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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...at Nationwide Children's Hospital, Columbus, Ohio 43205, USA Corresponding author: Parthun.1@osu.eduAbstractA large fraction of the interacts with the nuclear periphery through lamina-associated domains (LADs), repressive regions which play an important role in organization and gene regulation across...
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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
...have shown ablates the mitotic checkpoint and enhances the rate of chromosome missegregation (Hewitt et al. 2010; Kwiatkowski et al. 2010; Santaguida et al. 2010; Vasudevan et al. 2020). We hypothesized that transient exposure to AZ3146 could have two potential benefits. First, by increasing...
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Research: Redistribution of lamina-associated domains reshapes binding of pioneer factor FOXA2 in development of nonalcoholic fatty liver disease
- Xiaolong Wei,
- Megan A. Murphy,
- Nihal A. Reddy,
- Yi Hao,
- Taylor G. Eggertsen,
- Jeffrey J. Saucerman,
- and Irina M. Bochkis
Genome Res. November/December 2022 32: 1981-1992; Published in Advance December 15, 2022, doi:10.1101/gr.277149.122
...test the hypothesis that change in the expression of lamina-associated proteins and nuclear shape leads to redistribution of LADs, followed by altered binding of pioneer factor FOXA2 and by up-regulation of lipid synthesis and storage, culminating in steatosis in younger NAFLD patients (aged 21...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...regions make inter-chromosomal contacts, and gene-poor left and right arms are frequently located close to the nuclear lamina (Liu et al. 2011; Ho et al. 2014; Bian et al. 2020). At the megabase scale, the autosomes display A/B compartmentalization without loop-anchored TADs, which is consistent...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...reorganizes 3D architecture, facilitating long-range genomic interactions to modulate gene transcription, we next investigated whether the three ERBS categories display distinct patterns of chromatin interactions.To explore this, we used high-throughput chromosome conformation capture (Hi-C) in MCF-7 cells...
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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
.... These early-replicating domains are located across the entirety of the X Chromosome. The fraction of the X Chromosome that is earlier replicating in each cell type is shown above each corresponding bar.To facilitate cross-cell-type comparisons, we standardized replication timing along the reference to have...
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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
...classes (Supplemental Fig. S4D). Notably, Con SEs had the lowest average DNA methylation levels across all five developmental stages (Fig. 3H), supporting the transition of enhancers from basal to active states (Sharifi-Zarchi et al. 2017) and facilitating changes in cell identity (Guo et al. 2017). Given...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...whether physical and/or functional properties might explain the unparalleled linkage conservation seen on the mammalian X Chromosome. Third, we asked whether the remarkable number of intrachromosomal rearrangements that occurred in the mouse lineage facilitated the substantial shift in the ampliconic gene...
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Research: Vertebrates show coordinated elevated expression of mitochondrial and nuclear genes after birth
- Hadar Medini and
- Dan Mishmar
Genome Res. March 2025 35: 459-474; Published in Advance March 4, 2025, doi:10.1101/gr.279700.124
...Hadar Medini and Dan Mishmar Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel Corresponding author: dmishmar@bgu.ac.ilAbstractInteractions between mitochondrial and nuclear factors are essential to life. Nevertheless, the importance of coordinated...
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Research: Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptors
- James L. Shepherdson,
- Ryan Z. Friedman,
- Yiqiao Zheng,
- Chi Sun,
- Inez Y. Oh,
- David M. Granas,
- Barak A. Cohen,
- Shiming Chen,
- and Michael A. White
Genome Res. February 2024 34: 243-255; Published in Advance February 14, 2024, doi:10.1101/gr.278133.123
...by motifs or motif families for CRX/OTX2, NRL (leucine zipper), NEUROD1 (E-box binding factor), RORB (nuclear receptor), MAZ/SP4 (C2H2 zinc finger), MEF2D (MADS-box), RAX (Q50 homeodomain), and GFI1 (C2H2 zinc finger repressor). In sum, prior analyses show that enhancers are characterized by high...
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