1
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Naderi J, Magalhaes AP, Kibar G, Stik G, Zhang Y, Mackowiak SD, Wieler HM, Rossi F, Buschow R, Christou-Kent M, Alcoverro-Bertran M, Graf T, Vingron M, Hnisz D. An activity-specificity trade-off encoded in human transcription factors. Nat Cell Biol 2024; 26:1309-1321. [PMID: 38969762 PMCID: PMC11321997 DOI: 10.1038/s41556-024-01411-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/20/2024] [Indexed: 07/07/2024]
Abstract
Transcription factors (TFs) control specificity and activity of gene transcription, but whether a relationship between these two features exists is unclear. Here we provide evidence for an evolutionary trade-off between the activity and specificity in human TFs encoded as submaximal dispersion of aromatic residues in their intrinsically disordered protein regions. We identified approximately 500 human TFs that encode short periodic blocks of aromatic residues in their intrinsically disordered regions, resembling imperfect prion-like sequences. Mutation of periodic aromatic residues reduced transcriptional activity, whereas increasing the aromatic dispersion of multiple human TFs enhanced transcriptional activity and reprogramming efficiency, promoted liquid-liquid phase separation in vitro and more promiscuous DNA binding in cells. Together with recent work on enhancer elements, these results suggest an important evolutionary role of suboptimal features in transcriptional control. We propose that rational engineering of amino acid features that alter phase separation may be a strategy to optimize TF-dependent processes, including cellular reprogramming.
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Affiliation(s)
- Julian Naderi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Alexandre P Magalhaes
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gözde Kibar
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Gregoire Stik
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Yaotian Zhang
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sebastian D Mackowiak
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hannah M Wieler
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Francesca Rossi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Rene Buschow
- Microscopy Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marie Christou-Kent
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marc Alcoverro-Bertran
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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2
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Meyer K, Lammers NC, Bugaj LJ, Garcia HG, Weiner OD. Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation. Nat Commun 2023; 14:6929. [PMID: 37903793 PMCID: PMC10616176 DOI: 10.1038/s41467-023-42643-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
YAP is a transcriptional regulator that controls pluripotency, cell fate, and proliferation. How cells ensure the selective activation of YAP effector genes is unknown. This knowledge is essential to rationally control cellular decision-making. Here we leverage optogenetics, live-imaging of transcription, and cell fate analysis to understand and control gene activation and cell behavior. We reveal that cells decode the steady-state concentrations and timing of YAP activation to control proliferation, cell fate, and expression of the pluripotency regulators Oct4 and Nanog. While oscillatory YAP inputs induce Oct4 expression and proliferation optimally at frequencies that mimic native dynamics, cellular differentiation requires persistently low YAP levels. We identify the molecular logic of the Oct4 dynamic decoder, which acts through an adaptive change sensor. Our work reveals how YAP levels and dynamics enable multiplexing of information transmission for the regulation of developmental decision-making and establishes a platform for the rational control of these behaviors.
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Affiliation(s)
- Kirstin Meyer
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas C Lammers
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Orion D Weiner
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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3
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Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Dev Cell 2023; 58:1898-1916.e9. [PMID: 37557175 PMCID: PMC10592203 DOI: 10.1016/j.devcel.2023.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/09/2023] [Accepted: 07/13/2023] [Indexed: 08/11/2023]
Abstract
Chromatin accessibility is integral to the process by which transcription factors (TFs) read out cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive accessibility and those that do not. Deep learning models that learn complex sequence rules provide an unprecedented opportunity to dissect this problem. Using zygotic genome activation in Drosophila as a model, we analyzed high-resolution TF binding and chromatin accessibility data with interpretable deep learning and performed genetic validation experiments. We identify a hierarchical relationship between the pioneer TF Zelda and the TFs involved in axis patterning. Zelda consistently pioneers chromatin accessibility proportional to motif affinity, whereas patterning TFs augment chromatin accessibility in sequence contexts where they mediate enhancer activation. We conclude that chromatin accessibility occurs in two tiers: one through pioneering, which makes enhancers accessible but not necessarily active, and the second when the correct combination of TFs leads to enhancer activation.
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Affiliation(s)
- Kaelan J Brennan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sabrina Krueger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA
| | - Hsiao-Yun Liu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Ally W H Yang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jason A Morrison
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA; Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS 66160, USA.
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4
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Alamos S, Reimer A, Westrum C, Turner MA, Talledo P, Zhao J, Luu E, Garcia HG. Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient. Cell Syst 2023; 14:220-236.e3. [PMID: 36696901 PMCID: PMC10125799 DOI: 10.1016/j.cels.2022.12.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/03/2022] [Accepted: 12/21/2022] [Indexed: 01/26/2023]
Abstract
How enhancers interpret morphogen gradients to generate gene expression patterns is a central question in developmental biology. Recent studies have proposed that enhancers can dictate whether, when, and at what rate promoters engage in transcription, but the complexity of endogenous enhancers calls for theoretical models with too many free parameters to quantitatively dissect these regulatory strategies. To overcome this limitation, we established a minimal promoter-proximal synthetic enhancer in embryos of Drosophila melanogaster. Here, a gradient of the Dorsal activator is read by a single Dorsal DNA binding site. Using live imaging to quantify transcriptional activity, we found that a single binding site can regulate whether promoters engage in transcription in a concentration-dependent manner. By modulating the binding-site affinity, we determined that a gene's decision to transcribe and its transcriptional onset time can be explained by a simple model where the promoter traverses multiple kinetic barriers before transcription can ensue.
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Affiliation(s)
- Simon Alamos
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Armando Reimer
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
| | - Clay Westrum
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - Meghan A Turner
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Paul Talledo
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jiaxi Zhao
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - Emma Luu
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA; Department of Physics, University of California at Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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5
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Xie J, Wang W, Yang T, Zhang Q, Zhang Z, Zhu X, Li N, Zhi L, Ma X, Zhang S, Liu Y, Wang X, Li F, Zhao Y, Jia X, Zhou J, Jiang N, Li G, Liu M, Liu S, Li L, Zeng A, Du M, Zhang Z, Li J, Zhang Z, Li Z, Zhang H. Large-scale genomic and transcriptomic profiles of rice hybrids reveal a core mechanism underlying heterosis. Genome Biol 2022; 23:264. [PMID: 36550554 PMCID: PMC9773586 DOI: 10.1186/s13059-022-02822-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Heterosis is widely used in agriculture. However, its molecular mechanisms are still unclear in plants. Here, we develop, sequence, and record the phenotypes of 418 hybrids from crosses between two testers and 265 rice varieties from a mini-core collection. RESULTS Phenotypic analysis shows that heterosis is dependent on genetic backgrounds and environments. By genome-wide association study of 418 hybrids and their parents, we find that nonadditive QTLs are the main genetic contributors to heterosis. We show that nonadditive QTLs are more sensitive to the genetic background and environment than additive ones. Further simulations and experimental analysis support a novel mechanism, homo-insufficiency under insufficient background (HoIIB), underlying heterosis. We propose heterosis in most cases is not due to heterozygote advantage but homozygote disadvantage under the insufficient genetic background. CONCLUSION The HoIIB model elucidates that genetic background insufficiency is the intrinsic mechanism of background dependence, and also the core mechanism of nonadditive effects and heterosis. This model can explain most known hypotheses and phenomena about heterosis, and thus provides a novel theory for hybrid rice breeding in future.
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Affiliation(s)
- Jianyin Xie
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Weiping Wang
- grid.496830.00000 0004 7648 0514State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125 China
| | - Tao Yang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Quan Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhifang Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xiaoyang Zhu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Ni Li
- grid.496830.00000 0004 7648 0514State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125 China
| | - Linran Zhi
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xiaoqian Ma
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Shuyang Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Yan Liu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xueqiang Wang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Fengmei Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,grid.428986.90000 0001 0373 6302Sanya Nanfan Research Institute of Hainan University, Sanya, 572024 China
| | - Yan Zhao
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xuewei Jia
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jieyu Zhou
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Ningjia Jiang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,Sanya Institute of China Agricultural University, Sanya, 572024 China
| | - Gangling Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Miaosong Liu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Shijin Liu
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Lin Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - An Zeng
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,grid.428986.90000 0001 0373 6302Sanya Nanfan Research Institute of Hainan University, Sanya, 572024 China ,Sanya Institute of China Agricultural University, Sanya, 572024 China
| | - Mengke Du
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,grid.428986.90000 0001 0373 6302Sanya Nanfan Research Institute of Hainan University, Sanya, 572024 China
| | - Zhanying Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jinjie Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Ziding Zhang
- grid.22935.3f0000 0004 0530 8290State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193 China
| | - Zichao Li
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,Sanya Institute of China Agricultural University, Sanya, 572024 China ,grid.22935.3f0000 0004 0530 8290State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193 China
| | - Hongliang Zhang
- grid.22935.3f0000 0004 0530 8290Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China ,grid.428986.90000 0001 0373 6302Sanya Nanfan Research Institute of Hainan University, Sanya, 572024 China ,Sanya Institute of China Agricultural University, Sanya, 572024 China
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6
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Kim YJ, Rhee K, Liu J, Jeammet S, Turner MA, Small SJ, Garcia HG. Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer. eLife 2022; 11:73395. [PMID: 36503705 PMCID: PMC9836395 DOI: 10.7554/elife.73395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
A challenge in quantitative biology is to predict output patterns of gene expression from knowledge of input transcription factor patterns and from the arrangement of binding sites for these transcription factors on regulatory DNA. We tested whether widespread thermodynamic models could be used to infer parameters describing simple regulatory architectures that inform parameter-free predictions of more complex enhancers in the context of transcriptional repression by Runt in the early fruit fly embryo. By modulating the number and placement of Runt binding sites within an enhancer, and quantifying the resulting transcriptional activity using live imaging, we discovered that thermodynamic models call for higher-order cooperativity between multiple molecular players. This higher-order cooperativity captures the combinatorial complexity underlying eukaryotic transcriptional regulation and cannot be determined from simpler regulatory architectures, highlighting the challenges in reaching a predictive understanding of transcriptional regulation in eukaryotes and calling for approaches that quantitatively dissect their molecular nature.
