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Research: Systematic transcriptome analysis associated with physiological and chronological aging in Caenorhabditis elegans
- Seokjin Ham,
- Sieun S. Kim,
- Sangsoon Park,
- Eun Ji E. Kim,
- Sujeong Kwon,
- Hae-Eun H. Park,
- Yoonji Jung,
- and Seung-Jae V. Lee
Genome Res. November/December 2022 32: 2003-2014; Published in Advance November 9, 2022, doi:10.1101/gr.276515.121
...regions increased during aging (Fig. 1B,C). In addition, the expressed intron levels of individual nonoverlapping genes increased (Supplemental Fig. S1A,B). In contrast, the fraction of exonic RNA-seq reads decreased during aging (Fig. 1D). These results indicate that aging is associated...
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Research: Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast
- Danny A. Bitton,
- Sophie R. Atkinson,
- Charalampos Rallis,
- Graeme C. Smith,
- David A. Ellis,
- Yuan Y.C. Chen,
- Michal Malecki,
- Sandra Codlin,
- Jean-François Lemay,
- Cristina Cotobal,
- François Bachand,
- Samuel Marguerat,
- Juan Mata,
- and Jürg Bähler
Genome Res. June 2015 25: 884-896; Published in Advance April 16, 2015, doi:10.1101/gr.185371.114
...with increasing numbers of introns between the joint exons (Supplemental Fig. S7). About 94% of circRNAs (238/254) originated from genes containing three or more exons (Supplemental Fig. S8), in line with reports that flanking introns facilitate circularization (Jeck et al. 2013; Ivanov et al. 2014; Liang...
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Resource: Identification of the long, edited dsRNAome of LPS-stimulated immune cells
- Matthew G. Blango and
- Brenda L. Bass
Genome Res. June 2016 26: 852-862; Published in Advance April 21, 2016, doi:10.1101/gr.203992.116
...RNAs (circRNAs) is promoted by complementary Alu repeats in flanking introns (Dubin et al. 1995; Liang and Wilusz 2014; Zhang et al. 2014; Ivanov et al. 2015). Not surprisingly, these Alu repeats are hyperedited, and knockdown of ADAR1 increases the levels of a subset of circRNAs (Ivanov et al. 2015...
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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
...for investigation into its noncanonical functions.Toward this, we performed a systematic analysis of single-cell RNA-seq (scRNA-seq) and chromatin accessibility (scATAC-seq) data to characterize XIST expression in male and female tissues from healthy human individuals, including data from child and adult hearts...
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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
...splicing, known as back-splicing, stitches the 3′ end of a downstream exon to the 5′ end of an upstream exon via a back-splicing junction (BSJ), forming a closed circular structure called circular RNA (circRNA). Both canonical and back-splicing junctions may experience alternative splicing; consequently...
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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
...the circRNAs that match exon boundaries. Confirming previously reported results (Jeck et al. 2013; Zhang et al. 2014; Ivanov et al. 2015), Figure 2C shows that introns next to circRNA regions are significantly larger than introns not adjacent to circRNAs: on average 2.33 and 2.27 times larger, respectively...
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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
...selection—namely, cassette exon, intron retention, alternative 5′ splice site, and alternative 3′ splice site—can all be found in circRNAs (Zhang et al. 2016). Because the function of a circRNA depends on its exact sequence, for example, in determining the presence of miRNA response elements (MREs...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
...—can further expand the known atlas of immunogenic dsRNAs and characterize their roles in different cell types and cellular conditions. These methods may also be adapted to facilitate the identification of immunogenic circRNAs and ncRNAs, which, to our knowledge, has not previously been subject to review...
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Resource: Diverse alternative back-splicing and alternative splicing landscape of circular RNAs
- Xiao-Ou Zhang,
- Rui Dong,
- Yang Zhang,
- Jia-Lin Zhang,
- Zheng Luo,
- Jun Zhang,
- Ling-Ling Chen,
- and Li Yang
Genome Res. September 2016 26: 1277-1287; Published in Advance June 30, 2016, doi:10.1101/gr.202895.115
...Genome Research www..org Figure 1. An upgraded computational pipeline (CIRCexplorer2) to systematically identify alternative (back-)splicing in back-spliced circular RNAs (circRNAs). (A) Schematic diagrams of two types of alternative back-splicing. Colored bars, exons. Black lines, introns. Red polylines...
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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
...; Rahimi et al. 2021). CircRNAs also present challenges to representation in standard linear browsers to identify their distinct biology compared to linear RNA species. An analogous challenge applies to intragenic trans-spliced RNAs, where a transcript contains noncollinear splicing, e.g., exons may...
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