian Viehweger,
- Sebastian Krautwurst,
- Kevin Lamkiewicz,
- Ramakanth Madhugiri,
- John Ziebuhr,
- Martin Hölzer,
- and Manja Marz
Genome Res. September 2019 29: 1545-1554; Published in Advance August 22, 2019, doi:10.1101/gr.247064.118
...Direct RNA nanopore sequencing of full-length coronavirus s provides novel insights into structural variants and enables modification analysis Adrian Viehweger1,2,5, Sebastian Krautwurst1,2,5, Kevin Lamkiewicz1,2, Ramakanth Madhugiri3, John Ziebuhr2,3, Martin Hölzer1,2 and Manja Marz1,2,4 1RNA...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...in 109 genes, of which 57% had enzyme functions (Supplemental Table 3). The FIE-containing protein domains belong to 95 functional families (Supplemental Tables 2, 4). There were fewer functional families than genes because FunVar groups domains in different gene paralogs that share a common function...
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