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Affiliation(s)
- Yang Joon Kim
- Chan Zuckerberg Biohub, San Francisco, United States
| | - Kaitlin Rhee
- Department of Chemical Biology, University of California, Berkeley, Berkeley, United States
| | - Jonathan Liu
- Department of Physics, University of California, Berkeley, Berkeley, United States
| | - Selene Jeammet
- Department of Biology, Ecole Polytechnique, Paris, France
| | - Meghan A Turner
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Stephen J Small
- Department of Biology, New York University, New York, United States
| | - Hernan G Garcia
- Chan Zuckerberg Biohub, San Francisco, United States.,Department of Physics, University of California, Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, United States
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7
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Shahein A, López-Malo M, Istomin I, Olson EJ, Cheng S, Maerkl SJ. Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance. Nat Commun 2022; 13:5273. [PMID: 36071116 PMCID: PMC9452512 DOI: 10.1038/s41467-022-32971-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/25/2022] [Indexed: 11/10/2022] Open
Abstract
Binding to binding site clusters has yet to be characterized in depth, and the functional relevance of low-affinity clusters remains uncertain. We characterized transcription factor binding to low-affinity clusters in vitro and found that transcription factors can bind concurrently to overlapping sites, challenging the notion of binding exclusivity. Furthermore, small clusters with binding sites an order of magnitude lower in affinity give rise to high mean occupancies at physiologically-relevant transcription factor concentrations. To assess whether the observed in vitro occupancies translate to transcriptional activation in vivo, we tested low-affinity binding site clusters in a synthetic and native gene regulatory network in S. cerevisiae. In both systems, clusters of low-affinity binding sites generated transcriptional output comparable to single or even multiple consensus sites. This systematic characterization demonstrates that clusters of low-affinity binding sites achieve substantial occupancies, and that this occupancy can drive expression in eukaryotic promoters.
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Affiliation(s)
- Amir Shahein
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Maria López-Malo
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ivan Istomin
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Evan J Olson
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Shiyu Cheng
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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8
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Rodriguez K, Do A, Senay-Aras B, Perales M, Alber M, Chen W, Reddy GV. Concentration-dependent transcriptional switching through a collective action of cis-elements. SCIENCE ADVANCES 2022; 8:eabo6157. [PMID: 35947668 PMCID: PMC9365274 DOI: 10.1126/sciadv.abo6157] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Gene expression specificity of homeobox transcription factors has remained paradoxical. WUSCHEL activates and represses CLAVATA3 transcription at lower and higher concentrations, respectively. We use computational modeling and experimental analysis to investigate the properties of the cis-regulatory module. We find that intrinsically each cis-element can only activate CLAVATA3 at a higher WUSCHEL concentration. However, together, they repress CLAVATA3 at higher WUSCHEL and activate only at lower WUSCHEL, showing that the concentration-dependent interactions among cis-elements regulate both activation and repression. Biochemical experiments show that two adjacent functional cis-elements bind WUSCHEL with higher affinity and dimerize at relatively lower levels. Moreover, increasing the distance between cis-elements prolongs WUSCHEL monomer binding window, resulting in higher CLAVATA3 activation. Our work showing a constellation of optimally spaced cis-elements of defined affinities determining activation and repression thresholds in regulating CLAVATA3 transcription provides a previously unknown mechanism of cofactor-independent regulation of transcription factor binding in mediating gene expression specificity.
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Affiliation(s)
- Kevin Rodriguez
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Albert Do
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Betul Senay-Aras
- Department of Mathematics, University of California Riverside, Riverside, CA 92521, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Mariano Perales
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
| | - Mark Alber
- Department of Mathematics, University of California Riverside, Riverside, CA 92521, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Weitao Chen
- Department of Mathematics, University of California Riverside, Riverside, CA 92521, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92521, USA
| | - G. Venugopala Reddy
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA 92521, USA
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9
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Choi Y, Luo Y, Lee S, Jin H, Yoon HJ, Hahn Y, Bae J, Lee HH. FOXL2 and FOXA1 cooperatively assemble on the TP53 promoter in alternative dimer configurations. Nucleic Acids Res 2022; 50:8929-8946. [PMID: 35920317 PMCID: PMC9410875 DOI: 10.1093/nar/gkac673] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/13/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Although both the p53 and forkhead box (FOX) family proteins are key transcription factors associated with cancer progression, their direct relationship is unknown. Here, we found that FOX family proteins bind to the non-canonical homotypic cluster of the p53 promoter region (TP53). Analysis of crystal structures of FOX proteins (FOXL2 and FOXA1) bound to the p53 homotypic cluster indicated that they interact with a 2:1 stoichiometry accommodated by FOX-induced DNA allostery. In particular, FOX proteins exhibited distinct dimerization patterns in recognition of the same p53-DNA; dimer formation of FOXA1 involved protein–protein interaction, but FOXL2 did not. Biochemical and biological functional analyses confirmed the cooperative binding of FOX proteins to the TP53 promoter for the transcriptional activation of TP53. In addition, up-regulation of TP53 was necessary for FOX proteins to exhibit anti-proliferative activity in cancer cells. These analyses reveal the presence of a discrete characteristic within FOX family proteins in which FOX proteins regulate the transcription activity of the p53 tumor suppressor via cooperative binding to the TP53 promoter in alternative dimer configurations.
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Affiliation(s)
- Yuri Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea
| | - Yongyang Luo
- School of Pharmacy, Chung-Ang University, Seoul 06974, Korea
| | - Seunghwa Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Hanyong Jin
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, Jilin Province, China
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Jeehyeon Bae
- School of Pharmacy, Chung-Ang University, Seoul 06974, Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea
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10
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Carmon S, Jonas F, Barkai N, Schejter ED, Shilo BZ. Generation and timing of graded responses to morphogen gradients. Development 2021; 148:273784. [PMID: 34918740 PMCID: PMC8722393 DOI: 10.1242/dev.199991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/17/2021] [Indexed: 11/20/2022]
Abstract
Morphogen gradients are known to subdivide a naive cell field into distinct zones of gene expression. Here, we examine whether morphogens can also induce a graded response within such domains. To this end, we explore the role of the Dorsal protein nuclear gradient along the dorsoventral axis in defining the graded pattern of actomyosin constriction that initiates gastrulation in early Drosophila embryos. Two complementary mechanisms for graded accumulation of mRNAs of crucial zygotic Dorsal target genes were identified. First, activation of target-gene expression expands over time from the ventral-most region of high nuclear Dorsal to lateral regions, where the levels are lower, as a result of a Dorsal-dependent activation probability of transcription sites. Thus, sites that are activated earlier will exhibit more mRNA accumulation. Second, once the sites are activated, the rate of RNA Polymerase II loading is also dependent on Dorsal levels. Morphological restrictions require that translation of the graded mRNA be delayed until completion of embryonic cell formation. Such timing is achieved by large introns, which provide a delay in production of the mature mRNAs. Spatio-temporal regulation of key zygotic genes therefore shapes the pattern of gastrulation.
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Affiliation(s)
- Shari Carmon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eyal D Schejter
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ben-Zion Shilo
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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11
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Mechanisms of Binding Specificity among bHLH Transcription Factors. Int J Mol Sci 2021; 22:ijms22179150. [PMID: 34502060 PMCID: PMC8431614 DOI: 10.3390/ijms22179150] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 12/25/2022] Open
Abstract
The transcriptome of every cell is orchestrated by the complex network of interaction between transcription factors (TFs) and their binding sites on DNA. Disruption of this network can result in many forms of organism malfunction but also can be the substrate of positive natural selection. However, understanding the specific determinants of each of these individual TF-DNA interactions is a challenging task as it requires integrating the multiple possible mechanisms by which a given TF ends up interacting with a specific genomic region. These mechanisms include DNA motif preferences, which can be determined by nucleotide sequence but also by DNA’s shape; post-translational modifications of the TF, such as phosphorylation; and dimerization partners and co-factors, which can mediate multiple forms of direct or indirect cooperative binding. Binding can also be affected by epigenetic modifications of putative target regions, including DNA methylation and nucleosome occupancy. In this review, we describe how all these mechanisms have a role and crosstalk in one specific family of TFs, the basic helix-loop-helix (bHLH), with a very conserved DNA binding domain and a similar DNA preferred motif, the E-box. Here, we compile and discuss a rich catalog of strategies used by bHLH to acquire TF-specific genome-wide landscapes of binding sites.
