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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
...fide full-length ones but are absent in the current WormBase. The main purpose of this study was not to capture as many isoforms as possible but to demonstrate the capacity of the direct RNA sequencing technology in characterizing transcriptome complexity and in identifying novel RNA modifications...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...the transcriptome (Eisenberg and Levanon 2018; Duan 2025). Editing events taking place in coding sequences (CDSs)might alter the genomically encoded amino acid and lead to nonsynonymous changes, namely, “recoding” (Alon et al. 2015). Genome-wide profiling of RNA editing sites has been performed in several metazoans...
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Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
- Marcus J. Viscardi,
- Enisha Sehgal,
- and Joshua A. Arribere
Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
...full-length mRNAs and degradation intermediatesTo assess the roles of deadenylation, endonucleolytic cleavage, and decapping on NMD targets, we turned to whole-transcript, native RNA sequencing. Long-read sequencing offers key advantages over short-read sequencing, namely, (1) the ability to sequence...
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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
...for the identification and quantification of sample-specific APA events in a transcriptome-wide manner by enriching the 3′ end of RNA transcripts, followed by high-throughput sequencing (3′ end-seq), such as 3P-seq, Aseq, Poly(A)-seq, and 3′ READS (Jan et al. 2011; Derti et al. 2012; Martin et al. 2012; Hoque et al...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...direct RNA-seq method can potentially overcome these issues while also identifying RNA modifications in the native molecule. However, sequencing throughput from current direct RNA protocols is still relatively low compared to cDNA-based protocols (∼20 M reads in direct RNA protocols [Oxford Nanopore...
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Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
- Giulia F. Del Gobbo and
- Kym M. Boycott
Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
...; Murdock et al. 2021; Yépez et al. 2022). However, previous studies have relied on SRS, which has limited ability to reconstruct full-length mRNA transcripts, making it challenging to interpret the exact impact of splice-altering variants or fully resolve novel gene fusions. Long-read RNA-seq in contrast...
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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
...′ ends of RNA molecules to ensure full-length sequencing.In principle, nanopore directRNA sequencing allows for full-length sequencing by bypassing terminal end or length biases created during library preparation. Additionally, directRNA sequencing can identify RNA modifications (e.g., the 5′ cap...
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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
...; Brar and Weissman 2015), to uncover the complete transcriptome and translatome of S. pombe. Oxford Nanopore Technologies (ONT) direct RNA (dRNA) sequencing (dRNA-seq) offers several important advantages over previous RNA-seq approaches: (1) It provides an unbiased snapshot of the native polyadenylated...
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Resource: The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution
- Adam D. Warner,
- Louis Gevirtzman,
- LaDeana W. Hillier,
- Brent Ewing,
- and Robert H. Waterston
Genome Res. June 2019 29: 1036-1045; Published in Advance May 23, 2019, doi:10.1101/gr.243394.118
..., the differential expression of transcription factors and the differential association of genes enriched in a tissue suggest a direct regulatory relationship.DiscussionWe have dissected gene expression with lineage and tissue/organ resolution by producing deeply sequenced RNA-seq libraries from early in embryonic...
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