101
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Amândio AR, Lopez-Delisle L, Bolt CC, Mascrez B, Duboule D. A complex regulatory landscape involved in the development of mammalian external genitals. eLife 2020; 9:e52962. [PMID: 32301703 PMCID: PMC7185996 DOI: 10.7554/elife.52962] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/17/2020] [Indexed: 02/04/2023] Open
Abstract
Developmental genes are often controlled by large regulatory landscapes matching topologically associating domains (TADs). In various contexts, the associated chromatin backbone is modified by specific enhancer-enhancer and enhancer-promoter interactions. We used a TAD flanking the mouse HoxD cluster to study how these regulatory architectures are formed and deconstructed once their function achieved. We describe this TAD as a functional unit, with several regulatory sequences acting together to elicit a transcriptional response. With one exception, deletion of these sequences didn't modify the transcriptional outcome, a result at odds with a conventional view of enhancer function. The deletion and inversion of a CTCF site located near these regulatory sequences did not affect transcription of the target gene. Slight modifications were nevertheless observed, in agreement with the loop extrusion model. We discuss these unexpected results considering both conventional and alternative explanations relying on the accumulation of poorly specific factors within the TAD backbone.
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Affiliation(s)
- Ana Rita Amândio
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of GenevaGenevaSwitzerland
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
- Department of Genetics and Evolution, University of GenevaGenevaSwitzerland
- Collège de FranceParisFrance
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102
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Xu D, Gokcumen O, Khurana E. Loss-of-function tolerance of enhancers in the human genome. PLoS Genet 2020; 16:e1008663. [PMID: 32243438 PMCID: PMC7159235 DOI: 10.1371/journal.pgen.1008663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 04/15/2020] [Accepted: 02/12/2020] [Indexed: 12/21/2022] Open
Abstract
Previous studies have surveyed the potential impact of loss-of-function (LoF) variants and identified LoF-tolerant protein-coding genes. However, the tolerance of human genomes to losing enhancers has not yet been evaluated. Here we present the catalog of LoF-tolerant enhancers using structural variants from whole-genome sequences. Using a conservative approach, we estimate that individual human genomes possess at least 28 LoF-tolerant enhancers on average. We assessed the properties of LoF-tolerant enhancers in a unified regulatory network constructed by integrating tissue-specific enhancers and gene-gene interactions. We find that LoF-tolerant enhancers tend to be more tissue-specific and regulate fewer and more dispensable genes relative to other enhancers. They are enriched in immune-related cells while enhancers with low LoF-tolerance are enriched in kidney and brain/neuronal stem cells. We developed a supervised learning approach to predict the LoF-tolerance of all enhancers, which achieved an area under the receiver operating characteristics curve (AUROC) of 98%. We predict 3,519 more enhancers would be likely tolerant to LoF and 129 enhancers that would have low LoF-tolerance. Our predictions are supported by a known set of disease enhancers and novel deletions from PacBio sequencing. The LoF-tolerance scores provided here will serve as an important reference for disease studies. Enhancers are elements where transcription factors bind and regulate the expression of protein-coding genes. Although multiple previous studies have focused on which genes can tolerate loss-of-function (LoF), none has systematically evaluated the tolerance of all enhancers in the human genome to LoF. Individual studies have shown a broad range of phenotypic effects of enhancer LoF. The phenotypic effects of enhancer LoF likely fall into a spectrum where deletion of LoF-tolerant enhancers would not elicit substantial phenotypic impact, while some enhancers are likely to cause fitness defects when deleted. Here we report a systematic computational approach that uses machine learning and properties of enhancers in a unified human regulatory network with tissue-specific annotations to predict the LoF-tolerance of all enhancers identified in the human genome. The LoF-tolerance scores of enhancers provided in this study can significantly facilitate the interpretation and prioritization of non-coding sequence variants for disease and functional studies.
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Affiliation(s)
- Duo Xu
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, United States of America
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, United States of America
- Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, New York, United States of America
- Meyer Cancer Center, Weill Cornell Medicine, New York, New York, United States of America
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, New York, United States of America
| | - Ekta Khurana
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, United States of America
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, United States of America
- Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, New York, United States of America
- Meyer Cancer Center, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
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103
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Li Y, Tao T, Du L, Zhu X. Three-dimensional genome: developmental technologies and applications in precision medicine. J Hum Genet 2020; 65:497-511. [PMID: 32152365 DOI: 10.1038/s10038-020-0737-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/20/2020] [Accepted: 02/22/2020] [Indexed: 12/17/2022]
Abstract
In the 20th century, our familiar structure of DNA was the double helix. Due to technical limitations, we do not have a good way to understand the finer structure of the genome, let alone its transcriptional regulation. Until the advent of 3C technologies, we were no longer blind to this one. Three-dimensional (3D) genomics is a new subject, which mainly studies the 3D structure and transcriptional regulation of eukaryotic genomes. Now, this field mainly has Hi-C series and CHIA-PET series technologies. Through 3D genomics, we can understand the basic structure of DNA, understand the growth and development of organisms and the occurrence of diseases, so as to promote human medical and health undertakings. The review introduces the main research techniques of 3D genomics and their characteristics, the latest development of 3D genome structure, the relationship between diseases and 3D genome structure, the applications of 3D genome in precision medicine, and the development of the 4D nucleome project.
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Affiliation(s)
- Yingqi Li
- Marine Medical Research Institute of Guangdong Zhanjiang (GDZJMMRI), Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China
| | - Tao Tao
- Department of Gastroenterology, Zibo Central Hospital, Zibo, 255000, China
| | - Likun Du
- First Affiliated Hospital, Heilongjiang University of Traditional Chinese Medicine, Harbin, 150040, China.
| | - Xiao Zhu
- Marine Medical Research Institute of Guangdong Zhanjiang (GDZJMMRI), Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang, 524023, China.
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104
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Barth NKH, Li L, Taher L. Independent Transposon Exaptation Is a Widespread Mechanism of Redundant Enhancer Evolution in the Mammalian Genome. Genome Biol Evol 2020; 12:1-17. [PMID: 31950992 PMCID: PMC7093719 DOI: 10.1093/gbe/evaa004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2020] [Indexed: 02/07/2023] Open
Abstract
Many regulatory networks appear to involve partially redundant enhancers. Traditionally, such enhancers have been hypothesized to originate mainly by sequence duplication. An alternative model postulates that they arise independently, through convergent evolution. This mechanism appears to be counterintuitive to natural selection: Redundant sequences are expected to either diverge and acquire new functions or accumulate mutations and become nonfunctional. Nevertheless, we show that at least 31% of the redundant enhancer pairs in the human genome (and 17% in the mouse genome) indeed originated in this manner. Specifically, for virtually all transposon-derived redundant enhancer pairs, both enhancer partners have evolved independently, from the exaptation of two different transposons. In addition to conferring robustness to the system, redundant enhancers could provide an evolutionary advantage by fine-tuning gene expression. Consistent with this hypothesis, we observed that the target genes of redundant enhancers exhibit higher expression levels and tissue specificity as compared with other genes. Finally, we found that although enhancer redundancy appears to be an intrinsic property of certain mammalian regulatory networks, the corresponding enhancers are largely species-specific. In other words, the redundancy in these networks is most likely a result of convergent evolution.
