Searching journal content for articles similar to Ehrenberg et al. 13 (11): 2375.

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  1. Method: Cross-species analysis of enhancer logic using deep learning
    • Liesbeth Minnoye,
    • Ibrahim Ihsan Taskiran,
    • David Mauduit,
    • Maurizio Fazio,
    • Linde Van Aerschot,
    • Gert Hulselmans,
    • Valerie Christiaens,
    • Samira Makhzami,
    • Monika Seltenhammer,
    • Panagiotis Karras,
    • Aline Primot,
    • Edouard Cadieu,
    • Ellen van Rooijen,
    • Jean-Christophe Marine,
    • Giorgia Egidy,
    • Ghanem-Elias Ghanem,
    • Leonard Zon,
    • Jasper Wouters,
    • and Stein Aerts
    Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
    ...affinity, understanding this “enhancer logic” can help interpret the functional role of enhancers within a gene regulatory network. Several techniques exist to study the enhancer code, including (1) motif discovery tools (Bailey et al. 2009; Heinz et al. 2010; Thomas-Chollier et al. 2011, 2012; Janky et al...
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  2. Research: A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes
    • Joe R. Harman,
    • Ross Thorne,
    • Max Jamilly,
    • Marta Tapia,
    • Nicholas T. Crump,
    • Siobhan Rice,
    • Ryan Beveridge,
    • Edward Morrissey,
    • Marella F.T.R. de Bruijn,
    • Irene Roberts,
    • Anindita Roy,
    • Tudor A. Fulga,
    • and Thomas A. Milne
    Genome Res. July 2021 31: 1159-1173; Published in Advance June 4, 2021, doi:10.1101/gr.268490.120
    ...targets in feed-forward loops and cascade motifsBecause RUNX1 is part of the core KMT2A-AFF1 network, we wanted to interrogate the regulatory logic of combined KMT2A-AFF1:RUNX1 activity in the GRN. Nascent RNA-seq in RUNX1 KDs identified 5212 DEGs (Supplemental Data S3), the majority of which were bound...
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  3. Method: A synergistic DNA logic predicts genome-wide chromatin accessibility
    • Tatsunori Hashimoto,
    • Richard I. Sherwood,
    • Daniel D. Kang,
    • Nisha Rajagopal,
    • Amira A. Barkal,
    • Haoyang Zeng,
    • Bart J.M. Emons,
    • Sharanya Srinivasan,
    • Tommi Jaakkola,
    • and David K. Gifford
    Genome Res. October 2016 26: 1430-1440; Published in Advance July 25, 2016, doi:10.1101/gr.199778.115
    ...A synergistic DNA logic predicts genome-wide chromatin accessibility Tatsunori Hashimoto 1 , 3 , Richard I. Sherwood 2 , 3 , Daniel D. Kang 1 , 3 , Nisha Rajagopal 1 , Amira A. Barkal 1 , 2 , Haoyang Zeng 1 , Bart J...
  4. 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
    ...Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic Annelien Verfaillie 1 , Dmitry Svetlichnyy 1 , Hana Imrichova 1 , Kristofer Davie 1 , Mark Fiers 2 , Zeynep Kalender Atak 1 , Gert Hulselmans 1...
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  5. Research: The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions
    • Julie Dubois-Chevalier,
    • Vanessa Dubois,
    • Hélène Dehondt,
    • Parisa Mazrooei,
    • Claire Mazuy,
    • Aurélien A. Sérandour,
    • Céline Gheeraert,
    • Penderia Guillaume,
    • Eric Baugé,
    • Bruno Derudas,
    • Nathalie Hennuyer,
    • Réjane Paumelle,
    • Guillemette Marot,
    • Jason S. Carroll,
    • Mathieu Lupien,
    • Bart Staels,
    • Philippe Lefebvre,
    • and Jérôme Eeckhoute
    Genome Res. June 2017 27: 985-996; Published in Advance April 11, 2017, doi:10.1101/gr.217075.116
    ...), as our model system to tackle this question. Using integrative cistromic, epigenomic, transcriptomic, and interactomic analyses, we reveal a logical organization where trans-regulatory modules (TRMs), which consist of subsets of preferentially and coordinately corecruited TRs, assemble into hierarchical...
  6. 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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  7. Research: 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. January 2017 27: 87-94; Published in Advance December 13, 2016, doi:10.1101/gr.212316.116
    ...A, Segal E. 2012. Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat Biotechnol 30: 521–530. ↵Sharon E, van Dijk D, Kalma Y, Keren L, Manor O, Yakhini Z, Segal E. 2014. Probing the effect of promoters on noise in gene expression...
  8. Resource: Epigenomics of embryogenesis in turbot
    • Oscar Aramburu,
    • Belen G Pardo,
    • Ada Jimenez-Gonzalez,
    • Andrés Blanco-Hortas,
    • Daniel Macqueen,
    • Carmen Bouza,
    • and Paulino Martinez
    Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
    ...-priming before the onset of 370 transcription. To test the occurrence of more complex dynamics, the cis-371 regulatory logic of consensus ATAC peaks with their closest gene was tested 372 adapting the approach of Li et al. (2020), which considers three regulatory 373 logics: synchronization, repression...
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  9. Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
    • Daniela M. Riley,
    • Randa Elsayed,
    • Mark D. Walsh,
    • Simaran Johal,
    • Ying Lin,
    • Harry Walton,
    • Till Bretschneider,
    • Sascha Ott,
    • and Andrew C. Nelson
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
    ...suggests particular constraints on the regulatory logic and architecture of trans-dev gene CRMs, although the understanding of this is currently lacking. Although the importance and complete range of functions of HCNEs remain to be fully understood, many have been shown to direct tissue-specific gene...
  10. Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
    • Shelley Reich,
    • Tobias Loschko,
    • Julie Jung,
    • Samantha Nestel,
    • Ralf J. Sommer,
    • and Michael S. Werner
    Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
    ...expectations for when differential gene expression should matter. Here, we collated existing data into a gene-regulatory network (GRN) and performed developmental transcriptomics across different environmental conditions, genetic backgrounds, and mutants to assess the regulatory logic of mouth-form plasticity...
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