Searching journal content for articles similar to Gandin et al. 26 (5): 636.

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  1. Method: A versatile type VI CRISPR-based approach for targeted m6A demethylation in mRNAs
    • Panagiotis G. Adamopoulos,
    • Konstantina Athanasopoulou,
    • and Andreas Scorilas
    Genome Res. January 2026 36: 169-182; Published in Advance December 11, 2025, doi:10.1101/gr.280476.125
    ....55% of the identified m6A sites were detected within 3′ untranslated regions (UTRs), whereas a significant proportion of 31.75% was found in the coding sequence (CDS) of mRNAs (Fig. 1B). Additionally, our findings indicate an increasing trend in the prevalence of m6A sites spanning from the translation initiation codon...
  2. Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
    • Philipp Rentzsch,
    • Aaron Kollotzek,
    • Kaushik Ram Ganapathy,
    • Pejman Mohammadi,
    • and Tuuli Lappalainen
    Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
    ..., as recently exemplified by the gene encoding the transcription factor SOX9 (Naqvi et al. 2023), these regulatory changes are associated with differences in phenotype and disease risk (Albert and Kruglyak 2015). To our knowledge, there exist currently no assays that measure the viable dosage range of mRNA...
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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
    ...was relatively uniform, with a higher concentration toward the 5′ end (Fig. 3A). In contrast, in MT-mRNA, the m3C sites were depleted near both the 5′ and 3′ ends of the RNA (Fig. 3A), which correspond to the boundaries of the coding sequence (CDS), owing to the near absence of UTRs (Fig. 3B). Despite...
  4. Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
    • Ting-Ying Wu,
    • Ya-Ru Li,
    • Kai-Jyun Chang,
    • Jhen-Cheng Fang,
    • Daisuke Urano,
    • and Ming-Jung Liu
    Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
    ...decreased protein abundance but not mRNA abundance (WT vs. UCUUC/UCUCU mutations [mUCUUC/mUCUCU]) (Fig. 5A; Supplemental Fig. S8H). Mutating the CU-tract or “UCUUC”/”UCUCU” in the 5′ UTR–nonAUG TIS of Solyc06g009750.3.1 did not change translation efficiency (Supplemental Fig. S8F,G), implying other factors...
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  5. Research: Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context
    • Maria S. Benitez-Cantos,
    • Martina M. Yordanova,
    • Patrick B.F. O'Connor,
    • Alexander V. Zhdanov,
    • Sergey I. Kovalchuk,
    • Dmitri B. Papkovsky,
    • Dmitry E. Andreev,
    • and Pavel V. Baranov
    Genome Res. July 2020 30: 974-984; Published in Advance July 15, 2020, doi:10.1101/gr.257352.119
    ...evolutionarily conserved weak context (Loughran et al. 2018). Moreover, translation at fdAUG can be observed in those cases in which fdAUG is located downstream from CDS in the 3′ UTR as in the example of RPS19BP1 (Fig. 2D). Although it is possible that some nested or downstream ORFs code for functional peptides...
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  6. Research: The predicted RNA-binding protein regulome of axonal mRNAs
    • Raphaëlle Luisier,
    • Catia Andreassi,
    • Lisa Fournier,
    • and Antonella Riccio
    Genome Res. September 2023 33: 1497-1512; Published in Advance August 15, 2023, doi:10.1101/gr.277804.123
    .... The targeting of RNA transcripts to axons is one of the mechanisms that allows rapid local translation of proteins in response to extracellular signals. 3′ Untranslated regions (UTRs) of mRNA are noncoding sequences that play a critical role in determining transcript localization and translation by interacting...
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  7. Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
    • DongAhn Yoo,
    • Katherine M. Munson,
    • and Evan E. Eichler
    Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
    ...interactions between subtelomeric sequences among homologous and nonhomologous chromosomes (Hirai et al. 2019). The function of the subterminal caps is not known, although they have been proposed to help stabilize African great ape s by preventing or buffering against interchromosomal exchanges of more...
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  8. Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
    • Hsin-Yen Larry Wu,
    • Isaiah D. Kaufman,
    • and Polly Yingshan Hsu
    Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
    ...functions are provided to assign translated reading frames accurately: assign_frames()—assigns reading frames to Ribo-seq reads based on provided CDS ranges, enabling precise determination of translated codons. assign_frames_extended()—extends annotated frame assignments into UTRs, accommodating overlapping...
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  9. Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
    • Meilong Shi,
    • Chuanqi Teng,
    • Shan Zhang,
    • Xiaobo He,
    • Lingyun Xu,
    • Fengxian Han,
    • Rongqi Wen,
    • Ganjun Yu,
    • Jingwen Liu,
    • Yang Feng,
    • Yanfeng Wu,
    • Yan Ren,
    • Gang Jin,
    • and Jing Li
    Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
    ...analysis and identified genes positively correlated with different PLAAT4 isoforms (Fig. 6A). Our results revealed that genes specifically correlated with canonical PLAAT4 were enriched in virus defense functions (Supplemental Fig. S12A), whereas those correlated with LTR7-PLAAT4 isoform 1 were enriched...
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  10. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ...and transcriptomic levels, along with their regulatory effects on structural variations (SVs) and gene expression. Functional validation is performed using dual-luciferase assays and cell-based experiments. Our findings reveal that integrated HBV sequences form long concatemers, mediating inter- and intrachromosomal...
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