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Affiliation(s)
- Nicolai K H Barth
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Lifei Li
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Leila Taher
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
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105
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Abstract
Terminal regions of the early Drosophila embryo are patterned by the highly conserved ERK cascade, giving rise to the nonsegmented terminal structures of the future larva. In less than an hour, this signaling event establishes several gene expression boundaries and sets in motion a sequence of elaborate morphogenetic events. Genetic studies of terminal patterning discovered signaling components and transcription factors that are involved in numerous developmental contexts and deregulated in human diseases. This review summarizes current understanding of signaling and morphogenesis during terminal patterning and discusses several open questions that can now be rigorously investigated using live imaging, omics, and optogenetic approaches. The anatomical simplicity of the terminal patterning system and its amenability to a broad range of increasingly sophisticated genetic perturbations will continue to make it a premier quantitative model for studying multiple aspects of tissue patterning by dynamically controlled cell signaling pathways.
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106
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Tomoyasu Y, Halfon MS. How to study enhancers in non-traditional insect models. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb212241. [PMID: 32034049 DOI: 10.1242/jeb.212241] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcriptional enhancers are central to the function and evolution of genes and gene regulation. At the organismal level, enhancers play a crucial role in coordinating tissue- and context-dependent gene expression. At the population level, changes in enhancers are thought to be a major driving force that facilitates evolution of diverse traits. An amazing array of diverse traits seen in insect morphology, physiology and behavior has been the subject of research for centuries. Although enhancer studies in insects outside of Drosophila have been limited, recent advances in functional genomic approaches have begun to make such studies possible in an increasing selection of insect species. Here, instead of comprehensively reviewing currently available technologies for enhancer studies in established model organisms such as Drosophila, we focus on a subset of computational and experimental approaches that are likely applicable to non-Drosophila insects, and discuss the pros and cons of each approach. We discuss the importance of validating enhancer function and evaluate several possible validation methods, such as reporter assays and genome editing. Key points and potential pitfalls when establishing a reporter assay system in non-traditional insect models are also discussed. We close with a discussion of how to advance enhancer studies in insects, both by improving computational approaches and by expanding the genetic toolbox in various insects. Through these discussions, this Review provides a conceptual framework for studying the function and evolution of enhancers in non-traditional insect models.
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Affiliation(s)
| | - Marc S Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203, USA
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107
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Wang X, Goldstein DB. Enhancer Domains Predict Gene Pathogenicity and Inform Gene Discovery in Complex Disease. Am J Hum Genet 2020; 106:215-233. [PMID: 32032514 PMCID: PMC7010980 DOI: 10.1016/j.ajhg.2020.01.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/13/2020] [Indexed: 02/07/2023] Open
Abstract
Non-coding transcriptional regulatory elements are critical for controlling the spatiotemporal expression of genes. Here, we demonstrate that the sizes and number of enhancers linked to a gene reflect its disease pathogenicity. Moreover, genes with redundant enhancer domains are depleted of cis-acting genetic variants that disrupt gene expression, and they are buffered against the effects of disruptive non-coding mutations. Our results demonstrate that dosage-sensitive genes have evolved a robustness to the disruptive effects of genetic variation by expanding their regulatory domains. This solves a puzzle about why genes associated with human disease are depleted of cis-eQTLs (cis-expression quantitative trait loci), suggesting that this relationship might complicate gene identification in causal genome-wide association studies (GWASs) using eQTL information, and establishes a framework for identifying non-coding regulatory variation with phenotypic consequences.
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Affiliation(s)
- Xinchen Wang
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, 701 West 168th Street, New York, New York 10032, USA.
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, 701 West 168th Street, New York, New York 10032, USA; Department of Genetics and Development, Columbia University Medical Center, Hammer Health Sciences, 701 West 168th Street, New York, New York 10032, USA.
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108
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Enhancer jungles establish robust tissue-specific regulatory control in the human genome. Genomics 2019; 112:2261-2270. [PMID: 31887344 DOI: 10.1016/j.ygeno.2019.12.022] [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: 08/02/2019] [Revised: 12/23/2019] [Accepted: 12/25/2019] [Indexed: 11/21/2022]
Abstract
An increasing number of studies suggest that functionally redundant enhancers safeguard development via buffering gene expression against environmental and genetic perturbations. Here, we identified over-represented clusters of enhancers (enhancer jungles or EJs) in human B lymphoblastoid cells. We found that EJs tend to associate with genes involved in the activation of the immune system response. Although spanning multiple genes, the enhancers within an EJ tend to collaborate with each other on regulating a single gene. The employment of homotypic transcription factor binding sites (TFBSs) in EJ enhancers and heterotypic TFBSs between constituent enhancers within an EJ may safeguard a robust transcriptional output of the target gene. EJ enhancers evolve under a weaker selective pressure compared to regular enhancers (REs), and approximately 35% of EJs do not have orthologues in the mouse genome. In GM12878, these human-specific EJs appear to regulate genes associated with the adaptive immune system response, while the conserved EJs are associated with innate immunity. Recently acquired human EJs are associated with the higher level of target gene expression compared with conserved EJs, thus facilitating the environmental adaptation of the organism during evolution. In short, the existence of EJs is a common regulatory architecture conferring a robust regulatory control for key lineage genes.
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109
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Bell K, Skier K, Chen KH, Gergen JP. Two pair-rule responsive enhancers regulate wingless transcription in the Drosophila blastoderm embryo. Dev Dyn 2019; 249:556-572. [PMID: 31837063 DOI: 10.1002/dvdy.142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND While many developmentally relevant enhancers act in a modular fashion, there is growing evidence for nonadditive interactions between distinct cis-regulatory enhancers. We investigated if nonautonomous enhancer interactions underlie transcription regulation of the Drosophila segment polarity gene, wingless. RESULTS We identified two wg enhancers active at the blastoderm stage: wg 3613u, located from -3.6 to -1.3 kb upstream of the wg transcription start site (TSS) and 3046d, located in intron two of the wg gene, from 3.0 to 4.6 kb downstream of the TSS. Genetic experiments confirm that Even Skipped (Eve), Fushi-tarazu (Ftz), Runt, Odd-paired (Opa), Odd-skipped (Odd), and Paired (Prd) contribute to spatially regulated wg expression. Interestingly, there are enhancer specific differences in response to the gain or loss of function of pair-rule gene activity. Although each element recapitulates aspects of wg expression, a composite reporter containing both enhancers more faithfully recapitulates wg regulation than would be predicted from the sum of their individual responses. CONCLUSION These results suggest that the regulation of wg by pair-rule genes involves nonadditive interactions between distinct cis-regulatory enhancers.
