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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
...) interactions, and these interactions are commonly altered in cancer. Yet, the functional relationship between changes in 3D interactions associated with regulatory regions and differential gene expression appears context-dependent. In this study, we used HiChIP to capture changes in 3D interactions between...
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Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
- Leandros Boukas,
- Teresa Romeo Luperchio,
- Afrooz Razi,
- Kasper D. Hansen,
- and Hans T. Bjornsson
Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
...preferential chromatin disruption at CpG islands and at regulatory elements linked to aging. A sensitive analysis reveals that regulatory elements disrupted in B/T cells do show chromatin accessibility changes in neurons, but these are very subtle and of uncertain functional significance. Finally, we are able...
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Research: Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes
- Mohamed Belhocine,
- Mathieu Simonin,
- José David Abad Flores,
- Agata Cieslak,
- Iris Manosalva,
- Lydie Pradel,
- Charlotte Smith,
- Eve-Lyne Mathieu,
- Guillaume Charbonnier,
- Joost H.A. Martens,
- Hendrik G. Stunnenberg,
- Muhammad Ahmad Maqbool,
- Aneta Mikulasova,
- Lisa J. Russell,
- Daniel Rico,
- Denis Puthier,
- Pierre Ferrier,
- Vahid Asnafi,
- and Salvatore Spicuglia
Genome Res. July 2022 32: 1328-1342; Published in Advance June 23, 2021, doi:10.1101/gr.266924.120
.... 2016; Liu et al. 2016; Zhang et al. 2016a). Large epigenetic domains along the are also emerging as a new concept in defining tissue-specific gene regulation and in the control of normal development and cancer (Hnisz et al. 2017). Active chromatin marks usually restricted to cis-regulatory elements...
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Research: Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology
- Adebola Enikanolaiye,
- Julie Ruston,
- Rong Zeng,
- Christine Taylor,
- Marijke Schrock,
- Christie M. Buchovecky,
- Jay Shendure,
- Elif Acar,
- and Monica J. Justice
Genome Res. April 2020 30: 540-552; Published in Advance April 21, 2020, doi:10.1101/gr.258400.119
...(Cyp46a1), which produces 24S-OHC, a molecule essential for cholesterol turnover and a biomarker for abnormal cholesterol homeostasis in the Mecp2 brain (Lund et al. 2003; Buchovecky et al. 2013).Synapse functionMutations that affect synaptic function are expected from previous studies of RTT patients...
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Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
.... 2003; Rubenstein 2010) and that inhibitory neurons are overproduced in ASD patient-derived organoids (Mariani et al. 2015). These results suggest that the identified ASD-associated circRNA-miRNA axes may serve as an alternative pathway for gene-disrupting mutations to perturb key transcript levels...
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Research: U2AF1 mutations alter splice site recognition in hematological malignancies
- Janine O. Ilagan,
- Aravind Ramakrishnan,
- Brian Hayes,
- Michele E. Murphy,
- Ahmad S. Zebari,
- Philip Bradley,
- and Robert K. Bradley
Genome Res. January 2015 25: 14-26; Published in Advance September 29, 2014, doi:10.1101/gr.181016.114
...mutations exhibited different nucleotides prior to the AG of the 39 splice site (Przychodzen et al. 2013; Brooks et al. 2014), suggesting that U2AF1 mutations may cause specific alterations to the RNA splicing process. To determine how U2AF1 mutations alter RNA splicing in hematopoietic cells, we combined...
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Research: Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice
- Michael C. Saul,
- Christopher H. Seward,
- Joseph M. Troy,
- Huimin Zhang,
- Laura G. Sloofman,
- Xiaochen Lu,
- Patricia A. Weisner,
- Derek Caetano-Anolles,
- Hao Sun,
- Sihai Dave Zhao,
- Sriram Chandrasekaran,
- Saurabh Sinha,
- and Lisa Stubbs
Genome Res. June 2017 27: 959-972; Published in Advance March 29, 2017, doi:10.1101/gr.214221.116
...regulator ofWnt (Auld et al. 2012), andWnt intersects with ESRRAon both metabolic and behavioral axes. Notably, mutations in the Wnt effector, Tcf7l2, are associatedwith abnormal insulin and glucose homeostasis as well as deficits in fear learning (for review, see Nobrega 2013). Tcf7l2 is one of a small...
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Research: Whole-transcriptome sequencing identifies a distinct subtype of acute lymphoblastic leukemia with predominant genomic abnormalities of EP300 and CREBBP
- Maoxiang Qian,
- Hui Zhang,
- Shirley Kow-Yin Kham,
- Shuguang Liu,
- Chuang Jiang,
- Xujie Zhao,
- Yi Lu,
- Charnise Goodings,
- Ting-Nien Lin,
- Ranran Zhang,
- Takaya Moriyama,
- Zhaohong Yin,
- Zhenhua Li,
- Thuan Chong Quah,
- Hany Ariffin,
- Ah Moy Tan,
- Shuhong Shen,
- Deepa Bhojwani,
- Shaoyan Hu,
- Suning Chen,
- Huyong Zheng,
- Ching-Hon Pui,
- Allen Eng-Juh Yeoh,
- and Jun J. Yang
Genome Res. February 2017 27: 185-195; Published in Advance November 30, 2016, doi:10.1101/gr.209163.116
...of many hematologic malignancies. Often as initiating events, these structural abnormalities result in fusion proteins involving transcription factors important for hematopoietic differentiation and/or signaling molecules regulating cell proliferation and cell cycle. In contrast, epigenetic regulator...
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Research: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
- Phillippa C. Taberlay,
- Aaron L. Statham,
- Theresa K. Kelly,
- Susan J. Clark,
- and Peter A. Jones
Genome Res. September 2014 24: 1421-1432; Published in Advance June 10, 2014, doi:10.1101/gr.163485.113
...of promoters, CTCF sites, and enhancers could conversely acquire an abnormally active epigenetic signature. We identified a subset of regulatory elements that either gained H3K4me3 (at promoters), CTCF binding (at insulators), or H3K4me1 (at enhancers). Indeed, we found that promoters, CTCF sites...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...the coordinated interaction of multiple factors that ensure the fine-tuned regulation of gene expression.Among the regulatory mechanisms, cis-regulatory regions play a key role in the precise and timely recruitment of transcription factors and other regulatory molecules to activate and maintain appropriate...

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