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Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
- Cristian Groza,
- Bing Ge,
- Warren A. Cheung,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
...Carthy SA, Davies RM, et al. 2021. Twelve years of SAMtools and BCFtools. GigaScience 10: giab008. doi:10.1093/gigascience/giab008 ↵Daron J, Slotkin RK. 2017. EpiTEome: simultaneous detection of transposable element insertion sites and their DNA methylation levels. Genome Biol 18: 91. doi:10.1186/s13059...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...suggests a novel, non-XCI role of XIST in peripheral Schwann cells that is mediated by a newly recognized transcript.X-inactive specific transcript (XIST) is a long noncoding RNA (lncRNA) that serves as an important regulator of X Chromosome inactivation (XCI) in mammalian XX females (Loda and Heard 2019...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...on potentially misleading predictions.Prediction of potential regulatory sitesThis review focuses on gene-specific transcriptional regulation via direct TF binding to regulatory DNA sites. The initial task is thus to locate candidate DNA regions potentially involved in TF binding, and this starts...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...for downstream TFBS analysis, allowing the 142 identification of key regulatory motifs involved in the antiviral response. 143 To further characterise the genomic distribution of ATAC-seq and H3K27ac peaks, we 144 annotated consensus peaks relative to gene features and transcription start sites (TSS). The 145...
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Method: Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications
- Xudong Liu,
- Ying Ni,
- Lianwei Ye,
- Zhihao Guo,
- Lu Tan,
- Jun Li,
- Mengsu Yang,
- Sheng Chen,
- and Runsheng Li
Genome Res. November 2024 34: 2025-2038; Published in Advance October 2, 2024, doi:10.1101/gr.279012.124
...a “modification-aware” basecalling model for E. coli, starting from the super accuracy basecalling (SUP) model (dna_r10.4.1_e8.2_400bps_sup@v4.2.0), fine-tuned using methylation-free WGA reads (see Methods). To ensure that the “modification-aware” model does not have an extensive impact on WGS read quality, we...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...fragments. Studies using CRISPR-Cas9-induced centromeric DSBs in mammalian cells have shown activation of either homologous recombination (HR) or nonhomologous end joining (NHEJ) pathways (Tsouroula et al. 2016; Saayman et al. 2023). DNA-end resection, facilitated by the formation of DNA–RNA hybrids (R...
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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
...the pattern detected in female GSCs (DeLuca et al. 2020).Distinct replication timing profiles in GSC-like and CySC-like cellsChromatin organization plays an integral role in regulating transcription and DNA replication. Given the differences in chromatin landscapes between GSC-like and CySC-like cells, we...
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Research: Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma
- Huiwen Che,
- Peiyong Jiang,
- L.Y. Lois Choy,
- Suk Hang Cheng,
- Wenlei Peng,
- Rebecca W.Y. Chan,
- Jing Liu,
- Qing Zhou,
- W.K. Jacky Lam,
- Stephanie C.Y. Yu,
- So Ling Lau,
- Tak Y. Leung,
- John Wong,
- Vincent Wai-Sun Wong,
- Grace L.H. Wong,
- Stephen L. Chan,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. February 2024 34: 189-200; Published in Advance February 26, 2024, doi:10.1101/gr.278556.123
...of molecules, we assessed molecule ends in specific regions. The end frequencies of cfDNA at transcription start sites (TSSs) and regulatory regions that include DHSs and CTCF binding sites (Methods) were examined. As the expression level rose, the normalized end frequencies of long molecules gradually...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...al. 2005; Potthoff and Olson 2007; Zdobnov et al. 2020), with highly conserved DNA-binding domains (Carlsson and Mahlapuu 2002; Chang et al. 2015).View larger version: In this window In a new window Figure 1. Profiling transcription factor (TF) binding in F1 embryos of Drosophila melanogaster. (A...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
....24.0) (Wang et al. 2022) was used to annotate the location of the nested genes inside their host. A custom GTF file containing only the information about the host transcripts involved in host/nested gene pairs was used as a reference and a BED file containing the start and end coordinates of the nested genes...
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