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Affiliation(s)
- Kimberly Bell
- Department of Biochemistry and Cell Biology and the Center for Developmental Genetics, Stony Brook University, Stony Brook, New York
- Center for Excellence in Learning & Teaching, Stony Brook University, Stony Brook, New York
| | - Kevin Skier
- Department of Biochemistry and Cell Biology and the Center for Developmental Genetics, Stony Brook University, Stony Brook, New York
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Kevin H Chen
- Department of Biochemistry and Cell Biology and the Center for Developmental Genetics, Stony Brook University, Stony Brook, New York
- Boston University School of Medicine, Boston, Massachusetts
| | - John Peter Gergen
- Department of Biochemistry and Cell Biology and the Center for Developmental Genetics, Stony Brook University, Stony Brook, New York
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110
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Dunipace L, Ákos Z, Stathopoulos A. Coacting enhancers can have complementary functions within gene regulatory networks and promote canalization. PLoS Genet 2019; 15:e1008525. [PMID: 31830033 PMCID: PMC6932828 DOI: 10.1371/journal.pgen.1008525] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/26/2019] [Accepted: 11/15/2019] [Indexed: 11/18/2022] Open
Abstract
Developmental genes are often regulated by multiple enhancers exhibiting similar spatiotemporal outputs, which are generally considered redundantly acting though few have been studied functionally. Using CRISPR-Cas9, we created deletions of two enhancers, brk5' and brk3', that drive similar but not identical expression of the gene brinker (brk) in early Drosophila embryos. Utilizing both in situ hybridization and quantitative mRNA analysis, we investigated the changes in the gene network state caused by the removal of one or both of the early acting enhancers. brk5' deletion generally phenocopied the gene mutant, including expansion of the BMP ligand decapentaplegic (dpp) as well as inducing variability in amnioserosa tissue cell number suggesting a loss of canalization. In contrast, brk3' deletion presented unique phenotypes including dorsal expansion of several ventrally expressed genes and a decrease in amnioserosa cell number. Similarly, deletions were made for two enhancers associated with the gene short-gastrulation (sog), sog.int and sog.dist, demonstrating that they also exhibit distinct patterning phenotypes and affect canalization. In summary, this study shows that similar gene expression driven by coacting enhancers can support distinct, and sometimes complementary, functions within gene regulatory networks and, moreover, that phenotypes associated with individual enhancer deletion mutants can provide insight into new gene functions.
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Affiliation(s)
- Leslie Dunipace
- California Institute of Technology, Pasadena, CA, United States of America
| | - Zsuzsa Ákos
- California Institute of Technology, Pasadena, CA, United States of America
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111
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Racioppi C, Wiechecki KA, Christiaen L. Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices. eLife 2019; 8:49921. [PMID: 31746740 PMCID: PMC6952182 DOI: 10.7554/elife.49921] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/18/2019] [Indexed: 12/22/2022] Open
Abstract
During embryogenesis, chromatin accessibility profiles control lineage-specific gene expression by modulating transcription, thus impacting multipotent progenitor states and subsequent fate choices. Subsets of cardiac and pharyngeal/head muscles share a common origin in the cardiopharyngeal mesoderm, but the chromatin landscapes that govern multipotent progenitors competence and early fate choices remain largely elusive. Here, we leveraged the simplicity of the chordate model Ciona to profile chromatin accessibility through stereotyped transitions from naive Mesp+ mesoderm to distinct fate-restricted heart and pharyngeal muscle precursors. An FGF-Foxf pathway acts in multipotent progenitors to establish cardiopharyngeal-specific patterns of accessibility, which govern later heart vs. pharyngeal muscle-specific expression profiles, demonstrating extensive spatiotemporal decoupling between early cardiopharyngeal enhancer accessibility and late cell-type-specific activity. We found that multiple cis-regulatory elements, with distinct chromatin accessibility profiles and motif compositions, are required to activate Ebf and Tbx1/10, two key determinants of cardiopharyngeal fate choices. We propose that these 'combined enhancers' foster spatially and temporally accurate fate choices, by increasing the repertoire of regulatory inputs that control gene expression, through either accessibility and/or activity.
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Affiliation(s)
- Claudia Racioppi
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
| | - Keira A Wiechecki
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
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112
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Barr K, Reinitz J, Radulescu O. An in silico analysis of robust but fragile gene regulation links enhancer length to robustness. PLoS Comput Biol 2019; 15:e1007497. [PMID: 31730659 PMCID: PMC6881076 DOI: 10.1371/journal.pcbi.1007497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 11/27/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022] Open
Abstract
Organisms must ensure that expression of genes is directed to the appropriate tissues at the correct times, while simultaneously ensuring that these gene regulatory systems are robust to perturbation. This idea is captured by a mathematical concept called r-robustness, which says that a system is robust to a perturbation in up to r - 1 randomly chosen parameters. r-robustness implies that the biological system has a small number of sensitive parameters and that this number can be used as a robustness measure. In this work we use this idea to investigate the robustness of gene regulation using a sequence level model of the Drosophila melanogaster gene even-skipped. We consider robustness with respect to mutations of the enhancer sequence and with respect to changes of the transcription factor concentrations. We find that gene regulation is r-robust with respect to mutations in the enhancer sequence and identify a number of sensitive nucleotides. In both natural and in silico predicted enhancers, the number of nucleotides that are sensitive to mutation correlates negatively with the length of the sequence, meaning that longer sequences are more robust. The exact degree of robustness obtained is dependent not only on DNA sequence, but also on the local concentration of regulatory factors. We find that gene regulation can be remarkably sensitive to changes in transcription factor concentrations at the boundaries of expression features, while it is robust to perturbation elsewhere.
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Affiliation(s)
- Kenneth Barr
- Department of Genetic Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - John Reinitz
- Departments of Statistics, Ecology & Evolution, Molecular Genetics & Cell Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Ovidiu Radulescu
- LPHI UMR CNRS 5235, University of Montpellier, Montpellier, France
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113
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Xia JH, Wei GH. Enhancer Dysfunction in 3D Genome and Disease. Cells 2019; 8:cells8101281. [PMID: 31635067 PMCID: PMC6830074 DOI: 10.3390/cells8101281] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/10/2019] [Accepted: 10/14/2019] [Indexed: 12/13/2022] Open
Abstract
Spatiotemporal patterns of gene expression depend on enhancer elements and other factors during individual development and disease progression. The rapid progress of high-throughput techniques has led to well-defined enhancer chromatin properties. Various genome-wide methods have revealed a large number of enhancers and the discovery of three-dimensional (3D) genome architecture showing the distant interacting mechanisms of enhancers that loop to target gene promoters. Whole genome sequencing projects directed at cancer have led to the discovery of substantial enhancer dysfunction in misregulating gene expression and in tumor initiation and progression. Results from genome-wide association studies (GWAS) combined with functional genomics analyses have elucidated the functional impacts of many cancer risk-associated variants that are enriched within the enhancer regions of chromatin. Risk variants dysregulate the expression of enhancer variant-associated genes via 3D genomic interactions. Moreover, these enhancer variants often alter the chromatin binding affinity for cancer-relevant transcription factors, which in turn leads to aberrant expression of the genes associated with cancer susceptibility. In this review, we investigate the extent to which these genetic regulatory circuits affect cancer predisposition and how the recent development of genome-editing methods have enabled the determination of the impacts of genomic variation and alteration on cancer phenotype, which will eventually lead to better management plans and treatment responses to human cancer in the clinic.
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Affiliation(s)
- Ji-Han Xia
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland.
| | - Gong-Hong Wei
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90014 Oulu, Finland.
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114
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Ghavi-Helm Y. Functional Consequences of Chromosomal Rearrangements on Gene Expression: Not So Deleterious After All? J Mol Biol 2019; 432:665-675. [PMID: 31626801 DOI: 10.1016/j.jmb.2019.09.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/04/2019] [Accepted: 09/12/2019] [Indexed: 12/14/2022]
Abstract
Chromosomes are folded and organized into topologically associating domains (TADs) which provide a framework for the interaction of enhancers with the promoter of their target gene(s). Structural rearrangements observed during evolution or in disease contexts suggest that changes in genome organization strongly affect gene expression and can have drastic phenotypic effects. In this review, I will discuss how recent genomic engineering experiments reveal a more contrasted picture, suggesting that TADs are important but not always essential for gene expression regulation.
