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Research: MYC overexpression leads to increased chromatin interactions at super-enhancers and MYC binding sites
- Yi Xiang See,
- Kaijing Chen,
- and Melissa J. Fullwood
Genome Res. April 2022 32: 629-642; Published in Advance February 3, 2022, doi:10.1101/gr.276313.121
...with a more extensive network of chromatin interactions to multiple distant target genes (Cao et al. 2017), to serve as regulatory hubs to govern processes important to cell identity (Whyte et al. 2013). This led us to question whether MYC enhancer invasion might preferentially occur at super-enhancers...
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Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...with a published analysis that dissected the Sox2 locus in mouse embryonic stem cells (mESCs) (Brosh et al. 2023). Eighty synthetic payloads were delivered, replacing either the full 143 kb locus or 43 kb locus control region (LCR) required for Sox2 expression in mESCs, and included multiple categories...
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Research: Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes
- Yuvia A. Pérez-Rico,
- Valentina Boeva,
- Allison C. Mallory,
- Angelo Bitetti,
- Sara Majello,
- Emmanuel Barillot,
- and Alena Shkumatava
Genome Res. February 2017 27: 259-268; Published in Advance December 13, 2016, doi:10.1101/gr.203679.115
.... Super-enhancers delineate disease-associated regulatory nodes in T cells. Nature 520: 558–562. Vella P, Barozzi I, Cuomo A, Bonaldi T, Pasini D. 2012. Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells. Nucleic Acids Res 40: 3403–3418. Vermunt MW, Reinink P, Korving...
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Research: Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes
- Iris Zhu and
- David Landsman
Genome Res. October 2023 33: 1662-1672; Published in Advance October 26, 2023, doi:10.1101/gr.278130.123
.... 2018. Functional dissection of the enhancer repertoire in human embryonic stem cells. Cell Stem Cell 23: 276–288.e8. doi:10.1016/j.stem.2018.06.014 ↵Blinka S, Reimer MH Jr., Pulakanti K, Rao S. 2016. Super-enhancers at the Nanog locus differentially regulate neighboring pluripotency-associated genes...
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Research: A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells
- Gurdeep Singh,
- Shanelle Mullany,
- Sakthi D. Moorthy,
- Richard Zhang,
- Tahmid Mehdi,
- Ruxiao Tian,
- Andrew G. Duncan,
- Alan M. Moses,
- and Jennifer A. Mitchell
Genome Res. April 2021 31: 564-575; Published in Advance March 12, 2021, doi:10.1101/gr.272468.120
...reveals that pluripotent stem cell enhancers contain a conserved regulatory codeTo decipher the regulatory code in pluripotent cells, we investigated regions bound by multiple transcription factors in mouse and human embryonic stem cells (ESCs) (* in Fig. 1A), as these regions are more likely to show...
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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
...–Whitney U tests, with Benjamini–Hochberg correction for multiple testing, (***) corrected P-values < 0.001. See also Supplemental Figures S1 and S2 and Supplemental Table S1.To compare regulatory regions across the four study species, we used pairwise whole- alignments to identify promoters and enhancers...
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Research: Identification of a transcriptional signature found in multiple models of ASD and related disorders
- Samuel Thudium,
- Katherine Palozola,
- Éloïse L'Her,
- and Erica Korb
Genome Res. September 2022 32: 1642-1654; Published in Advance September 14, 2022, doi:10.1101/gr.276591.122
...corresponding to strong promoter-proximal enhancers, further indicating the presence of chromatin regulatory features that allow for the robust and highly regulated activation of target genes.View larger version: In this window In a new window Figure 4. Chromatin states in transcriptional signature genes. (A...
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Research: Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding
- Ian C. McDowell,
- Alejandro Barrera,
- Anthony M. D'Ippolito,
- Christopher M. Vockley,
- Linda K. Hong,
- Sarah M. Leichter,
- Luke C. Bartelt,
- William H. Majoros,
- Lingyun Song,
- Alexias Safi,
- D. Dewran Koçak,
- Charles A. Gersbach,
- Alexander J. Hartemink,
- Gregory E. Crawford,
- Barbara E. Engelhardt,
- and Timothy E. Reddy
Genome Res. September 2018 28: 1272-1284; Published in Advance August 10, 2018, doi:10.1101/gr.233346.117
...factors can increase methylation of the histone H3 lysine 4 (H3K4; SPI1 [Ghisletti et al. 2010; Heinz et al. 2010]; FOXA1 [Sérandour et al. 2011; Jozwik et al. 2016]). Once established, multiple genomic and epigenetic features mark the state of an active enhancer, including enhanced chromatin...
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Research: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal
- Juan L. Mateo,
- Debbie L.C. van den Berg,
- Maximilian Haeussler,
- Daniela Drechsel,
- Zachary B. Gaber,
- Diogo S. Castro,
- Paul Robson,
- Q. Richard Lu,
- Gregory E. Crawford,
- Paul Flicek,
- Laurence Ettwiller,
- Joachim Wittbrodt,
- François Guillemot,
- and Ben Martynoga
Genome Res. January 2015 25: 41-56; Published in Advance October 7, 2014, doi:10.1101/gr.173435.114
...or intermediate enhancer configuration in mouse embryonic stem cells (Fig. 1C,E; Creyghton et al. 2010; Zentner et al. 2011). Here we adopt the poised enhancer nomenclature for these clusters. All the putative enhancer clusters demonstrated a distinct “valley” shape, focused on the maximal point of DNase I...
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Research: Widespread cis-regulatory convergence between the extinct Tasmanian tiger and gray wolf
- Charles Y. Feigin,
- Axel H. Newton,
- and Andrew J. Pask
Genome Res. October 2019 29: 1648-1658; Published in Advance September 18, 2019, doi:10.1101/gr.244251.118
...; Dias et al. 2014; Wang et al. 2017).Convergence in thylacine and wolf brain enhancersGREAT analysis of TWARs also revealed significant enrichment of nearby brain-expressed genes (Supplemental Table S15), and several nervous system genes had multiple TWARs within their GREAT-defined gene regulatory...

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