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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
...region of Chromosome 2L (early-mid), the fourth chromosome (early), and the rDNA locus (early) (Fig. 5B). Although replication timing for the X Chromosome was found to be early-mid and the Y Chromosome to be late-mid in both GSC-like and CySC-like cells (Supplemental Table S5), the Z-scores revealed more...
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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. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...DNA loss and A B C D E Figure 5. Cell cycle regulation of DNA replication and gene expression. (A) Exemplary genomic locus from Chromosome 4 showing enrichment of gene expression at the early replicating regions. Collapsed E/L ratios from PARTAGE Repli-seq data, PARTAGE multifraction signals...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...the missegregation of a specific chromosome. (B) Copy numbers of CSMD1, MICU3, and CRISPLD1 (a gene located on the q arm of Chromosome 8), in trisomic proband clones that were transiently transfected with KaryoCreate plasmids. Mean ± SEM; data from representative trials are shown (n ≥ 3 total trials). Genomic DNA...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...upregulation of known DNA repair proteins as well as a global dynamic response of not yet characterized transcripts and proteins. Using artificial neural networks, we classify different expression trends in response to the damaging agents. These networks reveal both a core and specific global dynamic response...
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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
...suggests a novel, non-XCI role of XIST in peripheral Schwann cells that is mediated by a newly recognized transcript.X-inactive specific transcript (XIST) is a long noncoding RNA (lncRNA) that serves as an important regulator of X Chromosome inactivation (XCI) in mammalian XX females (Loda and Heard 2019...
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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: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...tissues, sexes, and chromosomes. P-values were calculated based on 1000 bootstrap replicates. (B) log2 (female expression level:male expression level) along the X Chromosome.DiscussionHi-C and long-read sequencing resolves a large, complex insect into chromosomesWe used a combination of long-read DNA...
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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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Research: An iPSC-based model of 47,XYY Jacobs syndrome reveals a DNA methylation-independent transcriptional dysregulation shared with male X aneuploid cells
- Veronica Astro,
- Kelly Yojanna Cardona-Londoño,
- Lorena Viridiana Cortés-Medina,
- Rawan Alghamdi,
- Gustavo Ramírez-Calderón,
- Fotios Kefalas,
- Jair Dilmé-Capó,
- Santiago Radío,
- and Antonio Adamo
Genome Res. July 2025 35: 1503-1517; Published in Advance June 10, 2025, doi:10.1101/gr.279716.124
...been linked to a global transcriptional impact in primary cells (Miao et al. 2023; Viuff et al. 2023), our findings in JS iPSCs could challenge this notion. The identification of highly similar patterns of DEGs in JS and KS prompts us to hypothesize that, in X Chromosome male aneuploidies, the DNA...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...-regulatory elements (CREs) in a spatiotemporal manner through precise gene regulatory networks (Lee and Young 2013; Levine et al. 2014; Long et al. 2016). Understanding these regulatory mechanisms beyond transcription may reveal critical aspects of how cellular changes during aging contribute to PD pathology...
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