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Affiliation(s)
- Yad Ghavi-Helm
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 Allée D'Italie, F-69364 Lyon, France.
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115
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Ginley-Hidinger M, Carleton JB, Rodriguez AC, Berrett KC, Gertz J. Sufficiency analysis of estrogen responsive enhancers using synthetic activators. Life Sci Alliance 2019; 2:2/5/e201900497. [PMID: 31570515 PMCID: PMC6769255 DOI: 10.26508/lsa.201900497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 01/06/2023] Open
Abstract
Enhancers bound by synthetic activators can recreate a transcriptional response to estrogen, drive different levels of gene expression, and work independently to regulate transcription. Multiple regulatory regions bound by the same transcription factor have been shown to simultaneously control a single gene’s expression. However, it remains unclear how these regulatory regions combine to regulate transcription. Here, we test the sufficiency of promoter-distal estrogen receptor α-binding sites (ERBSs) for activating gene expression by recruiting synthetic activators in the absence of estrogens. Targeting either dCas9-VP16(10x) or dCas9-p300(core) to ERBS induces H3K27ac and activates nearby expression in a manner similar to an estrogen induction, with dCas9-VP16(10x) acting as a stronger activator. The sufficiency of individual ERBSs is highly correlated with their necessity, indicating an inherent activation potential that is associated with the binding of RNA polymerase II and several transcription factors. By targeting ERBS combinations, we found that ERBSs work independently to control gene expression when bound by synthetic activators. The sufficiency results contrast necessity assays that show synergy between these ERBSs, suggesting that synergy occurs between ERBSs in terms of activator recruitment, whereas directly recruiting activators leads to independent effects on gene expression.
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Affiliation(s)
- Matthew Ginley-Hidinger
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Bioengineering, University of Utah, Salt Lake City, UT, USA
| | - Julia B Carleton
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Adriana C Rodriguez
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Kristofer C Berrett
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.,Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Jason Gertz
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA .,Department of Oncological Sciences, University of Utah, Salt Lake City, UT, USA
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116
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Ban H, Yokota D, Otosaka S, Kikuchi M, Kinoshita H, Fujino Y, Yabe T, Ovara H, Izuka A, Akama K, Yamasu K, Takada S, Kawamura A. Transcriptional autoregulation of zebrafish tbx6 is required for somite segmentation. Development 2019; 146:dev.177063. [PMID: 31444219 DOI: 10.1242/dev.177063] [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] [Received: 02/20/2019] [Accepted: 08/15/2019] [Indexed: 12/13/2022]
Abstract
The presumptive somite boundary in the presomitic mesoderm (PSM) is defined by the anterior border of the expression domain of Tbx6 protein. During somite segmentation, the expression domain of Tbx6 is regressed by Ripply-meditated degradation of Tbx6 protein. Although the expression of zebrafish tbx6 remains restricted to the PSM, the transcriptional regulation of tbx6 remains poorly understood. Here, we show that the expression of zebrafish tbx6 is maintained by transcriptional autoregulation. We find that a proximal-located cis-regulatory module, TR1, which contains two putative T-box sites, is required for somite segmentation in the intermediate body and for proper expression of segmentation genes. Embryos with deletion of TR1 exhibit significant reduction of tbx6 expression at the 12-somite stage, although its expression is initially observed. Additionally, Tbx6 is associated with TR1 and activates its own expression in the anterior PSM. Furthermore, the anterior expansion of tbx6 expression in ripply gene mutants is suppressed in a TR1-dependent manner. The results suggest that the autoregulatory loop of zebrafish tbx6 facilitates immediate removal of Tbx6 protein through termination of its own transcription at the anterior PSM.
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Affiliation(s)
- Hiroyuki Ban
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Daisuke Yokota
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Shiori Otosaka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Morimichi Kikuchi
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Hirofumi Kinoshita
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Yuuri Fujino
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Taijiro Yabe
- Exploratory Research Center on Life and Living Systems and National Institute for Basic Biology, National Institutes of Natural Sciences, Aichi 444-8787, Japan
| | - Hiroki Ovara
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Ayaka Izuka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Kagari Akama
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Kyo Yamasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Shinji Takada
- Exploratory Research Center on Life and Living Systems and National Institute for Basic Biology, National Institutes of Natural Sciences, Aichi 444-8787, Japan
| | - Akinori Kawamura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
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117
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Abstract
Mammalian genomes are extensively transcribed, which produces a large number of both coding and non-coding transcripts. Various RNAs are physically associated with chromatin, through being either retained in cis at their site of transcription or recruited in trans to other genomic regions. Driven by recent technological innovations for detecting chromatin-associated RNAs, diverse roles are being revealed for these RNAs and associated RNA-binding proteins (RBPs) in gene regulation and genome function. Such functions include locus-specific roles in gene activation and silencing, as well as emerging roles in higher-order genome organization, such as involvement in long-range enhancer-promoter interactions, transcription hubs, heterochromatin, nuclear bodies and phase transitions.
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Affiliation(s)
- Xiao Li
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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118
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Rice GR, Barmina O, Luecke D, Hu K, Arbeitman M, Kopp A. Modular tissue-specific regulation of doublesex underpins sexually dimorphic development in Drosophila. Development 2019; 146:dev178285. [PMID: 31285355 PMCID: PMC6679366 DOI: 10.1242/dev.178285] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/28/2019] [Indexed: 11/20/2022]
Abstract
The ability of a single genome to produce distinct and often dramatically different male and female forms is one of the wonders of animal development. In Drosophila melanogaster, most sexually dimorphic traits are controlled by sex-specific isoforms of the doublesex (dsx) transcription factor, and dsx expression is mostly limited to cells that give rise to sexually dimorphic traits. However, it is unknown how this mosaic of sexually dimorphic and monomorphic organs arises. Here, we characterize the cis-regulatory sequences that control dsx expression in the foreleg, which contains multiple types of sex-specific sensory organs. We find that separate modular enhancers are responsible for dsx expression in each sexually dimorphic organ. Expression of dsx in the sex comb is co-regulated by two enhancers with distinct spatial and temporal specificities that are separated by a genitalia-specific enhancer. The sex comb-specific enhancer from D. willistoni, a species that primitively lacks sex combs, is not active in the foreleg. Thus, the mosaic of sexually dimorphic and monomorphic organs depends on modular regulation of dsx transcription by dedicated cell type-specific enhancers.
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Affiliation(s)
- Gavin R Rice
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Olga Barmina
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - David Luecke
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - Kevin Hu
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - Michelle Arbeitman
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
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119
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Yevick HG, Miller PW, Dunkel J, Martin AC. Structural Redundancy in Supracellular Actomyosin Networks Enables Robust Tissue Folding. Dev Cell 2019; 50:586-598.e3. [PMID: 31353314 DOI: 10.1016/j.devcel.2019.06.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/08/2019] [Accepted: 06/21/2019] [Indexed: 12/31/2022]
Abstract
Tissue morphogenesis is strikingly robust. Yet, how tissues are sculpted under challenging conditions is unknown. Here, we combined network analysis, experimental perturbations, and computational modeling to determine how network connectivity between hundreds of contractile cells on the ventral side of the Drosophila embryo ensures robust tissue folding. We identified two network properties that mechanically promote robustness. First, redundant supracellular cytoskeletal network paths ensure global connectivity, even with network degradation. By forming many more connections than are required, morphogenesis is not disrupted by local network damage, analogous to the way redundancy guarantees the large-scale function of vasculature and transportation networks. Second, directional stiffening of edges oriented orthogonal to the folding axis promotes furrow formation at lower contractility levels. Structural redundancy and directional network stiffening ensure robust tissue folding with proper orientation.
