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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
...different cell types. This work has been cited extensively as evidence for housekeeping genes using common enhancers. The conclusion, however, was based on the work conducted on a few promoters in two Drosophila cell lines (Zabidi et al. 2015) and the STARR-seq system using a reporter gene to observe...
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Research: Genomic environments scale the activities of diverse core promoters
- Clarice K.Y. Hong and
- Barak A. Cohen
Genome Res. January 2022 32: 85-96; Published in Advance December 27, 2021, doi:10.1101/gr.276025.121
...and dev promoters used. Alternatively, the differences might be due to technical differences between the episomal MPRAs used previously and the -integrated assays used here, or to biological differences between Drosophila and human cells. Controlling the intrinsic strengths of different classes...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...organism Encyclopedia of Regulatory Networks) consortia to systematically assay TF binding events in vivo in two major model organisms, Drosophila melanogaster (fly) and Caenorhabditis elegans (worm). These data sets comprise 605 TFs identifying 3.6 M sites in the fly and 356 TFs identifying 0.9 M sites...
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Research: Systematic interrogation of human promoters
- Shira Weingarten-Gabbay,
- Ronit Nir,
- Shai Lubliner,
- Eilon Sharon,
- Yael Kalma,
- Adina Weinberger,
- and Eran Segal
Genome Res. February 2019 29: 171-183; Published in Advance January 8, 2019, doi:10.1101/gr.236075.118
...). With the growing appreciation of the importance of core promoters in determining gene expression, two recent studies measured the autonomous promoter activity of random native sequences -wide in human and Drosophila (Arnold et al. 2017; Cvetesic and Lenhard 2017; van Arensbergen et al. 2017). These approaches...
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Research: Damage-responsive elements in Drosophila regeneration
- Elena Vizcaya-Molina,
- Cecilia C. Klein,
- Florenci Serras,
- Rakesh K. Mishra,
- Roderic Guigó,
- and Montserrat Corominas
Genome Res. December 2018 28: 1852-1866; Published in Advance November 20, 2018, doi:10.1101/gr.233098.117
...by coordinated actions of genomic regions that control the activity of multiple sequence-specific DNA binding proteins. Using -wide approaches to interrogate chromatin function, we here identify the elements that regulate tissue recovery in Drosophila imaginal discs, which show a high regenerative capacity after...
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Resource: Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis
- Rui Yokomori,
- Kotaro Shimai,
- Koki Nishitsuji,
- Yutaka Suzuki,
- Takehiro G. Kusakabe,
- and Kenta Nakai
Genome Res. January 2016 26: 140-150; Published in Advance December 14, 2015, doi:10.1101/gr.184648.114
...to be associated with TATA boxes and CpG islands, respectively (Carninci et al. 2006). These two promoter classes have also been found in Drosophila melanogaster (Rach et al. 2009; Ni et al. 2010; Hoskins et al. 2011), but there is a difference in the associated motifs between human and Drosophila; the broad...
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Research: GC skew defines distinct RNA polymerase pause sites in CpG island promoters
- Wendy A. Kellner,
- Joshua S.K. Bell,
- and Paula M. Vertino
Genome Res. November 2015 25: 1600-1609; Published in Advance August 14, 2015, doi:10.1101/gr.189068.114
...supercoiling-dependent manner in vitro (Belotserkovskii et al. 2010), and promoter-proximal pausing has been correlated with local thermodynamic stability of the RNA:DNA duplex in Drosophila (Nechaev et al. 2010). Consistent with a tetheringmodel, Pol II paused in close proximity to the G-rich sequences...
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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: Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation
- Yujia Sun,
- Chung-Yi Nien,
- Kai Chen,
- Hsiao-Yun Liu,
- Jeff Johnston,
- Julia Zeitlinger,
- and Christine Rushlow
Genome Res. November 2015 25: 1703-1714; Published in Advance September 2, 2015, doi:10.1101/gr.192542.115
...motifs embedded in nucleosomes, Zld’s ability to reduce nucleosome occupancy and facilitate the binding of TFs certainly fulfills a pioneering role. The pioneering role we presented here for Zld during Drosophila ZGAmay be a general feature of key zygotic activators. For example, Pou5f3, which controls...
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Research: Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
- Valer Gotea,
- Axel Visel,
- John M. Westlund,
- Marcelo A. Nobrega,
- Len A. Pennacchio,
- and Ivan Ovcharenko
Genome Res. May 2010 20: 565-577; Published in Advance April 2, 2010, doi:10.1101/gr.104471.109
...has been extensively studied and used for predicting novel regulatory elements and their function, grouping of binding sites for the same transcription factor (TF) into homotypic clusters of TFBSs (HCTs) has been studied and observed almost exclusively in invertebrates, especially inDrosophila...
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