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12
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Ge W, Meier M, Roth C, Söding J. Bayesian Markov models improve the prediction of binding motifs beyond first order. NAR Genom Bioinform 2021; 3:lqab026. [PMID: 33928244 PMCID: PMC8057495 DOI: 10.1093/nargab/lqab026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/11/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific DNA motifs. Accurate models for predicting binding affinities are crucial for quantitatively understanding of transcriptional regulation. Motifs are commonly described by position weight matrices, which assume that each position contributes independently to the binding energy. Models that can learn dependencies between positions, for instance, induced by DNA structure preferences, have yielded markedly improved predictions for most TFs on in vivo data. However, they are more prone to overfit the data and to learn patterns merely correlated with rather than directly involved in TF binding. We present an improved, faster version of our Bayesian Markov model software, BaMMmotif2. We tested it with state-of-the-art motif discovery tools on a large collection of ChIP-seq and HT-SELEX datasets. BaMMmotif2 models of fifth-order achieved a median false-discovery-rate-averaged recall 13.6% and 12.2% higher than the next best tool on 427 ChIP-seq datasets and 164 HT-SELEX datasets, respectively, while being 8 to 1000 times faster. BaMMmotif2 models showed no signs of overtraining in cross-cell line and cross-platform tests, with similar improvements on the next-best tool. These results demonstrate that dependencies beyond first order clearly improve binding models for most TFs.
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Affiliation(s)
- Wanwan Ge
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Markus Meier
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Roth
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Johannes Söding
- Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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13
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Irizarry J, Stathopoulos A. Dynamic patterning by morphogens illuminated by cis-regulatory studies. Development 2021; 148:148/2/dev196113. [PMID: 33472851 DOI: 10.1242/dev.196113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Morphogen concentration changes in space as well as over time during development. However, how these dynamics are interpreted by cells to specify fate is not well understood. Here, we focus on two morphogens: the maternal transcription factors Bicoid and Dorsal, which directly regulate target genes to pattern Drosophila embryos. The actions of these factors at enhancers has been thoroughly dissected and provides a rich platform for understanding direct input by morphogens and their changing roles over time. Importantly, Bicoid and Dorsal do not work alone; we also discuss additional inputs that work with morphogens to control spatiotemporal gene expression in embryos.
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Affiliation(s)
- Jihyun Irizarry
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Angelike Stathopoulos
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Blvd., Pasadena, CA 91125, USA
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14
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Berndt AJ, Othonos KM, Lian T, Flibotte S, Miao M, Bhuiyan SA, Cho RY, Fong JS, Hur SA, Pavlidis P, Allan DW. A low affinity cis-regulatory BMP response element restricts target gene activation to subsets of Drosophila neurons. eLife 2020; 9:59650. [PMID: 33124981 PMCID: PMC7669266 DOI: 10.7554/elife.59650] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/29/2020] [Indexed: 11/19/2022] Open
Abstract
Retrograde BMP signaling and canonical pMad/Medea-mediated transcription regulate diverse target genes across subsets of Drosophila efferent neurons, to differentiate neuropeptidergic neurons and promote motor neuron terminal maturation. How a common BMP signal regulates diverse target genes across many neuronal subsets remains largely unresolved, although available evidence implicates subset-specific transcription factor codes rather than differences in BMP signaling. Here we examine the cis-regulatory mechanisms restricting BMP-induced FMRFa neuropeptide expression to Tv4-neurons. We find that pMad/Medea bind at an atypical, low affinity motif in the FMRFa enhancer. Converting this motif to high affinity caused ectopic enhancer activity and eliminated Tv4-neuron expression. In silico searches identified additional motif instances functional in other efferent neurons, implicating broader functions for this motif in BMP-dependent enhancer activity. Thus, differential interpretation of a common BMP signal, conferred by low affinity pMad/Medea binding motifs, can contribute to the specification of BMP target genes in efferent neuron subsets.
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Affiliation(s)
- Anthony Je Berndt
- Department of Food & Fuel for the 21st Century, University of California San Diego, San Diego, United States
| | - Katerina M Othonos
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | - Tianshun Lian
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | - Stephane Flibotte
- UBC/LSI Bioinformatics Facility, University of British Columbia, Vancouver, Canada
| | - Mo Miao
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | | | - Raymond Y Cho
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | - Justin S Fong
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | - Seo Am Hur
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
| | - Paul Pavlidis
- Department of Psychiatry, University of British Columbia, Vancouver, Canada
| | - Douglas W Allan
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, Canada
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15
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Elliott KH, Chen X, Salomone J, Chaturvedi P, Schultz PA, Balchand SK, Servetas JD, Zuniga A, Zeller R, Gebelein B, Weirauch MT, Peterson KA, Brugmann SA. Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks. eLife 2020; 9:e56450. [PMID: 33006313 PMCID: PMC7556880 DOI: 10.7554/elife.56450] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 10/01/2020] [Indexed: 12/17/2022] Open
Abstract
Despite a common understanding that Gli TFs are utilized to convey a Hh morphogen gradient, genetic analyses suggest craniofacial development does not completely fit this paradigm. Using the mouse model (Mus musculus), we demonstrated that rather than being driven by a Hh threshold, robust Gli3 transcriptional activity during skeletal and glossal development required interaction with the basic helix-loop-helix TF Hand2. Not only did genetic and expression data support a co-factorial relationship, but genomic analysis revealed that Gli3 and Hand2 were enriched at regulatory elements for genes essential for mandibular patterning and development. Interestingly, motif analysis at sites co-occupied by Gli3 and Hand2 uncovered mandibular-specific, low-affinity, 'divergent' Gli-binding motifs (dGBMs). Functional validation revealed these dGBMs conveyed synergistic activation of Gli targets essential for mandibular patterning and development. In summary, this work elucidates a novel, sequence-dependent mechanism for Gli transcriptional activity within the craniofacial complex that is independent of a graded Hh signal.
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Affiliation(s)
- Kelsey H Elliott
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research FoundationCincinnatiUnited States
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Joseph Salomone
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Graduate Program in Molecular and Developmental Biology, Cincinnati Children's Hospital Research FoundationCincinnatiUnited States
- Medical-Scientist Training Program, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Praneet Chaturvedi
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Preston A Schultz
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Sai K Balchand
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | | | - Aimée Zuniga
- Developmental Genetics, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Rolf Zeller
- Developmental Genetics, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | - Matthew T Weirauch
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
| | | | - Samantha A Brugmann
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Division of Plastic Surgery, Department of Surgery, Cincinnati Children’s Hospital Medical CenterCincinnatiUnited States
- Shriners Children’s HospitalCincinnatiUnited States
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16
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Abstract
Key discoveries in Drosophila have shaped our understanding of cellular "enhancers." With a special focus on the fly, this chapter surveys properties of these adaptable cis-regulatory elements, whose actions are critical for the complex spatial/temporal transcriptional regulation of gene expression in metazoa. The powerful combination of genetics, molecular biology, and genomics available in Drosophila has provided an arena in which the developmental role of enhancers can be explored. Enhancers are characterized by diverse low- or high-throughput assays, which are challenging to interpret, as not all of these methods of identifying enhancers produce concordant results. As a model metazoan, the fly offers important advantages to comprehensive analysis of the central functions that enhancers play in gene expression, and their critical role in mediating the production of phenotypes from genotype and environmental inputs. A major challenge moving forward will be obtaining a quantitative understanding of how these cis-regulatory elements operate in development and disease.
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Affiliation(s)
- Stephen Small
- Department of Biology, Developmental Systems Training Program, New York University, 10003 and
| | - David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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17
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Keller SH, Jena SG, Yamazaki Y, Lim B. Regulation of spatiotemporal limits of developmental gene expression via enhancer grammar. Proc Natl Acad Sci U S A 2020; 117:15096-15103. [PMID: 32541043 PMCID: PMC7334449 DOI: 10.1073/pnas.1917040117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The regulatory specificity of a gene is determined by the structure of its enhancers, which contain multiple transcription factor binding sites. A unique combination of transcription factor binding sites in an enhancer determines the boundary of target gene expression, and their disruption often leads to developmental defects. Despite extensive characterization of binding motifs in an enhancer, it is still unclear how each binding site contributes to overall transcriptional activity. Using live imaging, quantitative analysis, and mathematical modeling, we measured the contribution of individual binding sites in transcriptional regulation. We show that binding site arrangement within the Rho-GTPase component t48 enhancer mediates the expression boundary by mainly regulating the timing of transcriptional activation along the dorsoventral axis of Drosophila embryos. By tuning the binding affinity of the Dorsal (Dl) and Zelda (Zld) sites, we show that single site modulations are sufficient to induce significant changes in transcription. Yet, no one site seems to have a dominant role; rather, multiple sites synergistically drive increases in transcriptional activity. Interestingly, Dl and Zld demonstrate distinct roles in transcriptional regulation. Dl site modulations change spatial boundaries of t48, mostly by affecting the timing of activation and bursting frequency rather than transcriptional amplitude or bursting duration. However, modulating the binding site for the pioneer factor Zld affects both the timing of activation and amplitude, suggesting that Zld may potentiate higher Dl recruitment to target DNAs. We propose that such fine-tuning of dynamic gene control via enhancer structure may play an important role in ensuring normal development.
