Searching journal content for articles similar to Bhatt et al. 34 (2): 217.

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  1. Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
    • Zohar Rosenwasser,
    • Roni Cohen-Fultheim,
    • Ofir Shliefer,
    • Erez Y. Levanon,
    • and Eli Eisenberg
    Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
    ...), and similar results were reported for the mouse(Kiyosawa et al. 2003), Drosophila(Misra et al. 2002), Arabidopsis(Meyers et al. 2004; Wang et al. 2014), and rice s(Osato et al. 2003). In addition, many long intergenic non-coding RNAs (lincRNAs) have been identified as antisense transcripts, further...
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  2. Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
    • Richard D.W. Kelly,
    • Kristy R. Stengel,
    • Aditya Chandru,
    • Lyndsey C. Johnson,
    • Scott W. Hiebert,
    • and Shaun M. Cowley
    Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
    ...and elongating polymerase, suggesting an overall reduction in polymerase recruitment. Using enhancer RNA (eRNA) expression to measure enhancer activity, we find that LBH589-sensitive eRNAs are preferentially associated with superenhancers and PSN binding sites. These findings suggest that HDAC activity...
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  3. 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...
  4. Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
    • Haiyue Liu and
    • Lea H. Gregersen
    Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
    .... (2022).Notably, RNAPII elongation rates were generally higher in protein-coding genes than those in long noncoding RNA (lncRNA) genes (Fig. 4B). This difference was not attributed to gene length or GC contents (Supplemental Fig. S5A,B). Furthermore, no significant variation in elongation rates...
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  5. 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
    ...) depletion to ensure that the samples to be sequenced are enriched in miRNAs and not in rRNAs.miRNAs are short noncoding RNAs ∼22 nucleotides (nt) in length that play a crucial role in post-transcriptional regulation by targeting messenger RNA (mRNA) for degradation or translational repression (Shang et al...
  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
    ...for its proven efficacy in extracting local sequence motifs and hierarchical patterns from sequence data, which are hypothesized to be relevant features for modeling local RNA sequence conversion dynamics. The output of the CNN layers is flattened and passed to a fully connected dense layer, which...
  7. Perspective: Decrypting noncoding RNA interactions, structures, and functional networks
    • Muller Fabbri,
    • Leonard Girnita,
    • Gabriele Varani,
    • and George A. Calin
    Genome Res. September 2019 29: 1377-1388; Published in Advance August 21, 2019, doi:10.1101/gr.247239.118
    ...braveheart long non-coding RNA (Bvht) specifies the interaction with the CNBP/ZNF9 zinc-finger transcription factor and dramatically affects cardiomyocyte differentiation. This sequence is located in a motif named AGIL (from 5′-asymetric G-rich internal loop), and the deletion of 11 nt from this motif out...
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  8. Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
    • 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 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
    ...-wide profiling of RNA editing sites has been performed in several 50 metazoans, showing us highly distinct distributions of RNA editing events (Liscovitch-51 Brauer et al. 2017; Porath et al. 2017; Duan et al. 2023a; Zhang et al. 2023). While 52 extensive RNA editing on non-coding repetitive elements...
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  9. Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
    • Qiuhan Wen,
    • Zhen Wang,
    • Qi Bao,
    • Tianli Ding,
    • Haihan Zhang,
    • Jianbo Li,
    • Zhuang Liu,
    • Jieping Huang,
    • and Guoqiang Yi
    Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
    ...isoform detection. Future studies should consider employing long-read snRNA-seq technologies such as Oxford Nanopore Technologies (ONT) or Pacific Biosciences (PacBio) to overcome these limitations and provide more comprehensive insights. Second, our reliance on the CISBP-RNA database for RBP motifs...
  10. Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
    • Prashanthi Ravichandran,
    • Princy Parsana,
    • Rebecca Keener,
    • Kasper D. Hansen,
    • and Alexis Battle
    Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
    ...and AI Institute, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding author: ajbattle@jhu.eduAbstractGene coexpression networks (GCNs) describe relationships among genes that maintain cellular identity and homeostasis. However, typical RNA-seq experiments often lack sufficient sample...
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