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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 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...to mediate 57 consistent phenotypic outcomes there must also be consistent regulation of such genes by 58 cis-regulatory modules (CRMs). CRMs consist of clusters of transcription factor binding sites 59 (TFBSs) that regulate the expression of target genes through collective or competitive binding 60...
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Resource: Modeling transcriptional regulation of model species with deep learning
- Evan M. Cofer,
- João Raimundo,
- Alicja Tadych,
- Yuji Yamazaki,
- Aaron K. Wong,
- Chandra L. Theesfeld,
- Michael S. Levine,
- and Olga G. Troyanskaya
Genome Res. June 2021 31: 1097-1105; Published in Advance April 22, 2021, doi:10.1101/gr.266171.120
...remains a grand challenge of modern biology. Model species have long been at the forefront of biological discovery and biomedical innovation, but our knowledge of the cis-regulatory logic remains incomplete (Manolio et al. 2017). Many important questions remain: How should we mutate a fly enhancer...
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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
.... In fact, we reported a 671 high number of peak-gene pairs showing early opening cis-regulatory logic, 672 consistent with previous findings in medaka and mammals (Chereji et al., 2019; 673 Li et al., 2020) 674 As ontogeny continues post-hatching, several biological processes were not 675 enriched among...
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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
...potential binding sites and many candidate TFs. It is clear that the reactions underlying transcriptional regulation are much more complicated than the simple logic used to describe it. For example, characterization of mechanisms that control stochastic and noisy gene expression ( Elowitz et al. 2002...
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Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- Belle A. Moyers,
- E. Christopher Partridge,
- Mark Mackiewicz,
- Michael J. Betti,
- Roshan Darji,
- Sarah K. Meadows,
- Kimberly M. Newberry,
- Laurel A. Brandsmeier,
- Barbara J. Wold,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
...-acting proteins that bind cis-regulatory elements (CREs) in DNA to control gene expression. Here, we analyzed the genomic localization profiles of 529 sequence-specific TFs and 151 cofactors and chromatin regulators in the human cancer cell line HepG2, for a total of 680 broadly termed DNA-associated proteins...
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Research: Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis
- Arun B. Dutta,
- Daniel S. Lank,
- Roza K. Przanowska,
- Piotr Przanowski,
- Lixin Wang,
- Bao Nguyen,
- Ninad M. Walavalkar,
- Fabiana M. Duarte,
- and Michael J. Guertin
Genome Res. March 2023 33: 314-331; Published in Advance February 21, 2023, doi:10.1101/gr.277559.122
...(Takahashi and Yamanaka 2006). Sequence-specific TFs bind to conserved motifs (Ptashne 1967) in REs within promoters and enhancers to regulate different mechanistic steps in transcription (Fuda et al. 2009). TFs recruit cofactors such as chromatin-modifying enzymes and general transcription machinery to REs...
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Research: Enhancer–silencer transitions in the human genome
- Di Huang and
- Ivan Ovcharenko
Genome Res. March 2022 32: 437-448; Published in Advance February 1, 2022, doi:10.1101/gr.275992.121
..., they are enriched in the loci of transcriptional regulators, such as transcription factors (TFs) and chromatin remodeling genes. Dual-function REs consist of two intertwined but largely distinct sets of binding sites bound by either activating or repressing TFs, depending on the type of RE function in a given cell...
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Research: Transposable elements are the primary source of novelty in primate gene regulation
- Marco Trizzino,
- YoSon Park,
- Marcia Holsbach-Beltrame,
- Katherine Aracena,
- Katelyn Mika,
- Minal Caliskan,
- George H. Perry,
- Vincent J. Lynch,
- and Christopher D. Brown
Genome Res. October 2017 27: 1623-1633; Published in Advance August 30, 2017, doi:10.1101/gr.218149.116
...16802, USA Gene regulation shapes the evolution of phenotypic diversity. We investigated the evolution of liver promoters and enhancers in six primate species using ChIP-seq (H3K27ac and H3K4me1) to profile cis-regulatory elements (CREs) and using RNAseq to characterize gene expression in the same...
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Research: Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
- Pouya Kheradpour,
- Jason Ernst,
- Alexandre Melnikov,
- Peter Rogov,
- Li Wang,
- Xiaolan Zhang,
- Jessica Alston,
- Tarjei S. Mikkelsen,
- and Manolis Kellis
Genome Res. May 2013 23: 800-811; Published in Advance March 19, 2013, doi:10.1101/gr.144899.112
...a general strategy for deciphering cis -regulatory elements by systematic large-scale manipulation and provide quantitative enhancer activity measurements across thousands of constructs that can be mined to develop predictive models of gene expression. Footnotes ↵ 6 Corresponding author E...
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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
...regulation and illustrating functional principles of homeodomain binding sites that may be conserved in other cell types.Advances in high-throughput sequencing have enabled -wide mapping of cis-regulatory elements (CREs) in diverse cell types and tissues, providing powerful resources for studying the role...

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