Searching journal content for articles similar to Chen et al. 33 (12): 2108.

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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
...looping and high-order chromatin structure (Panigrahi and O'Malley 2021; Karr et al. 2022; Chen et al. 2024b). Furthermore, the DNA interactome at a particular gene locus is controlled by the availability of the transcription machinery, its correct localization, transcriptional complex formation...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
.... Here, 64 3 we studied DNA damage repair kinetics from a global transcriptomic and proteomic 65 perspective in the ciliate Tetrahymena thermophila (Tetrahymena) (Ruehle et al. 2016; Orias 66 et al. 2011). Tetrahymena possesses a unique nuclear architecture containing a 67 transcriptionally active...
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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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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...for downstream tasks, including prediction of transcription factor binding (Cazares et al. 2023), cell type–specific chromatin structure (Tan et al. 2023; Yang et al. 2023; Zhang et al. 2023; Gao et al. 2024; Grover et al. 2024), and gene expression (Karbalayghareh et al. 2022; Zhang et al. 2023). Therefore...
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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
...throughout the S phase, with some regions replicating early and others late (Fig. 4B,C). The 2 and 3 Chromosomes comprise 70%–80% of the Drosophila and display distinct chromatin landscapes between the chromosome arms and pericentromeric regions (Fig. 3B; Supplemental Fig. S4A). To examine replication...
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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
...was independently described by a recent report from Gorin and Goodman (2025).Characterization of XIST transcript sequence and regulation in peripheral nervesNext, we sought to investigate how XIST achieves such specific expression by comparing chromatin accessibility data from assay for transposase...
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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
...and proceeds along the gene body to transcribe RNA (Jonkers and Lis 2015; Core and Adelman 2019; Noe Gonzalez et al. 2021; Aoi and Shilatifard 2023). As with all steps in the transcription process, elongation is tightly regulated to ensure that RNAPII travels along the gene at a proper speed (i.e., elongation...
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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
..., population genomics, and diagnostic frameworks.Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a well-established method for studying the genomic localization of DNA-associated proteins. ChIP-seq is widely used to study histone modifications, chromatin regulators (CRs), transcription...
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Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
...-mRNAs) undergo several maturation steps before their release from chromatin. Most human pre-mRNAs have many introns that are removed through splicing, which takes place either cotranscriptionally or soon after transcription (Pandya-Jones and Black 2009; Tilgner et al. 2012; Yeom et al. 2021). Cleavage of the 3...
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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
...not accurately assess the length of stripes, always calculating the stripe starting position as directly on the main diagonal. StripeDiff (Gupta et al. 2022) detects differential stripes between experiments and reveals the connection between changes of chromatin stripe and chromatin modification, transcriptional...
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