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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. April 2026 36: 802-813; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...–specific, and changes during development in coordination with gene expression. Moreover, RT alterations are linked to abnormal gene expression, instability, and structural variation in multiple diseases, including cancer. However, mechanistic links between RT, large-scale 3D architecture, and transcriptional regulation...
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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
...relevance, integrating the origin of DNA and protein elements (cis and trans) to evaluate false-positive and false-negative risks across experimental systems. Moreover, we explore how perturbation strategies—gain and loss of function—can complement steady-state profiling to establish causality in gene...
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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...Revisiting models of enhancer–promoter communication in gene regulation Gilad Barshad1,2 and Charles G. Danko1,2 1Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA; 2Department of Biomedical Sciences, College of Veterinary Medicine...
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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
...control, and refining the computational strategy for detecting elongation progression. Together, these improvements significantly enhance the resolution and reliability of RNAPII elongation rate calculations at the single-gene level.Unlike previous methods that relied on data from only one (Veloso et al...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
...elements that underlie genetic effects on gene expression and metabolic traits. However, caQTL discovery has been limited by small sample sizes. Here, we map caQTLs in liver tissue from 138 human donors and identify caQTLs for 35,361 regulatory elements, including population-specific caQTLs driven...
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Research: The asymmetric distribution of RNA polymerase II and nucleosomes on replicated daughter genomes is caused by differences in replication timing between the lagging and the leading strand
- Rahima Ziane,
- Alain Camasses,
- and Marta Radman-Livaja
Genome Res. February 2022 32: 337-356; Published in Advance January 18, 2022, doi:10.1101/gr.275387.121
...to the gene copy that replicated first, while newly synthesized nucleosomes are assembled on the copy that replicated second. RNAPII enrichment then shifts to the sister copy that replicated second. The order of replication is largely determined by genic orientation: If transcription and replication...
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Research: Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
- Kyuha Choi,
- Xiaohui Zhao,
- Andrew J. Tock,
- Christophe Lambing,
- Charles J. Underwood,
- Thomas J. Hardcastle,
- Heïdi Serra,
- Juhyun Kim,
- Hyun Seob Cho,
- Jaeil Kim,
- Piotr A. Ziolkowski,
- Nataliya E. Yelina,
- Ildoo Hwang,
- Robert A. Martienssen,
- and Ian R. Henderson
Genome Res. April 2018 28: 532-546; Published in Advance March 12, 2018, doi:10.1101/gr.225599.117
..., with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant , we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...Suv39h-catalyzed H3K9me3 is critical for euchromatic organization and the maintenance of gene transcription Christine R. Keenan1,2,4,6, Hannah D. Coughlan1,2,4, Nadia Iannarella1, Andres Tapia del Fierro1,2, Andrew Keniry1,2, Timothy M. Johanson1,2, Wing Fuk Chan1,2,7, Alexandra L. Garnham1...
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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
...@cs.duke.eduAbstractEpigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy across the . Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely uncharted...
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Research: Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites
- Patrick D. Wilson,
- Xinyang Yu,
- Christopher R. Handelmann,
- and Michael J. Buck
Genome Res. March 2025 35: 404-416; Published in Advance February 10, 2025, doi:10.1101/gr.279541.124
...investigations into gene regulation and the potential development of therapeutic strategies targeting TP53 family dysfunction.MethodsPioneer-seq library designThe nucleosomes in the Pioneer-seq library were based on the widely used Widom-601 nucleosome-positioning sequence (Flaus 2011; Yu and Buck 2020...

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