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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
...transcripts can highlight how different isoforms of the same gene can be preferentially expressed in some cells. For example, the apoptosis regulator BCL2 has multiple splice variants (Warren et al. 2019) and shows distinct isoform usage patterns between clusters. In cluster 3, BCL2–201 dominates, with 69...
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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
...level of splicing junction events due to the limitation of the short-read sequencing technology.The recent development of long-read single-molecule sequencing technologies has enabled the capture of the full-length isoform diversity (Byrne et al. 2019), further facilitating the comparative analysis...
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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 known splice sites and junctions or at least one novel splice site); and 0.1% were categorized as either genic or fusions (Fig. 1B). Additionally, transcripts were categorized based on their productivity. We define productive transcripts as those encoding a full-length, canonical protein. Unproductive...
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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 any BSJ. The potential full-length circRNA transcript isoforms are then generated as those with all the involved forward- and backward-splicing junctions supported by sequencing reads using a graph searching algorithm. Because the BSJs identified in the first step of psirc can be defined by any pairs...
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Resource: Recent, full-length gene retrocopies are common in canids
- Kevin Batcher,
- Scarlett Varney,
- Daniel York,
- Matthew Blacksmith,
- Jeffrey M. Kidd,
- Robert Rebhun,
- Peter Dickinson,
- and Danika Bannasch
Genome Res. August 2022 32: 1602-1611; Published in Advance August 12, 2022, doi:10.1101/gr.276828.122
...-mers, which are present in spliced gene sequences but absent from the CanFam3.1 reference assembly (Fig. 1A). These sequences are only found in genomic DNA when a nonreference retroCNV is present (Fig. 1B). No mRNA-specific 30-mers were identified from single-exon genes (N = 1574) or genes with recent...
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Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
- Daffodil M. Canson,
- Michael T. Parsons,
- Gemma Moir-Meyer,
- Troy Dumenil,
- Gemma Montalban,
- Erica Lin,
- Terri P. McVeigh,
- Aimee L. Davidson,
- Shaun M. Bouckaert,
- Matt Trau,
- Darren Korbie,
- and Amanda B. Spurdle
Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
...exhibits excellent reproducibility across cDNA input and PCR cycle differences and is able to identify and quantitate transcripts that differed by a single base. Of the 193 BRCA1 and 72 BRCA2 variants profiled, 89% (237/265) had no publicly available RNA splicing data. Complete or near complete impact...
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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
...the two alleles while accounting for the technical variation associated with each minion run (Supplemental Table S2). The SNHG5 gene highlights this differential expression with transcripts of one allele always retaining the first intron of the gene and transcripts of the other allele either splicing...
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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
..., and clustered together by splice isoform. Our approach differs from FLAIR in several ways, including a series of filtering steps that reduces the impact of 3′ bias in our reads and allows us to consider only full-length transcripts. A recent publication examining the utility of dRNA-seq and cDNA nanopore...
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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
...isoform calling and a variation smaller than 10% in terms of isoform quantification.An underestimation of transcriptome complexity in C. elegansWith approximately three million full-length long reads and approximately another three million partial-length long reads, we identified 169,804 splicing...
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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
...–2476. doi:10.1093/gbe/evx154 ↵Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol 9: R7. doi:10.1186/gb-2008-9-1-r7 ↵Hu Q-L, Ye Y...

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