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Method: Long-read RNA sequencing reveals allele-specific N⁶-methyladenosine modifications
- Dayea Park and
- Can Cenik
Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
.... 2021). While the significance of allele-specific RNA expression is well-acknowledged, allele-specific RNA modification remains underexplored.N6-methyladenosine (m6A), the most prevalent RNA modification of mRNAs, has been suggested to impact diverse mechanisms to regulate gene expression (Lee et al...
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Method: Allele-specific RNA N⁶-methyladenosine modifications reveal functional genetic variants in human tissues
- Shuo Cao,
- Haoran Zhu,
- Jinru Cui,
- Sun Liu,
- Yuhe Li,
- Junfang Shi,
- Junyuan Mo,
- Zihan Wang,
- Hailan Wang,
- Jiaxin Hu,
- Lizhi Chen,
- Yuan Li,
- Laixin Xia,
- and Shan Xiao
Genome Res. August 2023 33: 1369-1380; Published in Advance September 15, 2023, doi:10.1101/gr.277704.123
...-dependent RNA structural switches regulate RNA–protein interactions. Nature 518: 560–564. doi:10.1038/nature14234 ↵Liu J, Dou X, Chen C, Chen C, Liu C, Xu MM, Zhao S, Shen B, Gao Y, Han D, et al. 2020a. N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription...
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Research: Acute depletion of METTL3 implicates N⁶-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome
- Guifeng Wei,
- Mafalda Almeida,
- Greta Pintacuda,
- Heather Coker,
- Joseph S. Bowness,
- Jernej Ule,
- and Neil Brockdorff
Genome Res. August 2021 31: 1395-1408; Published in Advance June 15, 2021, doi:10.1101/gr.271635.120
...splicing.RNA is subject to diverse post-transcriptional modifications that have emerged as new layers of gene regulation (Fu et al. 2014; Yue et al. 2015; Roundtree et al. 2017a). Among these, N6-methyladenosine (m6A) is the most prevalent and abundant internal RNA modification on mRNA. m6A was initially...
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Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
- Eleanor Elgood Hunt,
- Claudia Vivori,
- Richard Mitter,
- Vedis Agnadottir,
- and Folkert J. van Werven
Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
...Eleanor Elgood Hunt, Claudia Vivori, Richard Mitter, Vedis Agnadottir and Folkert J. van Werven The Francis Crick Institute, London, NW1 1AT, United Kingdom Corresponding author: folkert.vanwerven@crick.ac.ukAbstractTranscription initiation is a highly dynamic and tightly regulated process...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...a transposase domain derived from an Hsmar1 insertion conserved in primates, providing functional DNA-binding to target methylation (Cordaux et al. 2006). Such exaptation and domestication events can often be identified by the occurrence of chimeric transcripts, which are mRNAs with both gene- and TE...
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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...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...6BT, United Kingdom; 2Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom; 3Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, United Kingdom; 4University College London Cancer...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...in diverse adult and pediatric cancers. Accurate detection of fusion transcripts is essential in cancer clinical diagnostics and prognostics and for guiding therapeutic development. Most currently available methods for fusion transcript detection are compatible with Illumina RNA-seq involving highly accurate...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
..., Université de Lyon, Lyon 69007, France; 4Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, Villeurbanne 69622, France ↵5 These authors contributed equally to this work. Corresponding authors: domitille.chalopin-fillot@u-bordeaux.fr, sophie...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...Evolution of -wide methylation profiling technologies Carolina Montano1,2 and Winston Timp1 1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA; 2Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia...
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