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Affiliation(s)
- Samuel H Keller
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Siddhartha G Jena
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Yuji Yamazaki
- Yutaka Seino Distinguished Center for Diabetes Research, Kansai Electric Power Medical Research Institute, Kobe 650-0047, Japan
| | - Bomyi Lim
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104;
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18
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Cooper KL. Developmental and Evolutionary Allometry of the Mammalian Limb Skeleton. Integr Comp Biol 2020; 59:1356-1368. [PMID: 31180500 DOI: 10.1093/icb/icz082] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The variety of limb skeletal proportions enables a remarkable diversity of behaviors that include powered flight in bats and flipper-propelled swimming in whales using extremes of a range of homologous limb architectures. Even within human limbs, bone lengths span more than an order of magnitude from the short finger and toe bones to the long arm and leg bones. Yet all of this diversity arises from embryonic skeletal elements that are each a very similar size at formation. In this review article, I survey what is and is not yet known of the development and evolution of skeletal proportion at multiple hierarchical levels of biological organization. These include the cellular parameters of skeletal elongation in the cartilage growth plate, genes associated with differential growth, and putative gene regulatory mechanisms that would allow both covariant and independent evolution of the forelimbs and hindlimbs and of individual limb segments. Although the genetic mechanisms that shape skeletal proportion are still largely unknown, and most of what is known is limited to mammals, it is becoming increasingly apparent that the diversity of bone lengths is an emergent property of a complex system that controls elongation of individual skeletal elements using a genetic toolkit shared by all.
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Affiliation(s)
- Kimberly L Cooper
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093-0377, USA
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19
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Abstract
Transcription factors in the bHLH family are potentially relevant for tumor growth. Activation requires homodimerization or heterodimerization. Thus, the dimerization step is a likely significant drug target. The oligodendrocyte transcription factor 2 (OLIG2) is overexpressed in gliomas. Here, we developed a fluorescence cross-correlation spectroscopy protocol to examine 10 compounds selected using a pharmacophore-based computational strategy targeting OLIG2 dimerization. We showed that the potency to interact with OLIG2 dimerization in live cells correlates with carcinostatic efficacy. The data indicate a promising approach toward drug development targeting transcription factor overactivity and protein–protein interaction more generally. Transcription factors (TFs) are fundamental in the regulation of gene expression in the development and differentiation of cells. They may act as oncogenes and when overexpressed in tumors become plausible targets for the design of antitumor agents. Homodimerization or heterodimerization of TFs are required for DNA binding and the association interface between subunits, for the design of allosteric modulators, appears as a privileged structure for the pharmacophore-based computational strategy. Based on this strategy, a set of compounds were earlier identified as potential suppressors of OLIG2 dimerization and found to inhibit tumor growth in a mouse glioblastoma cell line and in a whole-animal study. To investigate whether the antitumor activity is due to the predicted mechanism of action, we undertook a study of OLIG2 dimerization using fluorescence cross-correlation spectroscopy (FCCS) of live HEK cells transfected with 2 spectrally different OLIG2 clones. The selected compounds showed an effect with potency, which correlated with the earlier observed antitumor activity. The OLIG2 proteins showed change in diffusion time under compound treatment in line with dissociation from DNA. The data suggest a general approach of drug discovery based on the design of allosteric modulators of protein–protein interaction.
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20
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Lammers NC, Galstyan V, Reimer A, Medin SA, Wiggins CH, Garcia HG. Multimodal transcriptional control of pattern formation in embryonic development. Proc Natl Acad Sci U S A 2020; 117:836-847. [PMID: 31882445 PMCID: PMC6969519 DOI: 10.1073/pnas.1912500117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Predicting how interactions between transcription factors and regulatory DNA sequence dictate rates of transcription and, ultimately, drive developmental outcomes remains an open challenge in physical biology. Using stripe 2 of the even-skipped gene in Drosophila embryos as a case study, we dissect the regulatory forces underpinning a key step along the developmental decision-making cascade: the generation of cytoplasmic mRNA patterns via the control of transcription in individual cells. Using live imaging and computational approaches, we found that the transcriptional burst frequency is modulated across the stripe to control the mRNA production rate. However, we discovered that bursting alone cannot quantitatively recapitulate the formation of the stripe and that control of the window of time over which each nucleus transcribes even-skipped plays a critical role in stripe formation. Theoretical modeling revealed that these regulatory strategies (bursting and the time window) respond in different ways to input transcription factor concentrations, suggesting that the stripe is shaped by the interplay of 2 distinct underlying molecular processes.
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Affiliation(s)
| | - Vahe Galstyan
- Biochemistry and Molecular Biophysics Option, California Institute of Technology, Pasadena, CA 91126
- Department of Physics, Columbia University, New York, NY 10027
| | - Armando Reimer
- Biophysics Graduate Group, University of California, Berkeley, CA 94720
| | - Sean A Medin
- Department of Physics, University of California, Berkeley, CA 94720
| | - Chris H Wiggins
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY 10027;
- Data Science Institute, Columbia University, New York, NY 10027
- Department of Systems Biology, Columbia University, New York, NY 10027
- Department of Statistics, Columbia University, New York, NY 10027
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California, Berkeley, CA 94720;
- Department of Physics, University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA 94720
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21
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Schloop AE, Bandodkar PU, Reeves GT. Formation, interpretation, and regulation of the Drosophila Dorsal/NF-κB gradient. Curr Top Dev Biol 2019; 137:143-191. [PMID: 32143742 DOI: 10.1016/bs.ctdb.2019.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The morphogen gradient of the transcription factor Dorsal in the early Drosophila embryo has become one of the most widely studied tissue patterning systems. Dorsal is a Drosophila homolog of mammalian NF-κB and patterns the dorsal-ventral axis of the blastoderm embryo into several tissue types by spatially regulating upwards of 100 zygotic genes. Recent studies using fluorescence microscopy and live imaging have quantified the Dorsal gradient and its target genes, which has paved the way for mechanistic modeling of the gradient. In this review, we describe the mechanisms behind the initiation of the Dorsal gradient and its regulation of target genes. The main focus of the review is a discussion of quantitative and computational studies of the Dl gradient system, including regulation of the Dl gradient. We conclude with a discussion of potential future directions.
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Affiliation(s)
- Allison E Schloop
- Genetics Program, North Carolina State University, Raleigh, NC, United States
| | - Prasad U Bandodkar
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States
| | - Gregory T Reeves
- Genetics Program, North Carolina State University, Raleigh, NC, United States; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States.
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22
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Abstract
Drosophila melanogaster embryos develop initially as a syncytium of totipotent nuclei and subsequently, once cellularized, undergo morphogenetic movements associated with gastrulation to generate the three somatic germ layers of the embryo: mesoderm, ectoderm, and endoderm. In this chapter, we focus on the first phase of gastrulation in Drosophila involving patterning of early embryos when cells differentiate their gene expression programs. This patterning process requires coordination of multiple developmental processes including genome reprogramming at the maternal-to-zygotic transition, combinatorial action of transcription factors to support distinct gene expression, and dynamic feedback between this genetic patterning by transcription factors and changes in cell morphology. We discuss the gene regulatory programs acting during patterning to specify the three germ layers, which involve the regulation of spatiotemporal gene expression coupled to physical tissue morphogenesis.
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Affiliation(s)
- Angelike Stathopoulos
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, United States.
| | - Susan Newcomb
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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23
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Garcia HG, Berrocal A, Kim YJ, Martini G, Zhao J. Lighting up the central dogma for predictive developmental biology. Curr Top Dev Biol 2019; 137:1-35. [PMID: 32143740 DOI: 10.1016/bs.ctdb.2019.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although the last 30years have witnessed the mapping of the wiring diagrams of the gene regulatory networks that dictate cell fate and animal body plans, specific understanding building on such network diagrams that shows how DNA regulatory regions control gene expression lags far behind. These networks have yet to yield the predictive power necessary to, for example, calculate how the concentration dynamics of input transcription factors and DNA regulatory sequence prescribes output patterns of gene expression that, in turn, determine body plans themselves. Here, we argue that reaching a predictive understanding of developmental decision-making calls for an interplay between theory and experiment aimed at revealing how the regulation of the processes of the central dogma dictate network connections and how network topology guides cells toward their ultimate developmental fate. To make this possible, it is crucial to break free from the snapshot-based understanding of embryonic development facilitated by fixed-tissue approaches and embrace new technologies that capture the dynamics of developmental decision-making at the single cell level, in living embryos.
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Affiliation(s)
- Hernan G Garcia
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States; Department of Physics, University of California at Berkeley, Berkeley, CA, United States; Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, United States; Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, United States.
| | - Augusto Berrocal
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States
| | - Yang Joon Kim
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, United States
| | - Gabriella Martini
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, United States
| | - Jiaxi Zhao
- Department of Physics, University of California at Berkeley, Berkeley, CA, United States
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24
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Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system. Nat Immunol 2019; 20:1372-1380. [PMID: 31451789 PMCID: PMC6754753 DOI: 10.1038/s41590-019-0471-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/16/2019] [Indexed: 12/12/2022]
Abstract
In multicellular organisms, duplicated genes can diverge through tissue-specific gene expression patterns, as exemplified by highly regulated expression of Runx transcription factor paralogs with apparent functional redundancy. Here we asked what cell type-specific biologies might be supported by the selective expression of Runx paralogs during Langerhans cell and inducible regulatory T cell differentiation. We uncovered functional non-equivalence between Runx paralogs. Selective expression of native paralogs allowed integration of transcription factor activity with extrinsic signals, while non-native paralogs enforced differentiation even in the absence of exogenous inducers. DNA-binding affinity was controlled by divergent amino acids within the otherwise highly conserved RUNT domain, and evolutionary reconstruction suggested convergence of RUNT domain residues towards sub-maximal strength. Hence, the selective expression of gene duplicates in specialized cell types can synergize with the acquisition of functional differences to enable appropriate gene expression, lineage choice and differentiation in the mammalian immune system.
