Searching journal content for articles similar to Tran et al. 31 (6): 1035.

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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
.... 2007; Kemmeren et al. 2014), our approach offers new insights into the TF and nucleosome occupancies that are linked to transcriptional responses, significantly enhancing our understanding and modeling of GRNs.DiscussionTranscriptional regulation is, in part, controlled by chromatin. However, despite...
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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
...shared the same dynamic timescales. To simulate chromatin, we modeled 2.5 Mb of DNA as a 50-nm fiber with monomers of size 2.5 kb (Methods). Altogether, in our linked 1D extrusion and 3D polymer simulations, loop extruders can sequentially encounter and bypass dynamic barriers with corresponding impacts...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
..., and higher-resolution contact maps generated by in situ Hi-C have made it possible to study architectural stripes (Vian et al. 2018). Chromatin stripes are a chromatin architectural feature that captures the dynamic, ever-changing nature of the . The stripes reflect interactions between a single locus...
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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
...), and TRIPOD incorporate chromatin data, enhancing specificity. TFBShape and CRPTS account for DNA shape influences (Yang et al. 2014). Given the inherent challenges, modern prediction tools often incorporate machine learning to enhance traditional methods. Early tools like hidden Markov models and support...
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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
...traits are located in noncoding genomic regions (Hindorff et al. 2009), suggesting roles in transcriptional regulation. To elucidate this, it is imperative that we continue to identify genetic variants affecting TF occupancy and chromatin dynamics. To examine whether TOP is capable of sensitively...
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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
...-type testis tissue have made it difficult to generate comprehensive cell-type-specific genomic data sets defining their global transcriptional, chromatin, and replication landscapes. To address this, we developed cell-type-specific genomic strategies for testicular stem cells derived from a tumor model...
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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
...-associated factors and cellular perturbations differentially affect transcription elongation of individual genes.RNAPII elongation rates correlate with occupancy of RNAPII-associated factors and histone modificationsDuring the transcription cycle, elongating RNAPII complexes dynamically associate with multiple...
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Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
- Yichao Zhou,
- Venkatasai Rahul Dogiparthi,
- Hannah L. Harris,
- Suhita Ray,
- Avik Choudhuri,
- Song Yang,
- Yi Zhou,
- Leonard I. Zon,
- M. Jordan Rowley,
- and Kyle J. Hewitt
Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
...sample distance scores relative to controls indicates that chromatin profiles more closely resembled the pre-anemia state. To predict and evaluate transcription factor occupancy between these time points, we utilized ChromVAR (Schep et al. 2017). The highest variability scores at dynamically regulated...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...chromatin organization in facilitating MeCP2 function, investigators demonstrated in a MeCP2-mutant Rett syndrome mouse model that the ability of MeCP2 to engage in transcription repression relies on its ability to contact the TSS, even when MeCP2 is bound within the gene body itself (Figs. 2, 3B...
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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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