Searching journal content for articles similar to Dukler et al. 27 (11): 1816.

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  1. 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
    ...) demonstrated that introns are not always removed in the order in which they appear in the nascent transcript. Our recent work extended these results by studying posttranscriptional splicing order for three to six consecutive introns (Choquet et al. 2023) using long-read direct RNA nanopore sequencing (Garalde...
  2. Research: Dynamic A-to-I RNA editing in response to gut microbiome in honeybees
    • Yuange Duan,
    • Min Huang,
    • Lin Ye,
    • Ling Ma,
    • Yashuai Wu,
    • Yating Du,
    • Jiyao Liu,
    • Fan Song,
    • Li Tian,
    • Wanzhi Cai,
    • Hu Li,
    • Xin Zhou,
    • and Shiqi Luo
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
    ...of a single bacterium Lactobacillus or Bombilactobacillus instead of Gilliamella in GF bees successfully restores the Adar p.482 Ile >Met and the global editing level. Our work demonstrates the complex and dynamic transcriptomic diversity exerted by A-to-I RNA editing and discovers the axis of gut–Lactobacillus/Bombilactobacillus–brain–Adar–global...
  3. Resource: Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
    • Ishwarya Venkata Narayanan,
    • Karan Bedi,
    • Brian Magnuson,
    • Ariel McShane,
    • Mario Ashaka,
    • Michelle Paulsen,
    • Thomas E Wilson,
    • and Mats Ljungman
    Genome Res. March 26, 2026 gr.280892.125; Published in Advance March 26, 2026, doi:10.1101/gr.280892.125
    ...been reported in studies using long-read sequencing of nascent RNA, 91 where transcripts were found to be either fully spliced or completely unspliced , with a 92 smaller group of transcripts showing a mixture of spliced and unspliced introns (Herzel 93 et al. 2018; Drexler et al. 2020). However, after...
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  4. 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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  5. Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m3C sites in poly(A) RNA
    • Shuhei Mitsutomi,
    • Anzu Sugawara,
    • Masahide Seki,
    • Yutaka Suzuki,
    • Sotaro Miyao,
    • Haozhe Du,
    • Kenji Takahashi,
    • Yusuke Mizukami,
    • Kenzui Taniue,
    • and Nobuyoshi Akimitsu
    Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
    ...motif and coding sequences. METTL2A knockdown alters expression of S100A4 mRNA isoforms, which contains METTL2A-mediated m3C sites. Notably, many transcripts with METTL2A-mediated m3C sites are upregulated upon METTL2A knockdown. We reveal the transcriptome-wide presence of m3C sites in poly(A) RNA...
  6. Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    • Qiang Su,
    • Yi Long,
    • Deming Gou,
    • Junmin Quan,
    • Xiaoming Zhou,
    • and Qizhou Lian
    Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
    ...transcript by its GC-content, MFE, and tertiary structure, correlating these with model predictions and empirical sequencing counts (Fig. 4B). Unlike equal-molar spike-ins, natural k-mer counts are influenced by their global overlapping frequency across all isoforms. To isolate the effects of RNA structure...
  7. Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
    • Yanis Zekri,
    • Sebastian Gregoricchio,
    • Elif Yapıcı,
    • Chia-Chi Flora Huang,
    • Tunç Morova,
    • Umut Berkay Altıntaş,
    • Gozde Korkmaz,
    • Nathan A. Lack,
    • and Wilbert Zwart
    Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
    ..., underscoring the need for a comprehensive functional characterization.Traditional approaches to identify active enhancers often correlate transcription factor binding with chromatin accessibility, RNA polymerase II (RNAPII) recruitment, or enhancer-associated histone modifications (Andersson and Sandelin 2020...
  8. 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
    ...on mRNA stability, transcription, and translation efficiency (Mauer et al. 2017; Min et al. 2018; Cesaro et al. 2023). Specifically, m6A reader proteins such as YTHDC1 and YTHDC2, which interact with m6A sites on 3′ UTRs, enhance mRNA stability (Wang et al. 2014; Lee et al. 2021). Our study revealed...
  9. Method: Analysis of coding gene expression from small RNA sequencing
    • Aygun Azadova,
    • Anthonia Ekperuoh,
    • Greg N. Brooke,
    • and Antonio Marco
    Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
    ...a sample, reverse-transcribing it into stable cDNA, and finally sequencing using (mostly) Illumina technology (Bentley et al. 2008). RNA-seq has multiple technical variations, either to identify specific types of transcripts or to characterize other RNA products. For instance, small RNA sequencing (sRNA...
  10. 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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