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25
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Huang K, Xhani S, Albrecht AV, Ha VLT, Esaki S, Poon GMK. Mechanism of cognate sequence discrimination by the ETS-family transcription factor ETS-1. J Biol Chem 2019; 294:9666-9678. [PMID: 31048376 DOI: 10.1074/jbc.ra119.007866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/01/2019] [Indexed: 12/19/2022] Open
Abstract
Functional evidence increasingly implicates low-affinity DNA recognition by transcription factors as a general mechanism for the spatiotemporal control of developmental genes. Although the DNA sequence requirements for affinity are well-defined, the dynamic mechanisms that execute cognate recognition are much less resolved. To address this gap, here we examined ETS1, a paradigm developmental transcription factor, as a model for which cognate discrimination remains enigmatic. Using molecular dynamics simulations, we interrogated the DNA-binding domain of murine ETS1 alone and when bound to high-and low-affinity cognate sites or to nonspecific DNA. The results of our analyses revealed collective backbone and side-chain motions that distinguished cognate versus nonspecific as well as high- versus low-affinity cognate DNA binding. Combined with binding experiments with site-directed ETS1 mutants, the molecular dynamics data disclosed a triad of residues that respond specifically to low-affinity cognate DNA. We found that a DNA-contacting residue (Gln-336) specifically recognizes low-affinity DNA and triggers the loss of a distal salt bridge (Glu-343/Arg-378) via a large side-chain motion that compromises the hydrophobic packing of two core helices. As an intact Glu-343/Arg-378 bridge is the default state in unbound ETS1 and maintained in high-affinity and nonspecific complexes, the low-affinity complex represents a unique conformational adaptation to the suboptimization of developmental enhancers.
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Affiliation(s)
| | | | | | | | | | - Gregory M K Poon
- From the Department of Chemistry and .,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303
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26
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Rothenberg EV. Encounters across networks: Windows into principles of genomic regulation. Mar Genomics 2019; 44:3-12. [PMID: 30661741 DOI: 10.1016/j.margen.2019.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/06/2019] [Accepted: 01/06/2019] [Indexed: 12/13/2022]
Abstract
Gene regulatory networks account for the ability of the genome to program development in complex multi-cellular organisms. Such networks are based on principles of gene regulation by combinations of transcription factors that bind to specific cis-regulatory DNA sites to activate transcription. These cis-regulatory regions mediate logic processing at each network node, enabling progressive increases in organismal complexity with development. Gene regulatory network explanations of development have been shown to account for patterning and cell type diversification in fly and sea urchin embryonic systems, where networks are characterized by fast coupling between transcriptional inputs and changes in target gene transcription rates, and crucial cis-regulatory elements are concentrated relatively close to the protein coding sequences of the target genes, thus facilitating their identification. Stem cell-based development in post-embryonic mammalian systems also depends on gene networks, but differs from the fly and sea urchin systems. First, the number of regulatory elements per gene and the distances between regulatory elements and the genes they control are considerably larger, forcing searches via genome-wide transcription factor binding surveys rather than functional assays. Second, the intrinsic timing of network state transitions can be slowed considerably by the need to undo stem-cell chromatin configurations, which presumably add stability to stem-cell states but retard responses to transcription factor changes during differentiation. The dispersed, partially redundant cis-regulatory systems controlling gene expression and the slow state transition kinetics in these systems already reveal new insights and opportunities to extend understanding of the repertoire of gene networks and regulatory system logic.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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27
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Guo Z, Qin J, Zhou X, Zhang Y. Insect Transcription Factors: A Landscape of Their Structures and Biological Functions in Drosophila and beyond. Int J Mol Sci 2018; 19:ijms19113691. [PMID: 30469390 PMCID: PMC6274879 DOI: 10.3390/ijms19113691] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/16/2018] [Accepted: 11/16/2018] [Indexed: 12/17/2022] Open
Abstract
Transcription factors (TFs) play essential roles in the transcriptional regulation of functional genes, and are involved in diverse physiological processes in living organisms. The fruit fly Drosophila melanogaster, a simple and easily manipulated organismal model, has been extensively applied to study the biological functions of TFs and their related transcriptional regulation mechanisms. It is noteworthy that with the development of genetic tools such as CRISPR/Cas9 and the next-generation genome sequencing techniques in recent years, identification and dissection the complex genetic regulatory networks of TFs have also made great progress in other insects beyond Drosophila. However, unfortunately, there is no comprehensive review that systematically summarizes the structures and biological functions of TFs in both model and non-model insects. Here, we spend extensive effort in collecting vast related studies, and attempt to provide an impartial overview of the progress of the structure and biological functions of current documented TFs in insects, as well as the classical and emerging research methods for studying their regulatory functions. Consequently, considering the importance of versatile TFs in orchestrating diverse insect physiological processes, this review will assist a growing number of entomologists to interrogate this understudied field, and to propel the progress of their contributions to pest control and even human health.
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Affiliation(s)
- Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jianying Qin
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China.
| | - Xiaomao Zhou
- Longping Branch, Graduate School of Hunan University, Changsha 410125, China.
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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28
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Vincent BJ, Staller MV, Lopez-Rivera F, Bragdon MDJ, Pym ECG, Biette KM, Wunderlich Z, Harden TT, Estrada J, DePace AH. Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos. PLoS Genet 2018; 14:e1007644. [PMID: 30192762 PMCID: PMC6145585 DOI: 10.1371/journal.pgen.1007644] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 09/19/2018] [Accepted: 08/17/2018] [Indexed: 01/18/2023] Open
Abstract
Hunchback is a bifunctional transcription factor that can activate and repress gene expression in Drosophila development. We investigated the regulatory DNA sequence features that control Hunchback function by perturbing enhancers for one of its target genes, even-skipped (eve). While Hunchback directly represses the eve stripe 3+7 enhancer, we found that in the eve stripe 2+7 enhancer, Hunchback repression is prevented by nearby sequences-this phenomenon is called counter-repression. We also found evidence that Caudal binding sites are responsible for counter-repression, and that this interaction may be a conserved feature of eve stripe 2 enhancers. Our results alter the textbook view of eve stripe 2 regulation wherein Hb is described as a direct activator. Instead, to generate stripe 2, Hunchback repression must be counteracted. We discuss how counter-repression may influence eve stripe 2 regulation and evolution.
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Affiliation(s)
- Ben J. Vincent
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Max V. Staller
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Francheska Lopez-Rivera
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Meghan D. J. Bragdon
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Edward C. G. Pym
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kelly M. Biette
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Zeba Wunderlich
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Timothy T. Harden
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Javier Estrada
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Angela H. DePace
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
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29
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Rickels R, Shilatifard A. Enhancer Logic and Mechanics in Development and Disease. Trends Cell Biol 2018; 28:608-630. [PMID: 29759817 DOI: 10.1016/j.tcb.2018.04.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 12/31/2022]
Abstract
Enhancers are distally located genomic cis-regulatory elements that integrate spatiotemporal cues to coordinate gene expression in a tissue-specific manner during metazoan development. Enhancer function depends on a combination of bound transcription factors and cofactors that regulate local chromatin structure, as well as on the topological interactions that are necessary for their activity. Numerous genome-wide studies concur that the vast majority of disease-associated variations occur within non-coding genomic sequences, in other words the 'cis-regulome', and this underscores their relevance for human health. Advances in DNA sequencing and genome-editing technologies have dramatically expanded our ability to identify enhancers and investigate their properties in vivo, revealing an extraordinary level of interconnectivity underlying cis-regulatory networks. We discuss here these recently developed methodologies, as well as emerging trends and remaining questions in the field of enhancer biology, and how perturbation of enhancer activities/functions results in enhanceropathies.
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Affiliation(s)
- Ryan Rickels
- Simpson Querrey Center for Epigenetics, and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 East Superior Street, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics, and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 320 East Superior Street, Chicago, IL 60611, USA.
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30
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Capicua controls Toll/IL-1 signaling targets independently of RTK regulation. Proc Natl Acad Sci U S A 2018; 115:1807-1812. [PMID: 29432195 DOI: 10.1073/pnas.1713930115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The HMG-box protein Capicua (Cic) is a conserved transcriptional repressor that functions downstream of receptor tyrosine kinase (RTK) signaling pathways in a relatively simple switch: In the absence of signaling, Cic represses RTK-responsive genes by binding to nearly invariant sites in DNA, whereas activation of RTK signaling down-regulates Cic activity, leading to derepression of its targets. This mechanism controls gene expression in both Drosophila and mammals, but whether Cic can also function via other regulatory mechanisms remains unknown. Here, we characterize an RTK-independent role of Cic in regulating spatially restricted expression of Toll/IL-1 signaling targets in Drosophila embryogenesis. We show that Cic represses those targets by binding to suboptimal DNA sites of lower affinity than its known consensus sites. This binding depends on Dorsal/NF-κB, which translocates into the nucleus upon Toll activation and binds next to the Cic sites. As a result, Cic binds to and represses Toll targets only in regions with nuclear Dorsal. These results reveal a mode of Cic regulation unrelated to the well-established RTK/Cic depression axis and implicate cooperative binding in conjunction with low-affinity binding sites as an important mechanism of enhancer regulation. Given that Cic plays a role in many developmental and pathological processes in mammals, our results raise the possibility that some of these Cic functions are independent of RTK regulation and may depend on cofactor-assisted DNA binding.