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Affiliation(s)
- Hannah G Yevick
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Pearson W Miller
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Adam C Martin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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120
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Jia Y, Chng WJ, Zhou J. Super-enhancers: critical roles and therapeutic targets in hematologic malignancies. J Hematol Oncol 2019; 12:77. [PMID: 31311566 PMCID: PMC6636097 DOI: 10.1186/s13045-019-0757-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022] Open
Abstract
Super-enhancers (SEs) in a broad range of human cell types are large clusters of enhancers with aberrant high levels of transcription factor binding, which are central to drive expression of genes in controlling cell identity and stimulating oncogenic transcription. Cancer cells acquire super-enhancers at oncogene and cancerous phenotype relies on these abnormal transcription propelled by SEs. Furthermore, specific inhibitors targeting SEs assembly and activation have offered potential targets for treating various tumors including hematological malignancies. Here, we first review the identification, functional significance of SEs. Next, we summarize recent findings of SEs and SE-driven gene regulation in normal hematopoiesis and hematologic malignancies. The importance and various modes of SE-mediated MYC oncogene amplification are illustrated. Finally, we highlight the progress of SEs as selective therapeutic targets in basic research and clinical trials. Some open questions regarding functional significance and future directions of targeting SEs in the clinic will be discussed too.
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Affiliation(s)
- Yunlu Jia
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore.,Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, 310016, Zhejiang, China
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore.,Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), 1E, Kent Ridge Road, Singapore, 119228, Republic of Singapore
| | - Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Centre for Translational Medicine, Singapore, 117599, Republic of Singapore. .,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Republic of Singapore.
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121
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Tsai A, Alves MRP, Crocker J. Multi-enhancer transcriptional hubs confer phenotypic robustness. eLife 2019; 8:e45325. [PMID: 31294690 PMCID: PMC6650246 DOI: 10.7554/elife.45325] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/08/2019] [Indexed: 01/08/2023] Open
Abstract
We previously showed in Drosophila melanogaster embryos that low-affinity Ultrabithorax (Ubx)-responsive shavenbaby (svb) enhancers drive expression using localized transcriptional environments and that active svb enhancers on different chromosomes tended to colocalize (Tsai et al., 2017). Here, we test the hypothesis that these multi-enhancer 'hubs' improve phenotypic resilience to stress by buffering against decreases in transcription factor concentrations and transcriptional output. Deleting a redundant enhancer from the svb locus led to reduced trichome numbers in embryos raised at elevated temperatures. Using high-resolution fluorescence microscopy, we observed lower Ubx concentration and transcriptional output in this deletion allele. Transcription sites of the full svb cis-regulatory region inserted into a different chromosome colocalized with the svb locus, increasing Ubx concentration, the transcriptional output of svb, and partially rescuing the phenotype. Thus, multiple enhancers could reinforce a local transcriptional hub to buffer against environmental stresses and genetic perturbations, providing a mechanism for phenotypical robustness.
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Affiliation(s)
- Albert Tsai
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Mariana RP Alves
- European Molecular Biology LaboratoryHeidelbergGermany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of BiosciencesHeidelbergGermany
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122
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Repele A, Krueger S, Bhattacharyya T, Tuineau MY. The regulatory control of Cebpa enhancers and silencers in the myeloid and red-blood cell lineages. PLoS One 2019; 14:e0217580. [PMID: 31181110 PMCID: PMC6557489 DOI: 10.1371/journal.pone.0217580] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
Cebpa encodes a transcription factor (TF) that plays an instructive role in the development of multiple myeloid lineages. The expression of Cebpa itself is finely modulated, as Cebpa is expressed at high and intermediate levels in neutrophils and macrophages respectively and downregulated in non-myeloid lineages. The cis-regulatory logic underlying the lineage-specific modulation of Cebpa's expression level is yet to be fully characterized. Previously, we had identified 6 new cis-regulatory modules (CRMs) in a 78kb region surrounding Cebpa. We had also inferred the TFs that regulate each CRM by fitting a sequence-based thermodynamic model to a comprehensive reporter activity dataset. Here, we report the cis-regulatory logic of Cebpa CRMs at the resolution of individual binding sites. We tested the binding sites and functional roles of inferred TFs by designing and constructing mutated CRMs and comparing theoretical predictions of their activity against empirical measurements in a myeloid cell line. The enhancers were confirmed to be activated by combinations of PU.1, C/EBP family TFs, Egr1, and Gfi1 as predicted by the model. We show that silencers repress the activity of the proximal promoter in a dominant manner in G1ME cells, which are derived from the red-blood cell lineage. Dominant repression in G1ME cells can be traced to binding sites for GATA and Myb, a motif shared by all of the silencers. Finally, we demonstrate that GATA and Myb act redundantly to silence the proximal promoter. These results indicate that dominant repression is a novel mechanism for resolving hematopoietic lineages. Furthermore, Cebpa has a fail-safe cis-regulatory architecture, featuring several functionally similar CRMs, each of which contains redundant binding sites for multiple TFs. Lastly, by experimentally demonstrating the predictive ability of our sequence-based thermodynamic model, this work highlights the utility of this computational approach for understanding mammalian gene regulation.
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Affiliation(s)
- Andrea Repele
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Shawn Krueger
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Tapas Bhattacharyya
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
| | - Michelle Y Tuineau
- Department of Biology, University of North Dakota, Grand Forks, ND, United States of America
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123
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Qu J, Yi G, Zhou H. p63 cooperates with CTCF to modulate chromatin architecture in skin keratinocytes. Epigenetics Chromatin 2019; 12:31. [PMID: 31164150 PMCID: PMC6547520 DOI: 10.1186/s13072-019-0280-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 05/17/2019] [Indexed: 11/24/2022] Open
Abstract
The transcription factor p63 regulates epidermal genes and the enhancer landscape in skin keratinocytes. Its molecular function in controlling the chromatin structure is, however, not yet completely understood. Here, we integrated multi-omics profiles, including the transcriptome, transcription factor DNA-binding and chromatin accessibility, in skin keratinocytes isolated from EEC syndrome patients carrying p63 mutations, to examine the role of p63 in shaping the chromatin architecture. We found decreased chromatin accessibility in p63- and CTCF-bound open chromatin regions that potentially contributed to gene deregulation in mutant keratinocytes. Cooperation of p63 and CTCF seemed to assist chromatin interactions between p63-bound enhancers and gene promoters in skin keratinocytes. Our study suggests an intriguing model where cell type-specific transcription factors such as p63 cooperate with the genome organizer CTCF in the three-dimensional chromatin space to regulate the transcription program important for the proper cell identity.
