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Research: Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements
- Hosiana Abewe,
- Alexandra Richey,
- Jeffery M. Vahrenkamp,
- Matthew Ginley-Hidinger,
- Craig M. Rush,
- Noel Kitchen,
- Xiaoyang Zhang,
- and Jason Gertz
Genome Res. March 2025 35: 393-403; Published in Advance March 3, 2025, doi:10.1101/gr.279699.124
.... To determine the functional importance of specific regulatory regions, we used CRISPR-based Enhancer-i (Carleton et al. 2017) to block ER-bound enhancers from different classes of chromatin interactions or promoters that are part of an E2-upregulated gene cluster. With these studies, our main goal...
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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
...@cs.duke.eduAbstractEpigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy across the . Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely uncharted...
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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
...in the , similar to the situation with rDNA in yeast.Common with eukaryotes but unlike the euryarchaeon Haloferax, Bacteriovorax exhibits positive correlation between chromatin accessibility and active transcription, suggesting that displacing histones from promoters might play a regulatory role in this organism...
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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: Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes
- Anna Nordin,
- Chaitali Chakraborty,
- Mattias Jonasson,
- Orgena Dano,
- Gianluca Zambanini,
- Pierfrancesco Pagella,
- Silvia Remeseiro,
- and Claudio Cantù
Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
...with the increase in H3K4me3 (Sharifi-Zarchi et al. 2017). Many RUWs were decorated with H3K27ac, a marker of active enhancers (Adam et al. 2018): these increased upon Wnt/beta-catenin induction (Fig. 3A; Supplemental Fig. S2C). We recently did a time course study where we mapped chromatin accessibility via ATAC...
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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...biological contexts that are difficult to access in vivo, we were able to characterize the putative regulatory role of hundreds of GWAS loci, many of which had never been associated with an eQTL. Our results show that repurposing organoids for gene-environment interaction studies is a valuable...
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Resource: A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements
- Salam Idriss,
- Mohammad Hallal,
- Abdullah El-Kurdi,
- Hasan Zalzali,
- Inaam El-Rassi,
- Erik A. Ehli,
- Christel M. Davis,
- Philip E.D. Chung,
- Deena M.A. Gendoo,
- Eldad Zacksenhaus,
- Raya Saab,
- and Pierre Khoueiry
Genome Res. February 2023 33: 269-282; Published in Advance January 17, 2023, doi:10.1101/gr.277037.122
..., the role of epigenetic deregulation and cis-regulatory regions in PB pathogenesis and progression is largely unknown. Here, we generated -wide gene expression, chromatin accessibility, and H3K27ac profiles covering key time points of PB initiation and progression from pineal tissues of a mouse model...
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Research: Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features
- Marielle L. Bond,
- Eric S. Davis,
- Ivana Y. Quiroga,
- Anubha Dey,
- Manjari Kiran,
- Michael I. Love,
- Hyejung Won,
- and Douglas H. Phanstiel
Genome Res. August 2023 33: 1258-1268; Published in Advance September 12, 2023, doi:10.1101/gr.277397.122
...maps of chromatin accessibility, histone acetylation, transcription factor (TF) binding, and gene expression revealed insights into both the mechanisms and the functional impacts of differential looping during cellular differentiation. We find that regulatory features both at and between loop anchors...
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Research: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
..., allowing relatively free access to gene regulatory elements in the face of extensive physical compaction. In eukaryotes, the key principles of chromatin organization have been elucidated over the past half-century: A repeating nucleoprotein complex known as the nucleosome serves to compact ∼150 bp of DNA...
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Resource: Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis
- Yingshu Li,
- Yongjie Liu,
- Hang Yang,
- Ting Zhang,
- Kiyoshi Naruse,
- and Qiang Tu
Genome Res. June 2020 30: 924-937; Published in Advance June 26, 2020, doi:10.1101/gr.258871.119
...RNAs (lncRNAs) encoded in the ; we obtained the temporal expression profiles of all these genes during embryogenesis and identified those that use different isoforms across developmental stages. Furthermore, we acquired chromatin accessibility dynamics and investigated cis- and trans-regulatory logic...
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