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31
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Farley EK, Olson KM, Levine MS. Regulatory Principles Governing Tissue Specificity of Developmental Enhancers. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2018; 80:27-32. [PMID: 27325706 DOI: 10.1101/sqb.2015.80.027227] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Transcriptional enhancers are short segments of genomic DNA (50 bp to 1 kb in length) that can work over long distances (≥1 Mb) to regulate gene expression in specific cells and tissues. Genomic assays have identified on the order of 400,000 to one million putative enhancers in the human genome (e.g., ENCODE Consortium). This suggests that a typical gene is regulated by tens of enhancers, ensuring stringent regulation of gene expression in response to a variety of intrinsic and external signals. Despite the discovery of the first transcriptional enhancer more than 30 years ago, we know surprisingly little about how enhancers regulate gene expression. In particular, the relationship between primary DNA sequence and enhancer specificity remains obscure. Here we summarize recent high-throughput studies in whole embryos aimed at the systematic identification of the sequence and organizational constraints underlying enhancer function and specificity.
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Affiliation(s)
- Emma K Farley
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544
| | - Katrina M Olson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544
| | - Michael S Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544
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32
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Anderson C, Reiss I, Zhou C, Cho A, Siddiqi H, Mormann B, Avelis CM, Deford P, Bergland A, Roberts E, Taylor J, Vasiliauskas D, Johnston RJ. Natural variation in stochastic photoreceptor specification and color preference in Drosophila. eLife 2017; 6:29593. [PMID: 29251595 PMCID: PMC5745083 DOI: 10.7554/elife.29593] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/15/2017] [Indexed: 11/25/2022] Open
Abstract
Each individual perceives the world in a unique way, but little is known about the genetic basis of variation in sensory perception. In the fly eye, the random mosaic of color-detecting R7 photoreceptor subtypes is determined by stochastic on/off expression of the transcription factor Spineless (Ss). In a genome-wide association study, we identified a naturally occurring insertion in a regulatory DNA element in ss that lowers the ratio of SsON to SsOFF cells. This change in photoreceptor fates shifts the innate color preference of flies from green to blue. The genetic variant increases the binding affinity for Klumpfuss (Klu), a zinc finger transcriptional repressor that regulates ss expression. Klu is expressed at intermediate levels to determine the normal ratio of SsON to SsOFF cells. Thus, binding site affinity and transcription factor levels are finely tuned to regulate stochastic expression, setting the ratio of alternative fates and ultimately determining color preference.
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Affiliation(s)
- Caitlin Anderson
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - India Reiss
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Cyrus Zhou
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Annie Cho
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Haziq Siddiqi
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Benjamin Mormann
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
| | - Cameron M Avelis
- Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - Peter Deford
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Alan Bergland
- Department of Biology, University of Virginia, Charlottesville, United States
| | - Elijah Roberts
- Department of Biophysics, Johns Hopkins University, Baltimore, United States
| | - James Taylor
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Daniel Vasiliauskas
- Paris-Saclay Institute of Neuroscience, Université Paris Sud, Centre National de la Recherche Scientifque, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, Baltimore, United States
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33
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Tsai A, Muthusamy AK, Alves MR, Lavis LD, Singer RH, Stern DL, Crocker J. Nuclear microenvironments modulate transcription from low-affinity enhancers. eLife 2017; 6:28975. [PMID: 29095143 PMCID: PMC5695909 DOI: 10.7554/elife.28975] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/29/2017] [Indexed: 02/07/2023] Open
Abstract
Transcription factors bind low-affinity DNA sequences for only short durations. It is not clear how brief, low-affinity interactions can drive efficient transcription. Here, we report that the transcription factor Ultrabithorax (Ubx) utilizes low-affinity binding sites in the Drosophila melanogaster shavenbaby (svb) locus and related enhancers in nuclear microenvironments of high Ubx concentrations. Related enhancers colocalize to the same microenvironments independently of their chromosomal location, suggesting that microenvironments are highly differentiated transcription domains. Manipulating the affinity of svb enhancers revealed an inverse relationship between enhancer affinity and Ubx concentration required for transcriptional activation. The Ubx cofactor, Homothorax (Hth), was co-enriched with Ubx near enhancers that require Hth, even though Ubx and Hth did not co-localize throughout the nucleus. Thus, microenvironments of high local transcription factor and cofactor concentrations could help low-affinity sites overcome their kinetic inefficiency. Mechanisms that generate these microenvironments could be a general feature of eukaryotic transcriptional regulation.
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Affiliation(s)
- Albert Tsai
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Anand K Muthusamy
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | | | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Robert H Singer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, United States
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Justin Crocker
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,European Molecular Biology Laboratory, Heidelberg, Germany
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34
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Khoueiry P, Girardot C, Ciglar L, Peng PC, Gustafson EH, Sinha S, Furlong EE. Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity. eLife 2017; 6. [PMID: 28792889 PMCID: PMC5550276 DOI: 10.7554/elife.28440] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/21/2017] [Indexed: 12/15/2022] Open
Abstract
Sequence variation within enhancers plays a major role in both evolution and disease, yet its functional impact on transcription factor (TF) occupancy and enhancer activity remains poorly understood. Here, we assayed the binding of five essential TFs over multiple stages of embryogenesis in two distant Drosophila species (with 1.4 substitutions per neutral site), identifying thousands of orthologous enhancers with conserved or diverged combinatorial occupancy. We used these binding signatures to dissect two properties of developmental enhancers: (1) potential TF cooperativity, using signatures of co-associations and co-divergence in TF occupancy. This revealed conserved combinatorial binding despite sequence divergence, suggesting protein-protein interactions sustain conserved collective occupancy. (2) Enhancer in-vivo activity, revealing orthologous enhancers with conserved activity despite divergence in TF occupancy. Taken together, we identify enhancers with diverged motifs yet conserved occupancy and others with diverged occupancy yet conserved activity, emphasising the need to functionally measure the effect of divergence on enhancer activity.
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Affiliation(s)
- Pierre Khoueiry
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Charles Girardot
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Lucia Ciglar
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Pei-Chen Peng
- Carl R. Woese Institute of Genomic Biology, University of Illinois, Champaign, United States
| | - E Hilary Gustafson
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Saurabh Sinha
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.,Carl R. Woese Institute of Genomic Biology, University of Illinois, Champaign, United States
| | - Eileen Em Furlong
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
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35
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Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES. Systematic dissection of genomic features determining transcription factor binding and enhancer function. Proc Natl Acad Sci U S A 2017; 114:E1291-E1300. [PMID: 28137873 PMCID: PMC5321001 DOI: 10.1073/pnas.1621150114] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Enhancers regulate gene expression through the binding of sequence-specific transcription factors (TFs) to cognate motifs. Various features influence TF binding and enhancer function-including the chromatin state of the genomic locus, the affinities of the binding site, the activity of the bound TFs, and interactions among TFs. However, the precise nature and relative contributions of these features remain unclear. Here, we used massively parallel reporter assays (MPRAs) involving 32,115 natural and synthetic enhancers, together with high-throughput in vivo binding assays, to systematically dissect the contribution of each of these features to the binding and activity of genomic regulatory elements that contain motifs for PPARγ, a TF that serves as a key regulator of adipogenesis. We show that distinct sets of features govern PPARγ binding vs. enhancer activity. PPARγ binding is largely governed by the affinity of the specific motif site and higher-order features of the larger genomic locus, such as chromatin accessibility. In contrast, the enhancer activity of PPARγ binding sites depends on varying contributions from dozens of TFs in the immediate vicinity, including interactions between combinations of these TFs. Different pairs of motifs follow different interaction rules, including subadditive, additive, and superadditive interactions among specific classes of TFs, with both spatially constrained and flexible grammars. Our results provide a paradigm for the systematic characterization of the genomic features underlying regulatory elements, applicable to the design of synthetic regulatory elements or the interpretation of human genetic variation.
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Affiliation(s)
- Sharon R Grossman
- Broad Institute, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Health Sciences and Technology, Harvard Medical School, Boston, MA 02215
| | | | - Li Wang
- Broad Institute, Cambridge, MA 02142
| | - Jesse Engreitz
- Broad Institute, Cambridge, MA 02142
- Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | | | - Ryan Tewhey
- Broad Institute, Cambridge, MA 02142
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Alina Isakova
- Institute of Bioengineering, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Bart Deplancke
- Institute of Bioengineering, CH-1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Bradley E Bernstein
- Broad Institute, Cambridge, MA 02142
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Tarjei S Mikkelsen
- Broad Institute, Cambridge, MA 02142
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138
| | - Eric S Lander
- Broad Institute, Cambridge, MA 02142;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Systems Biology, Harvard Medical School, Boston, MA 02215
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36
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37
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Sandler JE, Stathopoulos A. Stepwise Progression of Embryonic Patterning. Trends Genet 2016; 32:432-443. [PMID: 27230753 DOI: 10.1016/j.tig.2016.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 01/23/2023]
Abstract
It is long established that the graded distribution of Dorsal transcription factor influences spatial domains of gene expression along the dorsoventral (DV) axis of Drosophila melanogaster embryos. However, the more recent realization that Dorsal levels also change with time raises the question of whether these dynamics are instructive. An overview of DV axis patterning is provided, focusing on new insights identified through quantitative analysis of temporal changes in Dorsal target gene expression from one nuclear cycle to the next ('steps'). Possible roles for the stepwise progression of this patterning program are discussed including (i) tight temporal regulation of signaling pathway activation, (ii) control of gene expression cohorts, and (iii) ensuring the irreversibility of the patterning and cell fate specification process.
