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Research: KDM1A maintains genome-wide homeostasis of transcriptional enhancers
- Saurabh Agarwal,
- Katherine M. Bonefas,
- Patricia M. Garay,
- Emily Brookes,
- Yumie Murata-Nakamura,
- Robert S. Porter,
- Todd S. Macfarlan,
- Bing Ren,
- and Shigeki Iwase
Genome Res. February 2021 31: 186-197; Published in Advance January 7, 2021, doi:10.1101/gr.234559.118
...and KMT2D (also known as MLL3 and MLL4) primes the enhancers with H3K4me1 (Herz et al. 2012; Hu et al. 2013; Lee et al. 2013). Changes in the epigenetic landscape further determine the identity of enhancers as either active or poised through the acetylation or trimethylation of histone H3 lysine 27 (H3K27...
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Resource: Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
- Aaron C. Daugherty,
- Robin W. Yeo,
- Jason D. Buenrostro,
- William J. Greenleaf,
- Anshul Kundaje,
- and Anne Brunet
Genome Res. December 2017 27: 2096-2107; Published in Advance November 15, 2017, doi:10.1101/gr.226233.117
...as a transcriptional activator, in part due to its ability to increase chromatin accessibility (Adkins et al. 2006). Like Drosophila GAF, C. elegans EOR-1 is a transcriptional activator in the Ras/ERK signaling pathway that has been suggested to also repress gene expression (Liu et al. 2011a). GAF and EOR-1 are also...
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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
...,000 enhancers active in at least one time point during the 12-h time course. Prior to dex exposure, the vast majority of enhancers were preprogrammed (H3K27ac+, 91%) and only a small minority of enhancers were poised (H3K27ac-, H3K4me1+, 3%) or latent (H3K27ac-, H3K4me1-, 5%), consistent with previous studies...
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Resource: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
- Timothy J. Durham,
- Riza M. Daza,
- Louis Gevirtzman,
- Darren A. Cusanovich,
- Olubusayo Bolonduro,
- William Stafford Noble,
- Jay Shendure,
- and Robert H. Waterston
Genome Res. October 2021 31: 1952-1969; Published in Advance April 22, 2021, doi:10.1101/gr.271791.120
...of differences in gene regulation across germ layers in Drosophila embryogenesis (Cusanovich et al. 2018b), the generation of an atlas of 85 different clusters of cells from 13 different mouse tissues (Cusanovich et al. 2018a), and the identification of cell types in hippocampal tissue from mice (Sinnamon et al...
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Research: Chromatin architecture reorganization during neuronal cell differentiation in Drosophila genome
- Keerthi T. Chathoth and
- Nicolae Radu Zabet
Genome Res. April 2019 29: 613-625; Published in Advance February 1, 2019, doi:10.1101/gr.246710.118
...between enhancers and promoters, divergent transcription, and insulator proteins on TAD border formation in Drosophila.ResultsCharacterization of TADs based on border conservation in DrosophilaTADs have been analyzed in Drosophila previously (Hou et al. 2012; Sexton et al. 2012; Li et al. 2015; Ulianov et...
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Research: Genome-wide phosphoacetylation of histone H3 at Drosophila enhancers and promoters
- Wendy A. Kellner,
- Edward Ramos,
- Kevin Van Bortle,
- Naomi Takenaka,
- and Victor G. Corces
Genome Res. June 2012 22: 1081-1088; Published in Advance April 16, 2012, doi:10.1101/gr.136929.111
...indicate that interaction between the enhancer and the promoter is dependent on the presence of JIL-1, 14-3-3, and CBP. Genome-wide analyses extend these conclusions to most Drosophila genes, showing that the presence of JIL-1, H3K9acS10ph, and H3K27acS28ph is a general feature of enhancers and promoters...
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Research: ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm
- Marta Bozek,
- Roberto Cortini,
- Andrea Ennio Storti,
- Ulrich Unnerstall,
- Ulrike Gaul,
- and Nicolas Gompel
Genome Res. May 2019 29: 771-783; Published in Advance April 8, 2019, doi:10.1101/gr.242362.118
...-Martinsried, Germany Corresponding author: gompel@bio.lmu.deAbstractEstablishment of spatial coordinates during Drosophila embryogenesis relies on differential regulatory activity of axis patterning enhancers. Concentration gradients of activator and repressor transcription factors (TFs) provide positional information...
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Research: Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes
- Sakthi D. Moorthy,
- Scott Davidson,
- Virlana M. Shchuka,
- Gurdeep Singh,
- Nakisa Malek-Gilani,
- Lida Langroudi,
- Alexandre Martchenko,
- Vincent So,
- Neil N. Macpherson,
- and Jennifer A. Mitchell
Genome Res. February 2017 27: 246-258; Published in Advance November 28, 2016, doi:10.1101/gr.210930.116
...of this super-enhancer have been shown to be involved in Sox2 regulation in neural tissues (Ferri et al. 2004; Iwafuchi-Doi et al. 2011). Robust enhancers separate from super-enhancers Aswe found that deletion of somepredicted super-enhancers had little (Macf1, Etl4) (Table 1) or no effect (the super-enhancer...
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Research: H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction
- Gillian C.A. Taylor,
- Ragnhild Eskeland,
- Betül Hekimoglu-Balkan,
- Madapura M. Pradeepa,
- and Wendy A. Bickmore
Genome Res. December 2013 23: 2053-2065; Published in Advance August 29, 2013, doi:10.1101/gr.155028.113
...and glial enhancers at the mouse Sox10 locus through transgenesis in zebrafish. PLoS Genet 4: e1000174. Bone JR, Lavender J, Richman R, Palmer MJ, Turner BM, Kuroda MI. 1994. Acetylated histone H4 on the male X chromosome is associated with dosage compensation in Drosophila. Genes Dev 8: 96–104. Cai Y, Jin...
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Research: Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
- Ozren Bogdanović,
- Steven W. Long,
- Simon J. van Heeringen,
- Arie B. Brinkman,
- Jose Luis Gómez-Skarmeta,
- Hendrik G. Stunnenberg,
- Peter L. Jones,
- and Gert Jan C. Veenstra
Genome Res. August 2011 21: 1313-1327; Published in Advance June 2, 2011, doi:10.1101/gr.114843.110
...regulated epigenetic mark associated with transcriptional repression. Next-generation sequencing of purified methylated DNA obtained from early Xenopus tropicalis embryos demonstrates that this genome is heavily methylated during blastula and gastrula stages. Although DNA methylation is largely absent...

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