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Affiliation(s)
- Jieqiong Qu
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Guoqiang Yi
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
- Present Address: Center for Animal Genomics, Agricultural Genome Institute at Shenzhen, Chinese
Academy of Agricultural Sciences, Shenzhen, 518124 China
| | - Huiqing Zhou
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
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124
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Schoenfelder S, Fraser P. Long-range enhancer–promoter contacts in gene expression control. Nat Rev Genet 2019; 20:437-455. [DOI: 10.1038/s41576-019-0128-0] [Citation(s) in RCA: 486] [Impact Index Per Article: 97.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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125
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Hamdan FH, Johnsen SA. Perturbing Enhancer Activity in Cancer Therapy. Cancers (Basel) 2019; 11:cancers11050634. [PMID: 31067678 PMCID: PMC6563029 DOI: 10.3390/cancers11050634] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/26/2019] [Accepted: 05/05/2019] [Indexed: 02/07/2023] Open
Abstract
Tight regulation of gene transcription is essential for normal development, tissue homeostasis, and disease-free survival. Enhancers are distal regulatory elements in the genome that provide specificity to gene expression programs and are frequently misregulated in cancer. Recent studies examined various enhancer-driven malignant dependencies and identified different approaches to specifically target these programs. In this review, we describe numerous features that make enhancers good transcriptional targets in cancer therapy and discuss different approaches to overcome enhancer perturbation. Interestingly, a number of approved therapeutic agents, such as cyclosporine, steroid hormones, and thiazolidinediones, actually function by affecting enhancer landscapes by directly targeting very specific transcription factor programs. More recently, a broader approach to targeting deregulated enhancer programs has been achieved via Bromodomain and Extraterminal (BET) inhibition or perturbation of transcription-related cyclin-dependent kinases (CDK). One challenge to enhancer-targeted therapy is proper patient stratification. We suggest that monitoring of enhancer RNA (eRNA) expression may serve as a unique biomarker of enhancer activity that can help to predict and monitor responsiveness to enhancer-targeted therapies. A more thorough investigation of cancer-specific enhancers and the underlying mechanisms of deregulation will pave the road for an effective utilization of enhancer modulators in a precision oncology approach to cancer treatment.
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Affiliation(s)
- Feda H Hamdan
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Steven A Johnsen
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
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126
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Yamada S, Whitney PH, Huang SK, Eck EC, Garcia HG, Rushlow CA. The Drosophila Pioneer Factor Zelda Modulates the Nuclear Microenvironment of a Dorsal Target Enhancer to Potentiate Transcriptional Output. Curr Biol 2019; 29:1387-1393.e5. [PMID: 30982648 DOI: 10.1016/j.cub.2019.03.019] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/07/2019] [Accepted: 03/12/2019] [Indexed: 12/31/2022]
Abstract
Connecting the developmental patterning of tissues to the mechanistic control of RNA polymerase II remains a long-term goal of developmental biology. Many key elements have been identified in the establishment of spatial-temporal control of transcription in the early Drosophila embryo, a model system for transcriptional regulation. The dorsal-ventral axis of the Drosophila embryo is determined by the graded distribution of Dorsal (Dl), a homolog of the nuclear factor κB (NF-κB) family of transcriptional activators found in humans [1, 2]. A second maternally deposited factor, Zelda (Zld), is uniformly distributed in the embryo and is thought to act as a pioneer factor, increasing enhancer accessibility for transcription factors, such as Dl [3-9]. Here, we utilized the MS2 live imaging system to evaluate the expression of the Dl target gene short gastrulation (sog) to better understand how a pioneer factor affects the kinetic parameters of transcription. Our experiments indicate that Zld modifies probability of activation, the timing of this activation, and the rate at which transcription occurs. Our results further show that this effective rate increase is due to an increased accumulation of Dl at the site of transcription, suggesting that transcription factor "hubs" induced by Zld [10] functionally regulate transcription.
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Affiliation(s)
- Shigehiro Yamada
- Department of Biology, New York University, New York, NY 10003, USA
| | - Peter H Whitney
- Department of Biology, New York University, New York, NY 10003, USA
| | - Shao-Kuei Huang
- Department of Biology, New York University, New York, NY 10003, USA
| | - Elizabeth C Eck
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cellular Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Department of Physics, University of California at Berkeley, Berkeley, CA 94720, USA; Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA 94720, USA
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127
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Ho EYK, Cao Q, Gu M, Chan RWL, Wu Q, Gerstein M, Yip KY. Shaping the nebulous enhancer in the era of high-throughput assays and genome editing. Brief Bioinform 2019; 21:836-850. [PMID: 30895290 DOI: 10.1093/bib/bbz030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/15/2019] [Accepted: 02/26/2019] [Indexed: 01/22/2023] Open
Abstract
Since the 1st discovery of transcriptional enhancers in 1981, their textbook definition has remained largely unchanged in the past 37 years. With the emergence of high-throughput assays and genome editing, which are switching the paradigm from bottom-up discovery and testing of individual enhancers to top-down profiling of enhancer activities genome-wide, it has become increasingly evidenced that this classical definition has left substantial gray areas in different aspects. Here we survey a representative set of recent research articles and report the definitions of enhancers they have adopted. The results reveal that a wide spectrum of definitions is used usually without the definition stated explicitly, which could lead to difficulties in data interpretation and downstream analyses. Based on these findings, we discuss the practical implications and suggestions for future studies.
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Affiliation(s)
| | - Qin Cao
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong
| | - Mengting Gu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Ricky Wai-Lun Chan
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong
| | - Qiong Wu
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong.,School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.,Program in Computational Biology and Bioinformatics.,Department of Computer Science, Yale University, New Haven, Connecticut, USA
| | - Kevin Y Yip
- Department of Biomedical Engineering.,Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong.,Hong Kong Bioinformatics Centre.,CUHK-BGI Innovation Institute of Trans-omics.,Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong
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128
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Redundant and Cryptic Enhancer Activities of the Drosophila yellow Gene. Genetics 2019; 212:343-360. [PMID: 30842209 DOI: 10.1534/genetics.119.301985] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/25/2019] [Indexed: 11/18/2022] Open
Abstract
Cis-regulatory sequences known as enhancers play a key role in regulating gene expression. Evolutionary changes in these DNA sequences contribute to phenotypic evolution. The Drosophila yellow gene, which is required for pigmentation, has emerged as a model system for understanding how cis-regulatory sequences evolve, providing some of the most detailed insights available into how activities of orthologous enhancers have diverged between species. Here, we examine the evolution of yellow cis-regulatory sequences on a broader scale, by comparing the distribution and function of yellow enhancer activities throughout the 5' intergenic and intronic sequences of Drosophila melanogaster, D. pseudoobscura, and D. willistoni We find that cis-regulatory sequences driving expression in a particular tissue are not as modular as previously described, but rather have many redundant and cryptic enhancer activities distributed throughout the regions surveyed. Interestingly, cryptic enhancer activities of sequences from one species often drove patterns of expression observed in other species, suggesting that the frequent evolutionary changes in yellow expression observed among Drosophila species may be facilitated by gaining and losing repression of preexisting cis-regulatory sequences.
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129
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Scholes C, Biette KM, Harden TT, DePace AH. Signal Integration by Shadow Enhancers and Enhancer Duplications Varies across the Drosophila Embryo. Cell Rep 2019; 26:2407-2418.e5. [PMID: 30811990 PMCID: PMC6597254 DOI: 10.1016/j.celrep.2019.01.115] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/06/2019] [Accepted: 01/30/2019] [Indexed: 01/07/2023] Open
Abstract
Transcription of developmental genes is controlled by multiple enhancers. Frequently, more than one enhancer can activate transcription from the same promoter in the same cells. How is regulatory information from multiple enhancers combined to determine the overall expression output? We measure nascent transcription driven by a pair of shadow enhancers, each enhancer of the pair separately, and each duplicated, using live imaging in Drosophila embryos. This set of constructs allows us to quantify the input-output function describing signal integration by two enhancers. We show that signal integration performed by these shadow enhancers and duplications varies across the expression pattern, implying that how their activities are combined depends on the transcriptional regulators bound to the enhancers in different parts of the embryo. Characterizing signal integration by multiple enhancers is a critical step in developing conceptual and computational models of gene expression at the locus level, where multiple enhancers control transcription together.
