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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
...-021-01126-w ↵Liu J, Yue Y, Han D, Wang X, Fu Y, Zhang L, Jia G, Yu M, Lu Z, Deng X, et al. 2014. A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol 10: 93–95. doi:10.1038/nchembio.1432 ↵Liu N, Dai Q, Zheng G, He C, Parisien M, Pan T. 2015. N6-methyladenosine...
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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
...by splicing-related mechanisms (Kristensen et al. 2019; Chen et al. 2022a). Two subclasses of circRNAs, exonic circRNAs (EcircRNAs) and exon–intron circRNAs (EIciRNAs) are generated by backsplicing, which is a form of noncanonical alternative splicing (AS) (Salzman et al. 2012; Li et al. 2015; Sibley et al...
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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...@iisermohali.ac.inAbstractIsoform diversity is known to enhance a gene's functional repertoire by producing protein variants with distinct functional implications. Despite numerous studies on transcriptome diversifying processes (alternative splicing/transcription), understanding their extent and correlated impact on proteome diversity...
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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
...critical insights into transcription dynamics. Here, we combine transient transcriptome sequencing with transcription start site sequencing (TT-TSS-seq) to accurately map and quantify transcription initiation sites from nascent transcripts. Because transient metabolic labeling yields low-input RNA, we...
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Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
...as rectangles and introns as horizontal lines. The arrow represents the transcription start site. Each dark or light blue arrow represents one read, with light blue reads highlighting AS of the orange exon. The alternative intron is shaded in orange and reads are sorted based on the excision status...
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Research: Evolution of transcript modification by N⁶-methyladenosine in primates
- Lijia Ma,
- Boxuan Zhao,
- Kai Chen,
- Amber Thomas,
- Jigyasa H. Tuteja,
- Xin He,
- Chuan He,
- and Kevin P. White
Genome Res. March 2017 27: 385-392; Published in Advance January 4, 2017, doi:10.1101/gr.212563.116
...-transcriptional processes on transcript evolution. Post-transcriptional modification of RNA by N6-methyladenosine (m6A) has been shown to be widespread throughout the transcriptome, and this reversible mark can affect transcript stability and translation dynamics. Here we analyze m6A mRNA modifications in lymphoblastoid...
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Research: Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts
- Isabela T. Pereira,
- Izabela Mamede,
- Paulo P. Amaral,
- Gloria R. Franco,
- and John L. Rinn
Genome Res. October 2025 35: 2189-2198; Published in Advance August 26, 2025, doi:10.1101/gr.280431.125
...to the inclusion of a specific exon in the GET isoform (Fig. 2A). This exemplifies how two isoforms from the same gene, even when mostly similar in sequence, can have discrete and nondiscrete sedimentation profiles in the same cell extract. Similarly, GET isoform Akap8-203 was found in mouse cell extracts as a GET...
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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...of alternative splicing patterns and histone post-translational modifications (hPTMs) across mouse brain development finds that enrichment of chromatin modifications correlates with, and predicts, alternative exon inclusion (Hu et al. 2017, 2020; Xu et al. 2017, 2018). Alternative splicing of neurexin I (Nrxn1...
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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...Haplotype-resolved telomere-to-telomere of Aphelenchus avenae implicates P5CS in nematode desiccation stress response Yali Zhang,1,2,3,4,7 Yayi Zhou,2,3,7 Yangyang Chen,2,3 Xueyu Wang,2,3 Boyan Hu,2,3 Shahid Siddique,4 Romnick A. Latina,4,5 Veronica I. Casey,4 Dexin Bo,2,3 Yucheng Liao,2,3 Min...
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