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Resource: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
- Michal Pawlak,
- Katarzyna Z. Kedzierska,
- Maciej Migdal,
- Karim Abu Nahia,
- Jordan A. Ramilowski,
- Lukasz Bugajski,
- Kosuke Hashimoto,
- Aleksandra Marconi,
- Katarzyna Piwocka,
- Piero Carninci,
- and Cecilia L. Winata
Genome Res. March 2019 29: 506-519; Published in Advance February 13, 2019, doi:10.1101/gr.244491.118
...-seq) (Buenrostro et al. 2013) to capture the dynamics of regulatory landscape throughout the progression of heart morphogenesis in vivo therefore unravelling the gene regulatory network driving key processes of heart development.ResultsCM transcriptome reveals strong dynamics at early stages of heart morphogenesis...
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Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
- Yichao Zhou,
- Venkatasai Rahul Dogiparthi,
- Hannah L. Harris,
- Suhita Ray,
- Avik Choudhuri,
- Song Yang,
- Yi Zhou,
- Leonard I. Zon,
- M. Jordan Rowley,
- and Kyle J. Hewitt
Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
...(Fig. 6E). These findings track accessibility during the early establishment and late resolution of a regeneration-dependent transcriptome in RBC precursors. Chromatin accessibility and transcriptional landscapes can be used to define mechanisms of hematopoietic differentiation within distinct...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...are largely unknown. Here, we profile -wide changes to gene expression and chromatin structure in cardiomyocytes derived from human pluripotent stem cells. We identify and characterize a gene regulatory element essential for regulating MYH6 expression, which encodes human fetal myosin. Using chromatin...
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Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
...that were discovered together in a GCOD oligogenic set. (CMs) Cardiomyocytes, (ECs) endothelial cells; (A/V) atrial/ventricular, (AHF) anterior heart field, (OFT) outflow tract, (RV) right ventricle.View this table: In this window In a new window Table 1. GCOD counts of significantly overtransmitted...
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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
...proposed to exhibit a range of divergent features compared with histones in archaea and eukaryotes. However, no functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription, and three...
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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...activation of regulatory regions during 313 the antiviral response. These findings provide a high-resolution view of chromatin state 314 13 dynamics, illustrating the diversity of regulatory landscapes and their functional relevance in 315 response to poly I:C stimulation. 316 To identify transcription...
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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
....Transcriptional regulation in eukaryotes is profoundly influenced by chromatin status, integrating diverse cellular signals to control gene expression (Berger 2007). Chromatin dynamics are modulated by multiple mechanisms, including histone modifications, DNA methylation, and chromatin remodeling complexes (Shilatifard 2006...
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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
...KAS-ATAC reveals the -wide single-stranded accessible chromatin landscape of the human Samuel H. Kim1,6, Georgi K. Marinov2,6 and William J. Greenleaf2,3,4,5 1Cancer Biology Programs, School of Medicine, Stanford University, Stanford, California 94305, USA; 2Department of Genetics, School...
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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
..., and higher-resolution contact maps generated by in situ Hi-C have made it possible to study architectural stripes (Vian et al. 2018). Chromatin stripes are a chromatin architectural feature that captures the dynamic, ever-changing nature of the . The stripes reflect interactions between a single locus...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...), or other regulatory elements, and constitute a substantial portion of lincRNAs (Khorkova et al. 2015; Choudhary et al. 2023). Despite their potential importance, the transcriptomic landscape and clinical relevance of TE-derived elements in PAAD remain poorly characterized, partly due to limited sample...
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