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Affiliation(s)
- Clarissa Scholes
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kelly M Biette
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Timothy T Harden
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Angela H DePace
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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130
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Yoshida H, Lareau CA, Ramirez RN, Rose SA, Maier B, Wroblewska A, Desland F, Chudnovskiy A, Mortha A, Dominguez C, Tellier J, Kim E, Dwyer D, Shinton S, Nabekura T, Qi Y, Yu B, Robinette M, Kim KW, Wagers A, Rhoads A, Nutt SL, Brown BD, Mostafavi S, Buenrostro JD, Benoist C. The cis-Regulatory Atlas of the Mouse Immune System. Cell 2019; 176:897-912.e20. [PMID: 30686579 PMCID: PMC6785993 DOI: 10.1016/j.cell.2018.12.036] [Citation(s) in RCA: 257] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/26/2018] [Accepted: 12/20/2018] [Indexed: 01/08/2023]
Abstract
A complete chart of cis-regulatory elements and their dynamic activity is necessary to understand the transcriptional basis of differentiation and function of an organ system. We generated matched epigenome and transcriptome measurements in 86 primary cell types that span the mouse immune system and its differentiation cascades. This breadth of data enable variance components analysis that suggests that genes fall into two distinct classes, controlled by either enhancer- or promoter-driven logic, and multiple regression that connects genes to the enhancers that regulate them. Relating transcription factor (TF) expression to the genome-wide accessibility of their binding motifs classifies them as predominantly openers or closers of local chromatin accessibility, pinpointing specific cis-regulatory elements where binding of given TFs is likely functionally relevant, validated by chromatin immunoprecipitation sequencing (ChIP-seq). Overall, this cis-regulatory atlas provides a trove of information on transcriptional regulation through immune differentiation and a foundational scaffold to define key regulatory events throughout the immunological genome.
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Affiliation(s)
- Hideyuki Yoshida
- Department of Immunology, Harvard Medical School, Boston, MA, USA; YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | | | | | - Samuel A Rose
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Barbara Maier
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksandra Wroblewska
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fiona Desland
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aleksey Chudnovskiy
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arthur Mortha
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Julie Tellier
- The Walter and Eliza Hall Institute and Department of Medical Biology, Melbourne University, Parkville, VIC, Australia
| | - Edy Kim
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
| | - Dan Dwyer
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Tsukasa Nabekura
- Department of Microbiology and Immunology, UCSF, San Francisco, CA, USA
| | - YiLin Qi
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bingfei Yu
- Department of Biological Sciences, UCSD, La Jolla, CA, USA
| | - Michelle Robinette
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Ki-Wook Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Amy Wagers
- Joslin Diabetes Center, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA USA
| | - Andrew Rhoads
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute and Department of Medical Biology, Melbourne University, Parkville, VIC, Australia
| | - Brian D Brown
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sara Mostafavi
- Department of Statistics and Department Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA USA.
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131
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Chong R, Insigne KD, Yao D, Burghard CP, Wang J, Hsiao YHE, Jones EM, Goodman DB, Xiao X, Kosuri S. A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions. Mol Cell 2019; 73:183-194.e8. [PMID: 30503770 PMCID: PMC6599603 DOI: 10.1016/j.molcel.2018.10.037] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/19/2018] [Accepted: 10/23/2018] [Indexed: 11/23/2022]
Abstract
Mutations that lead to splicing defects can have severe consequences on gene function and cause disease. Here, we explore how human genetic variation affects exon recognition by developing a multiplexed functional assay of splicing using Sort-seq (MFASS). We assayed 27,733 variants in the Exome Aggregation Consortium (ExAC) within or adjacent to 2,198 human exons in the MFASS minigene reporter and found that 3.8% (1,050) of variants, most of which are extremely rare, led to large-effect splice-disrupting variants (SDVs). Importantly, we find that 83% of SDVs are located outside of canonical splice sites, are distributed evenly across distinct exonic and intronic regions, and are difficult to predict a priori. Our results indicate extant, rare genetic variants can have large functional effects on splicing at appreciable rates, even outside the context of disease, and MFASS enables their empirical assessment at scale.
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Affiliation(s)
- Rockie Chong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kimberly D Insigne
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David Yao
- Department of Genetics, Stanford University, Stanford, CA 94035, USA
| | - Christina P Burghard
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jeffrey Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yun-Hua E Hsiao
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Eric M Jones
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel B Goodman
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xinshu Xiao
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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132
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Integrative view on how erythropoietin signaling controls transcription patterns in erythroid cells. Curr Opin Hematol 2019; 25:189-195. [PMID: 29389768 DOI: 10.1097/moh.0000000000000415] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE OF REVIEW Erythropoietin (EPO) is necessary and sufficient to trigger dynamic transcriptional patterns that drive the differentiation of erythroid precursor cells into mature, enucleated red cells. Because the molecular cloning and Food and Drug Administration approval for the therapeutic use of EPO over 30 years ago, a detailed understanding of how EPO works has advanced substantially. Yet, the precise epigenetic and transcriptional mechanisms by which EPO signaling controls erythroid expression patterns remains poorly understood. This review focuses on the current state of erythroid biology in regards to EPO signaling from human genetics and functional genomics perspectives. RECENT FINDINGS The goal of this review is to provide an integrative view of the gene regulatory underpinnings for erythroid expression patterns that are dynamically shaped during erythroid differentiation. Here, we highlight vignettes connecting recent insights into a genome-wide association study linking an EPO mutation to anemia, a study linking EPO-signaling to signal transducer and activator of transcription 5 (STAT5) chromatin occupancy and enhancers, and studies that examine the molecular mechanisms driving topological chromatin organization in erythroid cells. SUMMARY The genetic, epigenetic, and gene regulatory mechanisms underlying how hormone signal transduction influences erythroid gene expression remains only partly understood. A detailed understanding of these molecular pathways and how they intersect with one another will provide the basis for novel strategies to treat anemia and potentially other hematological diseases. As new regulators and signal transducers of EPO-signaling continue to emerge, new clinically relevant targets may be identified that improve the specificity and effectiveness of EPO therapy.
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133
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A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Cell 2019; 176:377-390.e19. [PMID: 30612741 DOI: 10.1016/j.cell.2018.11.029] [Citation(s) in RCA: 293] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/30/2018] [Accepted: 11/19/2018] [Indexed: 11/23/2022]
Abstract
Over one million candidate regulatory elements have been identified across the human genome, but nearly all are unvalidated and their target genes uncertain. Approaches based on human genetics are limited in scope to common variants and in resolution by linkage disequilibrium. We present a multiplex, expression quantitative trait locus (eQTL)-inspired framework for mapping enhancer-gene pairs by introducing random combinations of CRISPR/Cas9-mediated perturbations to each of many cells, followed by single-cell RNA sequencing (RNA-seq). Across two experiments, we used dCas9-KRAB to perturb 5,920 candidate enhancers with no strong a priori hypothesis as to their target gene(s), measuring effects by profiling 254,974 single-cell transcriptomes. We identified 664 (470 high-confidence) cis enhancer-gene pairs, which were enriched for specific transcription factors, non-housekeeping status, and genomic and 3D conformational proximity to their target genes. This framework will facilitate the large-scale mapping of enhancer-gene regulatory interactions, a critical yet largely uncharted component of the cis-regulatory landscape of the human genome.
