Searching journal content for articles similar to Toyoda et al. 13 (7): 1728.

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  1. Method: EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
    • Shuyu Zhang,
    • Quan Zou,
    • Mengting Niu,
    • Zhibin Lv,
    • Antony Stalin,
    • and Ximei Luo
    Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
    ...combinations, which provides experimental evidence for species-adaptive encoding strategies.DNA methylation is a form of DNA epigenetic modification, which modulates the genetic performance without changing the DNA sequence (Moore et al. 2013). Numerous studies have shown that DNA methylation can alter...
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  2. Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
    • Alexander J. Ritter,
    • Jolene M. Draper,
    • Christopher Vollmers,
    • and Jeremy R. Sanford
    Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
    ...using HiSeq 4000 PE150 (50 million to 100 million reads per library).Long-read Frac-seqFrom the same fractionated mRNA used prior for Illumina sequencing, full-length cDNA was prepared using the rolling circle amplification to concatemeric consensus (R2C2) method (Volden et al. 2018). Libraries were...
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  3. Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
    • Jonathan Cahn,
    • James P.B. Lloyd,
    • Ino D. Karemaker,
    • Pascal W.T.C. Jansen,
    • Jahnvi Pflueger,
    • Owen Duncan,
    • Jakob Petereit,
    • Ozren Bogdanovic,
    • A. Harvey Millar,
    • Michiel Vermeulen,
    • and Ryan Lister
    Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
    ...in the identification of all known mC readers as well as a variety of new candidate DNA methylation-binding proteins. We then focused on the characterization of their -wide binding pattern in vivo, and of high-order mutant plants lacking these proteins to interrogate the direct role of DNA methylation in Arabidopsis.ResultsIdentification...
  4. Resource: A systems view on DNA damage response kinetics in Tetrahymena
    • Emily Nischwitz,
    • Vivien A.C. Schoonenberg,
    • Rachel Mullner,
    • Albert Fradera-Sola,
    • Susanne Zimbelmann,
    • Joshua J. Smith,
    • and Falk Butter
    Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
    ...and Mochizuki 2009; Sandoval et al. 2015). To obtain transcriptome and proteome expression profiles, we harvested samples at 0, 1, 2, 3, 4, 6, and 8 h after treatment (0 h–8 h) in quadruplicate and performed mRNA sequencing (RNA-seq) and high-resolution quantitative mass spectrometry (MS) measurement (Fig. 1A...
  5. Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
    • Jennifer A. Urban,
    • Daniel Ringwalt,
    • John M. Urban,
    • Wingel Xue,
    • Ryan Gleason,
    • Keji Zhao,
    • and Xin Chen
    Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
    ...higher differentially expressed genes (DEGs) in the GSC-like cell cluster. The GSC-like transcriptome is differentially enriched for protein complexes involved in chromatin regulation, such as DNA replication, heterochromatin maintenance, and chromatin accessibility (Fig. 2F,G; Supplemental Fig. S3B...
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  6. Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
    • Kehan Lang,
    • Chenyang Jia,
    • Siyu Li,
    • Yi Guo,
    • Dingjun Hu,
    • and Shengquan Chen
    Genome Res. March 26, 2026 ; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
    ...sequencing (scRNA-seq) and single-cell DNA methylation (scDNAm) data face limitations, including unidirectionality, inadequate modeling of context-specific DNA methylation–expression associations, neglect of biological relevance in evaluation, and poor performance in limited paired training data. To fill...
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  7. Method: CodonBERT large language model for mRNA vaccines
    • Sizhen Li,
    • Saeed Moayedpour,
    • Ruijiang Li,
    • Michael Bailey,
    • Saleh Riahi,
    • Lorenzo Kogler-Anele,
    • Milad Miladi,
    • Jacob Miner,
    • Fabien Pertuy,
    • Dinghai Zheng,
    • Jun Wang,
    • Akshay Balsubramani,
    • Khang Tran,
    • Minnie Zacharia,
    • Monica Wu,
    • Xiaobo Gu,
    • Ryan Clinton,
    • Carla Asquith,
    • Joseph Skaleski,
    • Lianne Boeglin,
    • Sudha Chivukula,
    • Anusha Dias,
    • Tod Strugnell,
    • Fernando Ulloa Montoya,
    • Vikram Agarwal,
    • Ziv Bar-Joseph,
    • and Sven Jager
    Genome Res. July 2024 34: 1027-1035; Published in Advance July 1, 2024, doi:10.1101/gr.278870.123
    ...has been widely applied, including for optimizing recombinant protein drugs, nucleic acid therapies, gene therapy, mRNA therapy, and DNA/RNA vaccines (Al-Hawash et al. 2017; Webster et al. 2017; Mauro 2018). However, codon optimization alone does not consider several key properties that impact protein...
  8. Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
    • Marcus J. Viscardi,
    • Enisha Sehgal,
    • and Joshua A. Arribere
    Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
    ...truncated and dominantly acting proteins that harm cells. Eukaryotic cells protect themselves by degrading such mRNAs via the nonsense-mediated mRNA decay (NMD) pathway. The precise reactions by which cells attack NMD-target mRNAs remain obscure, precluding a biochemical understanding of NMD and hampering...
  9. Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
    • Aditi Singh,
    • Lilia Häußermann,
    • Christiane Emmerich,
    • Emily Nischwitz,
    • Brandon K.B. Seah,
    • Falk Butter,
    • Mariusz Nowacki,
    • and Estienne C. Swart
    Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
    ...Figure 4. Effects of ICOP knockdowns (KDs) on DNA excision. (A) mRNA expression levels in fragments per kilobase per million mapped reads (FPKM) compared between ICOPa and ICOPb KDs for transcripts early in development (40% old MAC fragmentation) or asynchronous (asyn.) cultures (*) in which new MACs...
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  10. 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
    ...with the most negative correlations with EIciRNAs (Supplemental Methods) showed that they were involved in pathways such as RNA splicing, mRNA metabolic process, and post-transcriptional regulation of gene expression (Supplemental Fig. S4F). Several RBPs, including HNRNPK, SNRNP70, SRSF1, and SRSF2, were core...
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