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Corrigendum: Corrigendum: Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators
- David van Dijk,
- Eilon Sharon,
- Maya Lotan-Pompan,
- Adina Weinberger,
- Eran Segal,
- and Lucas B. Carey
Genome Res. March 2017 27: 500; doi:10.1101/gr.220574.117
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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
...with changes in regulatory activity, but this relationship is obscured when considering mutations across multiple cis-regulatory elements (CREs). Taken together, these results demonstrate that the activity of CRX binding sites is highly dependent on sequence context, providing insight into photoreceptor gene...
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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
...).Predicted regulatory sites can be validated experimentally using reporter gene assays. In this assay, the transcriptional activity of a predicted promoter, or an enhancer, of a specific GOI can be investigated using plasmids that include the predicted regulatory sequence upstream of a reporter gene (for...
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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
....aerts@med.kuleuven.be Abstract Transcription factors regulate their target genes by binding to regulatory regions in the genome. Although the binding preferences of TP53 are known, it remains unclear what distinguishes functional enhancers from nonfunctional binding. In addition, the genome is scattered with recognition...
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Research: Drosophila poised enhancers are generated during tissue patterning with the help of repression
- Nina Koenecke,
- Jeff Johnston,
- Qiye He,
- Samuel Meier,
- and Julia Zeitlinger
Genome Res. January 2017 27: 64-74; Published in Advance November 14, 2016, doi:10.1101/gr.209486.116
...during tissue patterning. We discuss the possibility that the poised enhancer state is more generally the result of repression by transcriptional repressors. [Supplemental material is available for this article.] Understanding themechanisms by which cis-regulatory elements, or enhancers, activate...
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Method: Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks
- David R. Kelley,
- Jasper Snoek,
- and John L. Rinn
Genome Res. July 2016 26: 990-999; Published in Advance May 3, 2016, doi:10.1101/gr.200535.115
...prioritize variants predicted to drive the regulatory activity and devalue those predicted to be irrelevant bystanders. Second, rare variants that introduce a gain of function will often not overlap regulatory annotations in publicly available data. An accurate model for regulatory activity can predict...
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Research: A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen
- Sung Ho Yoon,
- Serdar Turkarslan,
- David J. Reiss,
- Min Pan,
- June A. Burn,
- Kyle C. Costa,
- Thomas J. Lie,
- Joseph Slagel,
- Robert L. Moritz,
- Murray Hackett,
- John A. Leigh,
- and Nitin S. Baliga
Genome Res. November 2013 23: 1839-1851; Published in Advance October 2, 2013, doi:10.1101/gr.153916.112
...are summarized in Supplemental Table S4. Biclustering analysis reveals complex transcriptional regulatory patterns of genes involved in the methanogenesis pathway We performed the network inference in two steps to first uncover the modular organization of genes based on their conditional coregulation and, second...
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Research: Multidimensional regulation of gene expression in the C. elegans embryo
- John Isaac Murray,
- Thomas J. Boyle,
- Elicia Preston,
- Dionne Vafeados,
- Barbara Mericle,
- Peter Weisdepp,
- Zhongying Zhao,
- Zhirong Bao,
- Max Boeck,
- and Robert H. Waterston
Genome Res. July 2012 22: 1282-1294; Published in Advance April 16, 2012, doi:10.1101/gr.131920.111
...in part by the TCF-LEF transcription factor POP-1. Other genes' reporters exhibited patterns correlated with tissue, position, and left–right asymmetry. Sequential patterns both within tissues and series of sublineages suggest regulatory pathways. Expression patterns often differ between embryonic...
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Resource: A spatial and temporal map of C. elegans gene expression
- W. Clay Spencer,
- Georg Zeller,
- Joseph D. Watson,
- Stefan R. Henz,
- Kathie L. Watkins,
- Rebecca D. McWhirter,
- Sarah Petersen,
- Vipin T. Sreedharan,
- Christian Widmer,
- Jeanyoung Jo,
- Valerie Reinke,
- Lisa Petrella,
- Susan Strome,
- Stephen E. Von Stetina,
- Menachem Katz,
- Shai Shaham,
- Gunnar Rätsch,
- and David M. Miller III
Genome Res. February 2011 21: 325-341; Published in Advance December 22, 2010, doi:10.1101/gr.114595.110
...corresponding to established gene models and revealed novel transcriptionally active regions (TARs) in noncoding domains that comprise at least 10% of the total C. elegans genome. Our results show that about 75% of transcripts with detectable expression are differentially expressed among developmental stages...
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ARTICLE: Extensive low-affinity transcriptional interactions in the yeast genome
- Amos Tanay
Genome Res. August 2006 16: 962-972; Published in Advance June 29, 2006, doi:10.1101/gr.5113606
...at the characterization of transcriptional networks on a genomic scale. The ultimate goal of many of these studies is to construct networks associating transcription factors with genes via well-defined binding sites. Weaker regulatory interactions other than those occurring at high-affinity binding sites are largely...

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