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Affiliation(s)
- Jeremy E Sandler
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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38
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Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers. Proc Natl Acad Sci U S A 2016; 113:6508-13. [PMID: 27155014 DOI: 10.1073/pnas.1605085113] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Transcriptional enhancers are short segments of DNA that switch genes on and off in response to a variety of intrinsic and extrinsic signals. Despite the discovery of the first enhancer more than 30 y ago, the relationship between primary DNA sequence and enhancer activity remains obscure. In particular, the importance of "syntax" (the order, orientation, and spacing of binding sites) is unclear. A high-throughput screen identified synthetic notochord enhancers that are activated by the combination of ZicL and ETS transcription factors in Ciona embryos. Manipulation of these enhancers elucidated a "regulatory code" of sequence and syntax features for notochord-specific expression. This code enabled in silico discovery of bona fide notochord enhancers, including those containing low-affinity binding sites that would be excluded by standard motif identification methods. One of the newly identified enhancers maps upstream of the known enhancer that regulates Brachyury (Ci-Bra), a key determinant of notochord specification. This newly identified Ci-Bra shadow enhancer contains binding sites with very low affinity, but optimal syntax, and therefore mediates surprisingly strong expression in the notochord. Weak binding sites are compensated by optimal syntax, whereas enhancers containing high-affinity binding affinities possess suboptimal syntax. We suggest this balance has obscured the importance of regulatory syntax, as noncanonical binding motifs are typically disregarded by enhancer detection methods. As a result, enhancers with low binding affinities but optimal syntax may be a vastly underappreciated feature of the regulatory genome.
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39
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Merabet S, Mann RS. To Be Specific or Not: The Critical Relationship Between Hox And TALE Proteins. Trends Genet 2016; 32:334-347. [PMID: 27066866 DOI: 10.1016/j.tig.2016.03.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Hox proteins are key regulatory transcription factors that act in different tissues of the embryo to provide specific spatial and temporal coordinates to each cell. These patterning functions often depend on the presence of the TALE-homeodomain class cofactors, which form cooperative DNA-binding complexes with all Hox proteins. How this family of cofactors contributes to the highly diverse and specific functions of Hox proteins in vivo remains an important unsolved question. We review here the most recent advances in understanding the molecular mechanisms underlying Hox-TALE function. In particular, we discuss the role of DNA shape, DNA-binding affinity, and protein-protein interaction flexibility in dictating Hox-TALE specificity. We propose several models to explain how these mechanisms are integrated with each other in the context of the many distinct functions that Hox and TALE factors carry out in vivo.
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Affiliation(s)
- Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, Centre National de Recherche Scientifique, Ecole Normale Supérieure de Lyon, France.
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Ursini G, Cavalleri T, Fazio L, Angrisano T, Iacovelli L, Porcelli A, Maddalena G, Punzi G, Mancini M, Gelao B, Romano R, Masellis R, Calabrese F, Rampino A, Taurisano P, Di Giorgio A, Keller S, Tarantini L, Sinibaldi L, Quarto T, Popolizio T, Caforio G, Blasi G, Riva MA, De Blasi A, Chiariotti L, Bollati V, Bertolino A. BDNF rs6265 methylation and genotype interact on risk for schizophrenia. Epigenetics 2016; 11:11-23. [PMID: 26889735 DOI: 10.1080/15592294.2015.1117736] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Epigenetic mechanisms can mediate gene-environment interactions relevant for complex disorders. The BDNF gene is crucial for development and brain plasticity, is sensitive to environmental stressors, such as hypoxia, and harbors the functional SNP rs6265 (Val(66)Met), which creates or abolishes a CpG dinucleotide for DNA methylation. We found that methylation at the BDNF rs6265 Val allele in peripheral blood of healthy subjects is associated with hypoxia-related early life events (hOCs) and intermediate phenotypes for schizophrenia in a distinctive manner, depending on rs6265 genotype: in ValVal individuals increased methylation is associated with exposure to hOCs and impaired working memory (WM) accuracy, while the opposite is true for ValMet subjects. Also, rs6265 methylation and hOCs interact in modulating WM-related prefrontal activity, another intermediate phenotype for schizophrenia, with an analogous opposite direction in the 2 genotypes. Consistently, rs6265 methylation has a different association with schizophrenia risk in ValVals and ValMets. The relationships of methylation with BDNF levels and of genotype with BHLHB2 binding likely contribute to these opposite effects of methylation. We conclude that BDNF rs6265 methylation interacts with genotype to bridge early environmental exposures to adult phenotypes, relevant for schizophrenia. The study of epigenetic changes in regions containing genetic variation relevant for human diseases may have beneficial implications for the understanding of how genes are actually translated into phenotypes.
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Affiliation(s)
- Gianluca Ursini
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy.,b Lieber Institute for Brain Development, Johns Hopkins University Medical Campus , Baltimore , MD , US
| | - Tommaso Cavalleri
- c Department of Clinical and Community Sciences, Università degli Studi di Milano , Milan , Italy.,d Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) Maggiore Hospital, Mangiagalli and Regina Elena Foundation , Milan , Italy
| | - Leonardo Fazio
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy
| | - Tiziana Angrisano
- e Istituto di Endocrinologia e Oncologia Sperimentale, IEOS, CNR, and Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli 'Federico II' , Naples
| | - Luisa Iacovelli
- f Department of Physiology and Pharmacology 'V. Erspamer', University of Rome 'Sapienza' , Rome , Italy
| | - Annamaria Porcelli
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy
| | - Giancarlo Maddalena
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy
| | - Giovanna Punzi
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy.,b Lieber Institute for Brain Development, Johns Hopkins University Medical Campus , Baltimore , MD , US
| | - Marina Mancini
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy
| | - Barbara Gelao
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy
| | - Raffaella Romano
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy
| | - Rita Masellis
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy
| | - Francesca Calabrese
- g Center of Neuropharmacology; Dipartimento di Scienze Farmacologiche e Biomolecolari; Università degli Studi di Milano , Milan , Italy
| | - Antonio Rampino
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy
| | - Paolo Taurisano
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy
| | - Annabella Di Giorgio
- h Department of Neuroradiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) 'Casa Sollievo della Sofferenza' , San Giovanni Rotondo , Italy
| | - Simona Keller
- e Istituto di Endocrinologia e Oncologia Sperimentale, IEOS, CNR, and Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli 'Federico II' , Naples
| | - Letizia Tarantini
- c Department of Clinical and Community Sciences, Università degli Studi di Milano , Milan , Italy.,d Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) Maggiore Hospital, Mangiagalli and Regina Elena Foundation , Milan , Italy
| | - Lorenzo Sinibaldi
- i Mendel Laboratory, Istituto di Ricoveroe Cura a Carattere Scientifico (IRCCS) 'Casa Sollievo della Sofferenza' , San Giovanni Rotondo , Italy
| | - Tiziana Quarto
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy.,j Cognitive Brain Research Unit, Institute of Behavioral Sciences, University of Helsinki , Helsinki , Finland
| | - Teresa Popolizio
- h Department of Neuroradiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) 'Casa Sollievo della Sofferenza' , San Giovanni Rotondo , Italy
| | - Grazia Caforio
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy
| | - Giuseppe Blasi
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy
| | - Marco A Riva
- g Center of Neuropharmacology; Dipartimento di Scienze Farmacologiche e Biomolecolari; Università degli Studi di Milano , Milan , Italy
| | - Antonio De Blasi
- k Department of Molecular Medicine, University of Rome 'Sapienza' , Rome , Italy
| | - Lorenzo Chiariotti
- e Istituto di Endocrinologia e Oncologia Sperimentale, IEOS, CNR, and Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli 'Federico II' , Naples
| | - Valentina Bollati
- c Department of Clinical and Community Sciences, Università degli Studi di Milano , Milan , Italy.,d Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS) Maggiore Hospital, Mangiagalli and Regina Elena Foundation , Milan , Italy
| | - Alessandro Bertolino
- a Psychiatric Neuroscience Group, Department of Basic Medical Science, Neuroscience and Sense Organs, University of Bari 'Aldo Moro' , Bari , Italy.,h Department of Neuroradiology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) 'Casa Sollievo della Sofferenza' , San Giovanni Rotondo , Italy
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Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors. Nat Genet 2016; 48:292-8. [DOI: 10.1038/ng.3509] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 01/15/2016] [Indexed: 12/13/2022]
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Crocker J, Noon EPB, Stern DL. The Soft Touch: Low-Affinity Transcription Factor Binding Sites in Development and Evolution. Curr Top Dev Biol 2016; 117:455-69. [PMID: 26969995 DOI: 10.1016/bs.ctdb.2015.11.018] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Transcription factor proteins regulate gene expression by binding to specific DNA regions. Most studies of transcription factor binding sites have focused on the highest affinity sites for each factor. There is abundant evidence, however, that binding sites with a range of affinities, including very low affinities, are critical to gene regulation. Here, we present the theoretical and experimental evidence for the importance of low-affinity sites in gene regulation and development. We also discuss the implications of the widespread use of low-affinity sites in eukaryotic genomes for robustness, precision, specificity, and evolution of gene regulation.
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Affiliation(s)
- Justin Crocker
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Ella Preger-Ben Noon
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.
