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Research: Functional characterization of enhancer activity during a long terminal repeat's evolution
- Alan Y. Du,
- Xiaoyu Zhuo,
- Vasavi Sundaram,
- Nicholas O. Jensen,
- Hemangi G. Chaudhari,
- Nancy L. Saccone,
- Barak A. Cohen,
- and Ting Wang
Genome Res. October 2022 32: 1840-1851; Published in Advance October 3, 2022, doi:10.1101/gr.276863.122
...is consistent with cell type–specific activity commonly seen in enhancers (Fig. 3A). Out of 1506 motif-focused sequences tested, 1004 were classified as active in HepG2, whereas only 52 were classified as active in K562. For genomic LTR18A, 786 (123 from hg19) were active in HepG2 and 31 (four from hg19) were...
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Research: Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
- Annelien Verfaillie,
- Dmitry Svetlichnyy,
- Hana Imrichova,
- Kristofer Davie,
- Mark Fiers,
- Zeynep Kalender Atak,
- Gert Hulselmans,
- Valerie Christiaens,
- and Stein Aerts
Genome Res. July 2016 26: 882-895; Published in Advance May 18, 2016, doi:10.1101/gr.204149.116
...of a single TP53 canonical motif. By combining machine learning with a meta-analysis of TP53 ChIP-seq data sets, we identified a core set of more than 1000 responsive enhancers in the human . This TP53 cistrome is invariably used between cell types and experimental conditions, whereas differences among...
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Research: High-throughput functional comparison of promoter and enhancer activities
- Thomas A. Nguyen,
- Richard D. Jones,
- Andrew R. Snavely,
- Andreas R. Pfenning,
- Rory Kirchner,
- Martin Hemberg,
- and Jesse M. Gray
Genome Res. August 2016 26: 1023-1033; Published in Advance June 16, 2016, doi:10.1101/gr.204834.116
...with a luciferase coding sequence in place of GFP. (D) Comparison of MPRA-based and luciferase-based enhancer activity measurements, with each shape representing a specific test sequence. Test sequences are artificial, with repeats of RFX (square), AP1 (circle), MYBL2 (triangle), and NFYshort (diamond) motifs...
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Research: Local sequence features that influence AP-1 cis-regulatory activity
- Hemangi G. Chaudhari and
- Barak A. Cohen
Genome Res. February 2018 28: 171-181; Published in Advance January 5, 2018, doi:10.1101/gr.226530.117
...near Activator Protein 1 (AP-1) binding sites that reside in DNase I Hypersensitive Sites (DHS) and regions annotated as Enhancers. In these regions, we found that sequence features directly adjacent to the core motif distinguish high from low activity AP-1 sites. Some nearby features are motifs...
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Research: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity
- Fumitaka Inoue,
- Martin Kircher,
- Beth Martin,
- Gregory M. Cooper,
- Daniela M. Witten,
- Michael T. McManus,
- Nadav Ahituv,
- and Jay Shendure
Genome Res. January 2017 27: 38-52; Published in Advance November 9, 2016, doi:10.1101/gr.212092.116
.... For example, the ENCODE Project Consortium and other efforts have identified thousands of candidate enhancers in mammalian s on the basis of such marks or their correlates (e.g., EP300 ChIP-seq, H3K27ac ChIP-seq, and DNase I hypersensitivity) in diverse cell lines and tissues (Visel et al. 2009; The ENCODE...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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Method: A universal framework for detecting cis-regulatory diversity in DNA regions
- Anushua Biswas and
- Leelavati Narlikar
Genome Res. September 2021 31: 1646-1662; Published in Advance July 19, 2021, doi:10.1101/gr.274563.120
.... Indeed, enrichment of CTCF and Su(Hw) in module 11 suggests this module harbors insulators. Similarly, dinucleotide repeats of GA (bound by GAGA binding factor Trl) and CA are known to be features of fly enhancers (Yanez-Cuna et al. 2014). One of the promoter modules is comprised of tRNAs, and cis...
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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
...-specific ones (Fig. 5C).View larger version: In this window In a new window Figure 5. Cell-type–specific enhancers correlate with cell-type–specific TAD borders. (A) Venn diagram representing the number of enhancers in neuronal and embryonic Drosophila cells as identified by STARR-seq. Enhancers were...
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Research: A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo
- Andrew E.O. Hughes,
- Connie A. Myers,
- and Joseph C. Corbo
Genome Res. October 2018 28: 1520-1531; Published in Advance August 29, 2018, doi:10.1101/gr.231886.117
...in mouse photoreceptors. First, we identified sequence features that predict CRX occupancy in vivo (as determined by ChIP-seq), and we compared these to sequence features that are correlated with enhancer activity (as measured by MPRA). In addition, we assayed the effect of inactivating mutations...
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Research: Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation
- Marina Veil,
- Lev Y. Yampolsky,
- Björn Grüning,
- and Daria Onichtchouk
Genome Res. March 2019 29: 383-395; Published in Advance January 23, 2019, doi:10.1101/gr.240572.118
...to the enhancers. Dinucleotide repeats that we detected on all TFBSs (Supplemental Fig. S2) and that had been previously characterized as general enhancer features (Yanez-Cuna et al. 2014) contribute to the periodic nucleosome positioning signal underlying HNAR center (Kaplan et al. 2009) and, at the same time...

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