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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: Accurate assembly of circular RNAs with TERRACE
- Tasfia Zahin,
- Qian Shi,
- Xiaofei Carl Zang,
- and Mingfu Shao
Genome Res. September 2024 34: 1365-1370; Published in Advance July 26, 2024, doi:10.1101/gr.279106.124
...RWM, Tan KE, Lim YY, Tsang ACM, Lo KW, et al. 2021. Quantifying full-length circular RNAs in cancer. Genome Res 31: 2340–2353. doi:10.1101/gr.275348.121 ↵Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, Zhang J, Chen LL, Yang L. 2016. Diverse alternative back-splicing and alternative splicing landscape...
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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
...purposes (Logan et al. 2011; Weng et al. 2013; Vollmers et al. 2015). However, RNA-seq, the current gold-standard for whole-transcriptome analysis, falls short of describing these immune receptors completely and accurately (Mose et al. 2016; Bolotin et al. 2017). Accurate and deep full-length c...
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Method: Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs
- Michiel de Hoon,
- Alessandro Bonetti,
- Charles Plessy,
- Yoshinari Ando,
- Chung-Chau Hon,
- Yuri Ishizu,
- Masayoshi Itoh,
- Sachi Kato,
- Dongyan Lin,
- Sho Maekawa,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Jay W. Shin,
- Jens Stolte,
- Ana Maria Suzuki,
- Michihira Tagami,
- Hazuki Takahashi,
- Supat Thongjuea,
- Alistair R.R. Forrest,
- Yoshihide Hayashizaki,
- Juha Kere,
- and Piero Carninci
Genome Res. September 2022 32: 1727-1735; Published in Advance August 12, 2022, doi:10.1101/gr.276647.122
...the background size distribution of all short capped RNAs aligning to mRNA or lncRNA transcripts. Full-length alignments, defined as those that extended over >90% of the mRNA or lncRNA transcript, were excluded. For each mRNA or lncRNA transcript, we counted the number of short capped RNAs aligning...
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Research: The circular RNome of primary breast cancer
- Marcel Smid,
- Saskia M. Wilting,
- Katharina Uhr,
- F. Germán Rodríguez-González,
- Vanja de Weerd,
- Wendy J.C. Prager-Van der Smissen,
- Michelle van der Vlugt-Daane,
- Anne van Galen,
- Serena Nik-Zainal,
- Adam Butler,
- Sancha Martin,
- Helen R. Davies,
- Johan Staaf,
- Marc J. van de Vijver,
- Andrea L. Richardson,
- Gaëten MacGrogan,
- Roberto Salgado,
- Gert G.G.M. van den Eynden,
- Colin A. Purdie,
- Alastair M. Thompson,
- Carlos Caldas,
- Paul N. Span,
- Fred C.G.J. Sweep,
- Peter T. Simpson,
- Sunil R. Lakhani,
- Steven Van Laere,
- Christine Desmedt,
- Angelo Paradiso,
- Jorunn Eyfjord,
- Annegien Broeks,
- Anne Vincent-Salomon,
- Andrew P. Futreal,
- Stian Knappskog,
- Tari King,
- Alain Viari,
- Anne-Lise Børresen-Dale,
- Hendrik G. Stunnenberg,
- Mike Stratton,
- John A. Foekens,
- Anieta M. Sieuwerts,
- and John W.M. Martens
Genome Res. March 2019 29: 356-366; Published in Advance January 28, 2019, doi:10.1101/gr.238121.118
...that were not recurring (χ2, P < 0.0001; 557 circRNAs; expected 207.3 circRNAs).Are circRNAs distinct molecules, specifically regulated, or splicing residues?Many of the circRNAs that are positively correlated with the expression level of the full-length linear transcript are thought to be a residue...
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Research: Antisense RNAs during early vertebrate development are divided in groups with distinct features
- Sanjana Pillay,
- Hazuki Takahashi,
- Piero Carninci,
- and Aditi Kanhere
Genome Res. June 2021 31: 995-1010; Published in Advance April 1, 2021, doi:10.1101/gr.262964.120
.... Group 1 NATs also show larger overlap and higher complementarity with the sense-strand mRNAs compared to other NATs. In addition, our transcriptomics data, quantifying RNA levels from cytoplasmic and nuclear compartments, indicates that Group 1 NATs are more abundant in the cytosol. Based...
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Research: A transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 ; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
....1002/j.1460-2075.1991.tb04916.x Osato N, Yamada H, Satoh K, Ooka H, Yamamoto M, Suzuki K, Kawai J, Carninci P, Ohtomo Y, Murakami K, et al. 2003. Antisense transcripts with rice full-length cDNAs.Genome Biol5: R5. doi:10.1186/gb-2003-5-1-r5 Ozsolak F, Milos PM. 2011. RNA sequencing: advances, challenges...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...glia (P-value = 1.24 × 10−4, AvgLog2FC = 0.37) compared with all other cell types, with the latter likely masked by the higher expression of the full-length XIST in female cells.To study if the newly discovered alternative promoter leads to alternative XIST transcripts, we analyzed bulk RNA-seq data...
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Resource: Generation and analysis of a mouse multitissue genome annotation atlas
- Matthew Adams and
- Christopher Vollmers
Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
...provides a blueprint for future annotation efforts of other organisms.ResultsGenerating accurate full-length cDNA data from 12 mouse tissuesWe constructed tissue-level, long-read transcriptome data using commercially available high-quality RNA (Takara Bio) from 12 mouse tissues (brain, eye, heart, kidney...
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Research: Systematic identification and characterization of exon–intron circRNAs
- Yinchun Zhong,
- Yan Yang,
- Xiaolin Wang,
- Bingbing Ren,
- Xueren Wang,
- Ge Shan,
- and Liang Chen
Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
...Table S1; Xin et al. 2021). Similar to the approach used by circtools to infer exon inclusion in circRNAs, we extracted the full-length of circRNAs detected by isoCirc, followed by quantifying their abundance in our RNase R+ HTS data and public RNase R– HTS data (Jakobi et al. 2019). It was found...
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