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Berndt AJE, Tang JCY, Ridyard MS, Lian T, Keatings K, Allan DW. Gene Regulatory Mechanisms Underlying the Spatial and Temporal Regulation of Target-Dependent Gene Expression in Drosophila Neurons. PLoS Genet 2015; 11:e1005754. [PMID: 26713626 PMCID: PMC4694770 DOI: 10.1371/journal.pgen.1005754] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 11/30/2015] [Indexed: 11/18/2022] Open
Abstract
Neuronal differentiation often requires target-derived signals from the cells they innervate. These signals typically activate neural subtype-specific genes, but the gene regulatory mechanisms remain largely unknown. Highly restricted expression of the FMRFa neuropeptide in Drosophila Tv4 neurons requires target-derived BMP signaling and a transcription factor code that includes Apterous. Using integrase transgenesis of enhancer reporters, we functionally dissected the Tv4-enhancer of FMRFa within its native cellular context. We identified two essential but discrete cis-elements, a BMP-response element (BMP-RE) that binds BMP-activated pMad, and a homeodomain-response element (HD-RE) that binds Apterous. These cis-elements have low activity and must be combined for Tv4-enhancer activity. Such combinatorial activity is often a mechanism for restricting expression to the intersection of cis-element spatiotemporal activities. However, concatemers of the HD-RE and BMP-RE cis-elements were found to independently generate the same spatiotemporal expression as the Tv4-enhancer. Thus, the Tv4-enhancer atypically combines two low-activity cis-elements that confer the same output from distinct inputs. The activation of target-dependent genes is assumed to 'wait' for target contact. We tested this directly, and unexpectedly found that premature BMP activity could not induce early FMRFa expression; also, we show that the BMP-insensitive HD-RE cis-element is activated at the time of target contact. This led us to uncover a role for the nuclear receptor, seven up (svp), as a repressor of FMRFa induction prior to target contact. Svp is normally downregulated immediately prior to target contact, and we found that maintaining Svp expression prevents cis-element activation, whereas reducing svp gene dosage prematurely activates cis-element activity. We conclude that the target-dependent FMRFa gene is repressed prior to target contact, and that target-derived BMP signaling directly activates FMRFa gene expression through an atypical gene regulatory mechanism.
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Affiliation(s)
- Anthony J. E. Berndt
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jonathan C. Y. Tang
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States America
| | - Marc S. Ridyard
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tianshun Lian
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathleen Keatings
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Douglas W. Allan
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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Abstract
The Drosophila blastoderm and the vertebrate neural tube are archetypal examples of morphogen-patterned tissues that create precise spatial patterns of different cell types. In both tissues, pattern formation is dependent on molecular gradients that emanate from opposite poles. Despite distinct evolutionary origins and differences in time scales, cell biology and molecular players, both tissues exhibit striking similarities in the regulatory systems that establish gene expression patterns that foreshadow the arrangement of cell types. First, signaling gradients establish initial conditions that polarize the tissue, but there is no strict correspondence between specific morphogen thresholds and boundary positions. Second, gradients initiate transcriptional networks that integrate broadly distributed activators and localized repressors to generate patterns of gene expression. Third, the correct positioning of boundaries depends on the temporal and spatial dynamics of the transcriptional networks. These similarities reveal design principles that are likely to be broadly applicable to morphogen-patterned tissues.
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Affiliation(s)
- James Briscoe
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Stephen Small
- Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
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Abstract
Transcriptional enhancers direct precise on-off patterns of gene expression during development. To explore the basis for this precision, we conducted a high-throughput analysis of the Otx-a enhancer, which mediates expression in the neural plate of Ciona embryos in response to fibroblast growth factor (FGF) signaling and a localized GATA determinant. We provide evidence that enhancer specificity depends on submaximal recognition motifs having reduced binding affinities ("suboptimization"). Native GATA and ETS (FGF) binding sites contain imperfect matches to consensus motifs. Perfect matches mediate robust but ectopic patterns of gene expression. The native sites are not arranged at optimal intervals, and subtle changes in their spacing alter enhancer activity. Multiple tiers of enhancer suboptimization produce specific, but weak, patterns of expression, and we suggest that clusters of weak enhancers, including certain "superenhancers," circumvent this trade-off in specificity and activity.
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Affiliation(s)
- Emma K Farley
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720-3200, USA. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
| | - Katrina M Olson
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720-3200, USA. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Wei Zhang
- Department of Medicine, University of California, San Diego, CA 92093-0688, USA
| | - Alexander J Brandt
- Department of Chemistry, University of California, Berkeley, CA 94720-3200, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720-3200, USA
| | - Michael S Levine
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720-3200, USA. Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
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Clifford J, Adami C. Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively. Phys Biol 2015; 12:056004. [PMID: 26331781 DOI: 10.1088/1478-3975/12/5/056004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein-DNA interactions at the sequence level is through position weight matrices (PWMs) that estimate the joint probability of a DNA binding site sequence by assuming positional independence within the DNA sequence. Here we construct conditional PWMs that depend on the motif signatures in the flanking DNA sequence, by conditioning known binding site loci on the presence or absence of additional binding sites in the flanking sequence of each site's locus. Pooling known sites with similar flanking sequence patterns allows for the estimation of the conditional distribution function over the binding site sequences. We apply our model to the Dorsal transcription factor binding sites active in patterning the Dorsal-Ventral axis of Drosophila development. We find that those binding sites that cooperate with nearby Twist sites on average contain about 0.5 bits of information about the presence of Twist transcription factor binding sites in the flanking sequence. We also find that Dorsal binding site detectors conditioned on flanking sequence information make better predictions about what is a Dorsal site relative to background DNA than detection without information about flanking sequence features.
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Affiliation(s)
- Jacob Clifford
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI, USA. BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
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Santhanam B, Cai H, Devreotes PN, Shaulsky G, Katoh-Kurasawa M. The GATA transcription factor GtaC regulates early developmental gene expression dynamics in Dictyostelium. Nat Commun 2015; 6:7551. [PMID: 26144553 PMCID: PMC4506546 DOI: 10.1038/ncomms8551] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/20/2015] [Indexed: 12/11/2022] Open
Abstract
In many systems, including the social amoeba Dictyostelium discoideum, development is often marked by dynamic morphological and transcriptional changes orchestrated by key transcription factors. However, efforts to examine sequential genome-wide changes of gene regulation in developmental processes have been fairly limited. Here we report the developmental regulatory dynamics of GtaC, a GATA-type zinc-finger transcription factor, through the analyses of serial ChIP- and RNA-sequencing data. GtaC is essential for developmental progression, decoding extracellular cAMP pulses during early development and may play a role in mediating cell-type differentiation at later stages. We find that GtaC exhibits temporally distinctive DNA-binding patterns concordant with each developmental stage. We identify direct GtaC targets and observe cotemporaneous GtaC-binding and developmental expression regulation. Our results suggest that GtaC regulates multiple physiological processes as Dictyostelium transitions from a group of unicellular amoebae to an integrated multicellular organism. Development involves dynamic transcriptional changes. By serial ChIP- and RNA-sequencing, here, the authors show that GtaC, a GATA type transcription factor, exhibits temporally distinctive DNA binding and regulation of gene expression concordant with the development in the social amoeba Dictyostelium discoideum.
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Affiliation(s)
- Balaji Santhanam
- 1] Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA [2] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Huaqing Cai
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Peter N Devreotes
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo. Proc Natl Acad Sci U S A 2015; 112:785-90. [PMID: 25564665 DOI: 10.1073/pnas.1413877112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hunchback (Hb) is a bifunctional transcription factor that activates and represses distinct enhancers. Here, we investigate the hypothesis that Hb can activate and repress the same enhancer. Computational models predicted that Hb bifunctionally regulates the even-skipped (eve) stripe 3+7 enhancer (eve3+7) in Drosophila blastoderm embryos. We measured and modeled eve expression at cellular resolution under multiple genetic perturbations and found that the eve3+7 enhancer could not explain endogenous eve stripe 7 behavior. Instead, we found that eve stripe 7 is controlled by two enhancers: the canonical eve3+7 and a sequence encompassing the minimal eve stripe 2 enhancer (eve2+7). Hb bifunctionally regulates eve stripe 7, but it executes these two activities on different pieces of regulatory DNA--it activates the eve2+7 enhancer and represses the eve3+7 enhancer. These two "shadow enhancers" use different regulatory logic to create the same pattern.
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50
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Ozdemir A, Ma L, White KP, Stathopoulos A. Su(H)-mediated repression positions gene boundaries along the dorsal-ventral axis of Drosophila embryos. Dev Cell 2015; 31:100-13. [PMID: 25313963 DOI: 10.1016/j.devcel.2014.08.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 06/10/2014] [Accepted: 08/05/2014] [Indexed: 12/22/2022]
Abstract
In Drosophila embryos, a nuclear gradient of the Dorsal (Dl) transcription factor directs differential gene expression along the dorsoventral (DV) axis, translating it into distinct domains that specify future mesodermal, neural, and ectodermal territories. However, the mechanisms used to differentially position gene expression boundaries along this axis are not fully understood. Here, using a combination of approaches, including mutant phenotype analyses and chromatin immunoprecipitation, we show that the transcription factor Suppressor of Hairless, Su(H), helps define dorsal boundaries for many genes expressed along the DV axis. Synthetic reporter constructs also provide molecular evidence that Su(H) binding sites support repression and act to counterbalance activation through Dl and the ubiquitous activator Zelda. Our study highlights a role for broadly expressed repressors, like Su(H), and organization of transcription factor binding sites within cis-regulatory modules as important elements controlling spatial domains of gene expression to facilitate flexible positioning of boundaries across the entire DV axis.
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Affiliation(s)
- Anil Ozdemir
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lijia Ma
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology and Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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