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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
...-translational modifications, play a crucial role in regulating programs integral to a cell's identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells in vivo remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst...
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Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models Yiqiao Zheng1,2,5, Gary D. Stormo3 and Shiming Chen2,4 1Molecular Genetics and Genomics Graduate Program, Division of Biology & Biomedical Sciences, Washington...
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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
..., SOX10, TCF4, ETS1, SREBF1, CEBPB, KLF2, and ETV5) were higher in either skeletal muscle or heart nonmyelinating Schwann cells. Analysis of the transcription regulatory programs by the SCENIC software predicted that FOXO1 (and YY1) could regulate XIST in heart and skeletal muscle Schwann cells...
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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
...governing PARP expression, 582 localization, and activity in cells. Crit Rev Biochem Mol Biol 55: 541–554. 583 Sandoval PY, Lee P-H, Meng X, Kapler GM. 2015. Checkpoint activation of an 584 unconventional DNA replication program in tetrahymena. PLoS Genet 11: 1005405. 585 Schärer OD. 2013. Nucleotide...
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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
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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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
...of the complex relationship between chromatin organization and transcription.Every eukaryotic encodes the information necessary for cellular viability and growth. Although the underlying instructions embedded in the DNA are identical among the cells of an organism, complex regulatory mechanisms transform...
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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
...-induced DNA damage (Andrade-Lima et al. 2015; Williamson et al. 2017; Cugusi et al. 2022). In addition, dysregulated transcriptional elongation has been implicated in developmental defects as well as disease and aging (Aoi and Shilatifard 2023; Debès et al. 2023).RNAPII elongation rates not only reflect...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...for substrate recognition (Grüne et al. 2003). ISWI complex partners determine the context of the complex activity and alter its remodeling efficiency (Längst et al. 1999; Toto et al. 2014). ISWI complexes have been shown to regulate DNA replication, transcription, DNA repair, and V(D)J cleavage...
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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...the same or distinct regulatory programs for their regenerative transcriptional reprogramming? An initial pairwise comparison to identify differentially expressed genes (DEGs) between time points for each major cell type revealed dynamic gene expression across all stages and cell types (Fig. 2A...
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Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
..., the complex of DNA and histone proteins that help to regulate transcription. Others encode transcription factors, whereas still others encode proteins that directly modify DNA itself. Thus, distinct groups of proteins with disparate functions in transcriptional regulation can lead to overlapping phenotypic...

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