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Research: Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon
- Koichi Kitao,
- Kenji Ichiyanagi,
- and So Nakagawa
Genome Res. June 2025 35: 1287-1300; Published in Advance May 8, 2025, doi:10.1101/gr.280007.124
...that are found in various vertebrates (Sotero-Caio et al. 2017). LINE-1 (L1) is the only active LINE in the human and has open reading frames (ORFs). The ORF2 protein (ORF2p) is an enzymatic protein containing endonuclease and reverse transcriptase domains. The ORF1 protein (ORF1p) is a nonenzymatic RNA...
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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
...-long analyzes various sequencing protocols to measure their effect on circRNA detection and concludes that the optimal procedure for circRNA detection using nanopore technology should include RNase R, A-tailing, reverse transcription with SMARTer RT under RNase H conditions, and 1 kb (long) fragment size...
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Research: Engineered LINE-1 retrotransposition in nondividing human neurons
- Angela Macia,
- Thomas J. Widmann,
- Sara R. Heras,
- Veronica Ayllon,
- Laura Sanchez,
- Meriem Benkaddour-Boumzaouad,
- Martin Muñoz-Lopez,
- Alejandro Rubio,
- Suyapa Amador-Cubero,
- Eva Blanco-Jimenez,
- Javier Garcia-Castro,
- Pablo Menendez,
- Philip Ng,
- Alysson R. Muotri,
- John L. Goodier,
- and Jose L. Garcia-Perez
Genome Res. March 2017 27: 335-348; Published in Advance December 13, 2016, doi:10.1101/gr.206805.116
...and other DNA rearrangements, an average human contains 80–100 potentially active retrotransposition-competent L1s (RC-L1s) (Brouha et al. 2003; Beck et al. 2010). LINE-1s are non-LTR retrotransposons that mobilize by a “copy-and-paste” mechanism using an intermediate RNA (Luan et al. 1993; Beck et al. 2011...
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Research: Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control
- Miguel L. Soares,
- Carol A. Edwards,
- Frances L. Dearden,
- Sacri R. Ferrón,
- Scott Curran,
- Jennifer A. Corish,
- Rebecca C. Rancourt,
- Sarah E. Allen,
- Marika Charalambous,
- Malcolm A. Ferguson-Smith,
- Willem Rens,
- David J. Adams,
- and Anne C. Ferguson-Smith
Genome Res. March 2018 28: 345-356; Published in Advance January 24, 2018, doi:10.1101/gr.221366.117
...retrotranspose. Nonetheless, it is conceivable that these elements could still produce RNA transcripts (see below).The LINE-1-rich repeat array bordering the Dlk1-Dio3 imprinted cluster is nuclear lamina associatedLINE-1s have been shown to be enriched in nuclear lamina-associated domains (LADs) (Meuleman et al...
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Research: Widespread formation of double-stranded RNAs in testis
- Andreas Werner,
- James E. Clark,
- Calum Samaranayake,
- John Casement,
- Hany S. Zinad,
- Shaymaa Sadeq,
- Surar Al-Hashimi,
- Martin Smith,
- Noora Kotaja,
- and John S. Mattick
Genome Res. July 2021 31: 1174-1186; Published in Advance June 22, 2021, doi:10.1101/gr.265603.120
...have identified three specific pathways that protect the oocyte , including piRNAs, RNA interference, and transcriptional silencing mechanisms controlling LINE-1 elements (Taborska et al. 2019). The dsRNA feeding into piRNA and endo-siRNA pathways in oocytes derives from repetitive elements; whether...
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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
...equally to this work. Corresponding authors: kwlo@cuhk.edu.hk, kevinyip@cse.cuhk.edu.hkAbstractCircular RNAs (circRNAs) are abundantly expressed in cancer. Their resistance to exonucleases enables them to have potentially stable interactions with different types of biomolecules. Alternative splicing can...
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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
...on reverse transcription to generate cDNA libraries from cellular RNA. Whereas an oligo(dT) primer that binds to the poly(A) tail can be used to reverse-transcribe polyadenylated RNA, current CAGE protocols make use of random primers to capture both polyadenylated and nonpolyadenylated RNA (The FANTOM...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...: synthetic tsRNA mimic and the pAWH vector to express the corresponding pre-tRNA. tsRNA sponge: synthetic RNA sequence that is reversely complementary to the tsRNA. Scramble sponge: synthetic RNA sequence that is randomly scrambled from the sponge. See Supplemental Tables S2–S5 for the sequences. (B) Summary...
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Research: Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs
- Joana Carlevaro-Fita,
- Taisia Polidori,
- Monalisa Das,
- Carmen Navarro,
- Tatjana I. Zoller,
- and Rory Johnson
Genome Res. February 2019 29: 208-222; Published in Advance December 26, 2018, doi:10.1101/gr.229922.117
...selection evidence. The latter are henceforth defined as RIDLs.Despite their overall abundance throughout the , presently active LINE-1 elements are relatively depleted in lncRNA exons (Fig. 3A). It is possible that this reflects selection against disruption to normal gene expression, in which numerous weak...
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Research: miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression
- Galen T. Martin,
- Edwin Solares,
- Jeanelle Guadardo-Mendez,
- Aline Muyle,
- Alexandros Bousios,
- and Brandon S. Gaut
Genome Res. November 2023 33: 1932-1946; Published in Advance November 2, 2023, doi:10.1101/gr.277459.122
...of California, Davis, California 95616, USA; 3CEFE, University of Montpellier, CNRS, EPHE, IRD, 34090 Montpellier, France; 4School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom ↵5 These authors contributed equally to this work. Corresponding author: bgaut@uci.eduAbstractRNA molecules...
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