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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
.... Finally, we determine cell-type-specific replication timing profiles, integrating our in vivo data sets with published data using cultured cell lines. Our results reveal that GSC-like cells display a distinct replication program, compared with somatic lineages, that aligns with chromatin state differences...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
.... By integrating transcription factor (TF)–target gene relationships, chromatin accessibility, and genetic variation, this framework aims to elucidate the cell type–specific regulatory mechanisms underlying AD progression, link genetic risk variants to cis-regulatory elements and target genes, and prioritize...
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Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
...Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS Qunlun Shen1,2, Shuqin Zhang1,3 and Shihua Zhang2,4,5 1School of Mathematical Sciences, Fudan University, Shanghai 200433, China; 2State Key Laboratory of Mathematical Sciences, Academy...
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Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
- Qiuhan Wen,
- Zhen Wang,
- Qi Bao,
- Tianli Ding,
- Haihan Zhang,
- Jianbo Li,
- Zhuang Liu,
- Jieping Huang,
- and Guoqiang Yi
Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
...), which are known to promote cell proliferation and inhibit apoptosis (Kota et al. 2021; Yang et al. 2021; Lachiondo-Ortega et al. 2022).Cell type–specific APA spectrum in skeletal muscleGiven the crucial role of the muscle differentiation in determining pork quantity and quality, we further investigated...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
...2016; Smith et al. 2016; Valton and Dekker 2016; Oksuz et al. 2021).In contrast to interphase chromatin, vertebrate mitotic chromosomes are often thought to all fold as arrays of loops that are sequence-independent, independent of cell type or organism, and regardless of the diversity of macroscopic...
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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
...these universal instructions into cell type–specific programs that are able to respond to developmental and environmental cues. In part, this regulation is mediated by epigenetic mechanisms, which alter the accessibility of the chromatin in conjunction with changes in transcription factor (TF) and nucleosome...
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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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Research: Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes
- Iris Zhu and
- David Landsman
Genome Res. October 2023 33: 1662-1672; Published in Advance October 26, 2023, doi:10.1101/gr.278130.123
...show functional enhancer conservation and turnover during cis-regulatory evolution. Nat Genet 46: 685–692. doi:10.1038/ng.3009 ↵Arvey A, Agius P, Noble WS, Leslie C. 2012. Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res 22: 1723–1734. doi:10.1101/gr...
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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: 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
...-accessible chromatin using sequencing (ATAC-seq) across cell types. We first turned to scATAC-seq data from the Human Heart Cell Atlas, which were generated using the 10x Multiome platform (Kanemaru et al. 2023). We recalled ATAC-seq peaks using MACS2 (Zhang et al. 2008) for each of the broad cell types defined...
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