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Resource: Epigenomics of embryogenesis in turbot
- Oscar Aramburu,
- Belen G Pardo,
- Ada Jimenez-Gonzalez,
- Andrés Blanco-Hortas,
- Daniel Macqueen,
- Carmen Bouza,
- and Paulino Martinez
Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
...The Onset of Zygotic Transcription: Chromatin Dynamics and Pioneer 552 Factor Activity During Early Embryogenesis 553 At the onset of embryogenesis, during the first synchronized mitotic divisions, 554 the embryo is transcriptionally quiescent, and development is driven by 555 maternal transcripts (Xu et al...
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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
...genetic variation impacts transcription factor (TF) binding remains a major challenge, limiting our ability to model disease-associated variants. Here, we used a highly controlled system of F1 crosses with extensive genetic diversity to profile allele-specific binding of four TFs at several time points...
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Method: Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression
- Howard J. Womersley,
- Daniel Muliaditan,
- Ramanuj DasGupta,
- and Lih Feng Cheow
Genome Res. January 2025 35: 162-177; Published in Advance December 2, 2024, doi:10.1101/gr.279105.124
...density profile from H3K4me3 snCUT&RUN samples showed similar profiles around transcriptional start sites (TSSs) to that of the bulk cell set, with corresponding patterns of nucleosome depletion (Supplemental Fig. S1A), indicating the high resolution of this assay. We next benchmarked snCUT&RUN...
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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
...cellular conditions such as hypoxia, starvation, DNA damage, etc., to determine the cellular context required for GOI expression.Originally the nuclear run-on technique was developed to detect the emergent transcripts that are in the process of being produced from the GOI. In this approach, intact nuclei...
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Method: Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data
- Kaixuan Luo,
- Jianling Zhong,
- Alexias Safi,
- Linda K. Hong,
- Alok K. Tewari,
- Lingyun Song,
- Timothy E. Reddy,
- Li Ma,
- Gregory E. Crawford,
- and Alexander J. Hartemink
Genome Res. June 2022 32: 1183-1198; Published in Advance May 24, 2022, doi:10.1101/gr.272203.120
..., North Carolina 27708, USA Corresponding author: amink@cs.duke.eduAbstractOver a thousand different transcription factors (TFs) bind with varying occupancy across the human . Chromatin immunoprecipitation (ChIP) can assay occupancy -wide, but only one TF at a time, limiting our ability to comprehensively...
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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...and buffers prior to the run (Fig. 1). Although both workflows can process a similar number of samples within a similar time frame, the incorporation of a liquid handler substantially reduces pipetting and handling errors, minimizing experimental variability, especially in larger-scale experiments. Our...
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Research: Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
- Hadi Rahmaninejad,
- Yao Xiao,
- Maxime M.C. Tortora,
- and Geoffrey Fudenberg
Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
...IP-seq and Hi-C maps are strongly influenced by the CTCF bound time. At high (90%) occupancy, long-lived barriers result in pronounced peaks in ChIP-seq profiles, as well as clearly defined TADs and dots in Hi-C maps, reminiscent of experimental observations (Fig. 1E,G). In contrast, if the barrier bound time...
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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
...).ResultsMNase-seq profiling reveals -wide chromatin changes in genetic perturbation experimentsTo investigate chromatin changes in response to the deletion of individual transcriptional regulators, we profiled -wide chromatin occupancy in 201 yeast knockout strains (Supplemental Fig. S1; Giaever et al. 2002; Giaever...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...measured from peak position in nascent transcription profiles, which approximates the maximum of the coverage (Gregersen et al. 2020). However, these peaks may not accurately reflect the exact distance traveled by RNAPII, as the signal likely comprises transcripts made from RNAPII complexes released...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...1 Title 1 Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals 2 conserved gene alterations linked to Parkinson’s disease 3 Running title: Substantia nigra aging linked to Parkinson 4 Kangli Wang1, Weikun Xia1, Yingli Gu1, Songpeng Zu1, Qian Yang2, Maria Luisa Amaral1...
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