Searching journal content for articles similar to Yu et al. 27 (7): 1238.

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  1. Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
    • Lianne B Cohen,
    • Tamara Hadzic,
    • Caitlin Sauer,
    • Julia R Gibbs,
    • and Zeba Wunderlich
    Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
    ...Methods 547 Genome-wide reporter library construction 548 To generate a -wide reporter library, genomic DNA was isolated from both male and 549 female iso-1 flies, fragmented via sonication, and size selected (500-750 bps). To prepare and 550 clone these fragments into the the pSTARR-seq fly plasmid (Add...
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  2. Mini-Review: Evolution of genome-wide methylation profiling technologies
    • Carolina Montano and
    • Winston Timp
    Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
    ..., Bruhm DC, Jensen SØ, Medina JE, Hruban C, White JR, et al. 2019. Genome-wide cell-free DNA fragmentation in patients with cancer. Nature 570: 385–389. doi:10.1038/s41586-019-1272-6 ↵De Coster W, Weissensteiner MH, Sedlazeck FJ. 2021. Towards population-scale long-read sequencing. Nat Rev Genet 22: 572...
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  3. Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
    • Marian F. Laughery,
    • Bastian Stark,
    • Benjamin Morledge-Hampton,
    • Steven A. Roberts,
    • and John J. Wyrick
    Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
    ...correlation between deamination and skin cancer mutations, there were some limitations. Specifically, the human cells used in this study were repair-competent, and thus, ongoing CPD repair could complicate analysis of deamination rates, and detection of lesions via cleavage by uracil DNA glycosylase (UDG...
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  4. Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
    • Samuel H. Kim,
    • Georgi K. Marinov,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
    ...abundances of accessible ssDNA and accessible DNA). (C) KAS-seq, ATAC-seq, and KAS-ATAC mitochondrial profiles in human GM12878 cells. (D) Fragment length distribution in biotin-ATAC-seq and KAS-ATAC libraries (GM12878 cells). (E) Genome-wide TSS metaprofiles for biotin-ATAC-seq and KAS-ATAC libraries (GM...
  5. Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
    • Kevin Moyung,
    • Yulong Li,
    • Heather K. MacAlpine,
    • Alexander J. Hartemink,
    • and David M. MacAlpine
    Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
    ...-axis, and fragment length is plotted on the y-axis, indicating nucleosome or TF-sized DNA. (C) Genome-wide map of chromatin changes in response to genetic perturbations. Loci with significant chromatin changes in response to a deletion are highlighted in purple (those reflecting the mutant deletion itself...
  6. Method: A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
    • Siyuan Chen,
    • Jiuming Wang,
    • Inkyung Jung,
    • Zhaowen Qiu,
    • Xin Gao,
    • and Yu Li
    Genome Res. August 2024 34: 1174-1184; Published in Advance August 13, 2024, doi:10.1101/gr.279274.124
    ...-cell data.The chromatin loop serves as a crucial structural variant that bridges promoters with regulatory regions, playing a pivotal role in DNA replication and gene transcription. It is closely related to DNA replication and gene transcription. Moreover, it serves as a vital regulator, enabling...
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  7. Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
    • Alejandro Martin-Trujillo,
    • Paras Garg,
    • Nihir Patel,
    • Bharati Jadhav,
    • and Andrew J. Sharp
    Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
    ...of quantitative trait loci (QTLs) often allows characterization of the functional consequences of sequence variation on gene expression (eQTLs) (Dixon et al. 2007; Göring et al. 2007; Stranger et al. 2007), DNA methylation (mQTLs) (Martin-Trujillo et al. 2020; Villicaña and Bell 2021), histone modifications (Mc...
  8. Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
    • Xuejing Wang and
    • Gerald Heckel
    Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
    ...; Braaker and Heckel 2009; Martínková et al. 2013; Lischer et al. 2014; Wang et al. 2023). New resequencing was performed for four samples. Sequence data from all samples are available at NCBI BioProject (https://www.ncbi.nlm.nih.gov/bioproject) under accession number PRJNA963218.DNA extraction...
  9. Method: Dynamics of intronic polyadenylation in the hematopoietic lineage and its regulation by DNA methylation
    • Richa Rashmi,
    • Abhinaya Muruganandham,
    • Pranita Borkar,
    • Sumana Mallick,
    • Taylor Hubbs,
    • Ari Aviles,
    • Daniel Chung,
    • and Irtisha Singh
    Genome Res. April 13, 2026 gr.281044.125; Published in Advance April 13, 2026, doi:10.1101/gr.281044.125
    ...of high-confidence IPA: RPKM ≥ 0.5, usage ≥ 10% in ≥10% samples) or "unused" 295 to control for sequence biases (Supplementary Fig. S6C). 296 297 Among 910 used and 1,820 unused PAS (>5.7M methylation sites), used PAS consistently 298 exhibited higher surrounding DNA methylation (Fig. 6A, KS-test, P...
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  10. 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
    ...observations in our example genes and other NMD targeted loci (Supplemental Fig. S4).Our data support the idea that SMG-5 and SMG-6 target a similar set of mRNAs (Fig. 1), with SMG-5 stimulating SMG-6-mediated cleavage (Fig. 3C) in C. elegans, as occurs in humans (Boehm et al. 2021).NMD-target m...
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