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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...-adipogenic progenitor cells, involving a total of 328 transcription factors acting at chromatin sites regulating 2025 genes. This web-accessible single-cell data set and regulatory circuitry map serve as a resource for understanding the molecular underpinnings of the metabolic and physiological effects of exercise...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...proteins in Fusarium graminearum, a globally significant fungal pathogen, reveals diverse roles in growth, development, and virulence. In-depth analyses of two H3K36-specific methyltransferases, Set2 and Ash1, uncover their distinct regulatory functions. Set2-mediated H3K36me3 is enriched in gene bodies...
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Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
- Song Zhang,
- Chao Wang,
- Shenghua Qin,
- Choulin Chen,
- Yongzhou Bao,
- Yuanyuan Zhang,
- Lingna Xu,
- Qingyou Liu,
- Yunxiang Zhao,
- Kui Li,
- Zhonglin Tang,
- and Yuwen Liu
Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
...and its potential target gene during myogenesis. Our findings reveal the dynamic regulatory features of SEs in skeletal muscle development and provide a general integrative framework for identifying critical enhancers underlying the formation of complex traits.Skeletal muscle, which constitutes nearly...
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Research: Single-cell analysis reveals transcriptional dynamics in healthy primary parathyroid tissue
- Aarthi Venkat,
- Maximillian J. Carlino,
- Betty R. Lawton,
- Manju L. Prasad,
- Matthew Amodio,
- Courtney E. Gibson,
- Caroline J. Zeiss,
- Scott E. Youlten,
- Smita Krishnaswamy,
- and Diane S. Krause
Genome Res. June 2024 34: 837-850; Published in Advance July 8, 2024, doi:10.1101/gr.278215.123
...from non-human primate parathyroid expression dynamics. Predicted cell–cell communication analysis reveals abundant endothelial cell interactions in the parathyroid cell microenvironment in both human and NHP parathyroid glands. We show abundant RARRES2 transcripts in both human adenoma and normal...
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Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
- Yidi Deng,
- Jiadong Mao,
- Jarny Choi,
- and Kim-Anh Le Cao
Genome Res. March 5, 2026 gr.281171.125; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
.... Caption next page. Figure 3. Dynamic coexpression network reveal key transcriptional program alternation during early hematopoiesis. (A) UMAP visualisation of bone marrow Lin− cells, depicting the transcriptional landscape of early hematopoiesis (Pellin et al., 2019). P: progenitor, GMP: granulocyte...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
..., reconstructing cell type–specific networks and allowing in silico T perturbations to reveal dynamic regulatory mechanisms. The knowledge-primed model SupirFactor (Tjärnberg et al. 2024) embeds the prior GRN directly into deep learning architectures, enabling biologically interpretable GRN predictions while...
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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
...a comparative analysis of 47,XYY and 47,XXY fibroblasts and iPSC transcriptomes. We reveal a transcriptional feedback mechanism tuning non-PAR X Chromosome gene (NPX) homologs in Y supernumerary cells, a phenomenon not detected in X aneuploid male iPSCs. By ectopically modulating the expression of selected NPY...
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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
..., as observed in cse2Δ and gal80Δ (Fig. 7D,E).View larger version: In this window In a new window Figure 7. Chromatin dynamics from genetic perturbations recapitulate transcriptional regulatory networks (TRNs). (A) TRN based on gene expression as a result of deleting BAS1 (|log2(FC)| > 0.85). Colored edges...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...aging. These include changes in DNA methylation, histone modifications, chromatin remodeling, and noncoding RNAs. Collectively, such alterations disrupt gene regulatory networks, leading to transcriptional dysregulation, loss of cellular homeostasis, and increased vulnerability to age-related diseases...
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Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...) that innervate skeletal muscles. However, certain MN groups including ocular MNs, are relatively resilient. To reveal key drivers of resilience versus vulnerability in ALS, we investigate the transcriptional dynamics of four distinct MN populations in SOD1G93A ALS mice using LCM-seq and single...
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