Searching journal content for articles similar to Macina et al. 5 (3): 225.

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  1. Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
    • Sheila Lutz,
    • Megan Lawler,
    • Samuel Amidon,
    • and Frank W Albert
    Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
    ...biparental crosses but has low power for 52 variants that are rare in the population. GWAS is also prone to confounding by population 53 structure (Peter et al. 2022) and by non-genetic, environmental factors (Young et al. 2019). The 54 regions identified by linkage mapping and GWAS typically contain...
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  2. 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
    ...in multiple and complex patterns, with integrated segments ranging from <1 kb to >3 kb in length (Li et al. 2022). These integrated segments were fragmented in different orientations, rarely with a complete (Zhuo et al. 2021). Moreover, except for the entire integration, the extended long reads sufficiently...
  3. Research: Loss of multilevel 3D genome organization during breast cancer progression
    • Roberto Rossini,
    • Saleh Oshaghi,
    • Maxim Nekrasov,
    • Aurélie Bellanger,
    • Renae Domaschenz,
    • Yasmin Dijkwel,
    • Mohamed Abdelhalim,
    • Rahul Agrawal,
    • Marit Ledsaak,
    • Philippe Collas,
    • Ragnhild Eskeland,
    • David Tremethick,
    • and Jonas Paulsen
    Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
    ...et al. 2025) CRISPR target track based on CRISPOR (Haeussler et al. 2016). The sgRNAs were cloned stepwise into a Lenti-multi-CRISPR plasmid that contains human codon-optimized Streptococcus pyogenes Cas9 (spCas9) followed by a porcine teschovirus-1 2A peptide (P2A) self-cleavage sequence upstream...
  4. Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
    • Jenna Kalleberg,
    • Jacob Rissman,
    • and Robert D. Schnabel
    Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
    ...the bovine genomic community run parallel to those for humans, including the 1000 Bull Genomes (1kBulls), Bovine Pan, and Ruminant Telomere-to-Telomere (RT2T) consortia (The 1000 Genomes Project Consortium 2010; Hayes and Daetwyler 2019; Jarvis et al. 2022; Kaminow et al. 2022; Nurk et al. 2022; Zhou et al...
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  5. Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
    • Xingmin Han,
    • Chenghui Xu,
    • Yiyi Ren,
    • Meiling Guo,
    • Jiayue Yan,
    • Xuan Wang,
    • Chao Liu,
    • Qin Gu,
    • Xing-Xing Shen,
    • Zhonghua Ma,
    • and Yun Chen
    Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
    ...in centromeric regions (Fig. 4D). Δset2 and Δash1 mutants displayed distinct, mutually exclusive H3K36me3 patterns, collectively recapitulating the wild-type H3K36me3 landscape. Specifically, H3K36me3 was mainly enriched in telomeric and centromere-proximal regions in Δset2, whereas Δash1 showed H3K36me3...
  6. Research: Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development
    • Hiroto S. Fukushima,
    • Hiroyuki Takeda,
    • and Ryohei Nakamura
    Genome Res. April 2023 33: 572-586; Published in Advance April 28, 2023, doi:10.1101/gr.277577.122
    ...accessibility after ZGA; (ii) H3K9me3 is globally erased but specifically retained at telomeric regions, which is required for maintenance of genomic stability during the cleavage stage. These results expand the understanding of diversity and conservation of reprogramming in vertebrates, and unveil previously...
  7. Review: Leveraging the power of long reads for targeted sequencing
    • Shruti V. Iyer,
    • Sara Goodwin,
    • and William Richard McCombie
    Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
    ...) wherein the authors performed Cas9 targeting and cleavage in agarose gel plugs to excise microbial segments of up to 100 kb for targeted cloning of gene clusters (Jiang et al. 2015; Jiang and Zhu 2016). CRISPR-mediated isolation of specific megabase-sized regions (CISMRs), developed by Bennett...
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  8. Research: Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing
    • Russell J. Butterfield,
    • Diane M. Dunn,
    • Brett Duval,
    • Sarah Moldt,
    • and Robert B. Weiss
    Genome Res. September 2023 33: 1439-1454; Published in Advance October 5, 2023, doi:10.1101/gr.277871.123
    ..., Salt Lake City, Utah 84112, USA Corresponding author: russell.butterfield@hsc.utah.eduAbstractFascioscapulohumeral muscular dystrophy (FSHD) is caused by a unique genetic mechanism that relies on contraction and hypomethylation of the D4Z4 macrosatellite array on the Chromosome 4q telomere allowing...
  9. LETTER: Characterization of Short Tandem Repeats from Thirty-One Human Telomeres
    • Marjorie Rosenberg,
    • Lester Hui,
    • Junli Ma,
    • Harris C. Nusbaum,
    • Kevin Clark,
    • Louise Robinson,
    • Laura Dziadzio,
    • Pamela M. Swain,
    • Tim Keith,
    • Thomas J. Hudson,
    • Leslie G. Biesecker,
    • and Jonathan Flint
    Genome Res. September 1, 1997 7: 917-923; doi:10.1101/gr.7.9.917
    ...demonstrated that they contain faithful representations of human telomeres. RARE site-specific cleavage has confirmed that half-YACs contain human telomeric and subtelomeric DNA for chromosomes 1q, 2p, 2q, 6q, 8q, 12q, 13q, 14q, 18p, 18q, and 21q (NIH/IMM Collaboration 1996). Cloned contigs of the 16p, 4p...
  10. 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
    ...the fundamental limitations of short-read sequencing for allele-specific analysis by detecting an increased number of single-nucleotide polymorphisms (SNPs) on a read, enabling its precise allelic assignment (Cho et al. 2014). This feature has been leveraged to characterize the genetic effects of rare and common...
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