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134
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Hoyer JS, Pruneda‐Paz JL, Breton G, Hassert MA, Holcomb EE, Fowler H, Bauer KM, Mreen J, Kay SA, Carrington JC. Functional dissection of the ARGONAUTE7 promoter. PLANT DIRECT 2019; 3:e00102. [PMID: 31245750 PMCID: PMC6508778 DOI: 10.1002/pld3.102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/29/2018] [Accepted: 11/09/2018] [Indexed: 05/27/2023]
Abstract
ARGONAUTES are the central effector proteins of RNA silencing which bind target transcripts in a small RNA-guided manner. Arabidopsis thaliana has 10 ARGONAUTE (AGO) genes, with specialized roles in RNA-directed DNA methylation, post-transcriptional gene silencing, and antiviral defense. To better understand specialization among AGO genes at the level of transcriptional regulation we tested a library of 1497 transcription factors for binding to the promoters of AGO1,AGO10, and AGO7 using yeast 1-hybrid assays. A ranked list of candidate DNA-binding TFs revealed binding of the AGO7 promoter by a number of proteins in two families: the miR156-regulated SPL family and the miR319-regulated TCP family, both of which have roles in developmental timing and leaf morphology. Possible functions for SPL and TCP binding are unclear: we showed that these binding sites are not required for the polar expression pattern of AGO7, nor for the function of AGO7 in leaf shape. Normal AGO7 transcription levels and function appear to depend instead on an adjacent 124-bp region. Progress in understanding the structure of this promoter may aid efforts to understand how the conserved AGO7-triggered TAS3 pathway functions in timing and polarity.
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Affiliation(s)
- J. Steen Hoyer
- Donald Danforth Plant Science CenterSt. LouisMissouri
- Computational and Systems Biology ProgramWashington UniversitySt. LouisMissouri
| | - Jose L. Pruneda‐Paz
- Division of Biological Sciences and Center for ChronobiologyUniversity of California San DiegoLa JollaCalifornia
| | - Ghislain Breton
- Division of Biological Sciences and Center for ChronobiologyUniversity of California San DiegoLa JollaCalifornia
- Department of Integrative Biology and PharmacologyMcGovern Medical SchoolHoustonTexas
| | | | | | - Halley Fowler
- Donald Danforth Plant Science CenterSt. LouisMissouri
| | | | - Jacob Mreen
- Donald Danforth Plant Science CenterSt. LouisMissouri
| | - Steve A. Kay
- Division of Biological Sciences and Center for ChronobiologyUniversity of California San DiegoLa JollaCalifornia
- Department of NeurologyUniversity of Southern CaliforniaLos AngelesCalifornia
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135
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Song W, Ovcharenko I. Dichotomy in redundant enhancers points to presence of initiators of gene regulation. BMC Genomics 2018; 19:947. [PMID: 30563465 PMCID: PMC6299655 DOI: 10.1186/s12864-018-5335-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/29/2018] [Indexed: 12/31/2022] Open
Abstract
Background The regulatory landscape of a gene locus often consists of several functionally redundant enhancers establishing phenotypic robustness and evolutionary stability of its regulatory program. However, it is unclear what mechanisms are employed by redundant enhancers to cooperatively orchestrate gene expression. Results By comparing redundant enhancers to single enhancers (enhancers present in a single copy in a gene locus), we observed that the DNA sequence encryption differs between these two classes of enhancers, suggesting a difference in their regulatory mechanisms. Initiator enhancers, which are a subset of redundant enhancers and show similar sequence encryption to single enhancers, differ from the rest of redundant enhancers in their sequence encryption, evolutionary conservation and proximity to target genes. Genes hosting initiator enhancers in their loci feature elevated levels of expression. Initiator enhancers show a high level of 3D chromatin contacts with both transcription start sites and regular enhancers, suggesting their roles as primary activators and intermediate catalysts of gene expression, through which the regulatory signals of redundant enhancers are propagated to the target genes. In addition, GWAS and eQTLs variants are significantly enriched in initiator enhancers compared to redundant enhancers, suggesting a key functional role these sequences play in gene regulation. Conclusions The specific characteristics and widespread abundance of initiator enhancers advocate for a possible universal hierarchical mechanism of tissue-specific gene regulation involving multiple redundant enhancers acting through initiator enhancers. Electronic supplementary material The online version of this article (10.1186/s12864-018-5335-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Song
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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136
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Halfon MS. Studying Transcriptional Enhancers: The Founder Fallacy, Validation Creep, and Other Biases. Trends Genet 2018; 35:93-103. [PMID: 30553552 DOI: 10.1016/j.tig.2018.11.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/15/2018] [Accepted: 11/21/2018] [Indexed: 12/21/2022]
Abstract
Transcriptional enhancers play a major role in regulating metazoan gene expression. Recent developments in genomics and next-generation sequencing have accelerated and revitalized the study of this important class of sequence elements. Increased interest and attention, however, has also led to troubling trends in the enhancer literature. In this Opinion, I describe some of these issues and show how they arise from shifting and nonuniform enhancer definitions, and genome-era biases. I discuss how they can lead to interpretative errors and an unduly narrow focus on certain aspects of enhancer biology to the potential exclusion of others.
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Affiliation(s)
- Marc S Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY, USA; NY State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA; Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY, USA; Department of Biomedical Informatics, University at Buffalo-State University of New York, Buffalo, NY, USA; Department of Molecular and Cellular Biology and Program in Cancer Genetics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
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137
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McGreal-Estrada RS, Wolf LV, Cvekl A. Promoter-enhancer looping and shadow enhancers of the mouse αA-crystallin locus. Biol Open 2018; 7:bio.036897. [PMID: 30404901 PMCID: PMC6310886 DOI: 10.1242/bio.036897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Gene regulation by enhancers is important for precise temporal and spatial gene expression. Enhancers can drive gene expression regardless of their location, orientation or distance from the promoter. Changes in chromatin conformation and chromatin looping occur to bring the promoter and enhancers into close proximity. αA-crystallin ranks among one of the most abundantly expressed genes and proteins in the mammalian lens. The αA-crystallin locus is characterized by a 16 kb chromatin domain marked by two distal enhancers, 5′ DCR1 and 3′ DCR3. Here we used chromatin conformation capture (3C) analysis and transgenic approaches to analyze temporal control of the mouse αA-crystallin gene. We find that DCR1 is necessary, but not sufficient alone to drive expression at E10.5 in the mouse lens pit. Chromatin looping revealed interaction between the promoter and the region 3′ to DCR1, identifying a novel enhancer region in the αA-crystallin locus. We determined that this novel enhancer region, DCR1S, recapitulates the temporal control by DCR1. Acting as shadow enhancers, DCR1 and DCR1S are able to control expression in the lens vesicle at E11.5. It remains to be elucidated however, which region of the αA-crystallin locus is responsible for expression in the lens pit at E10.5. Summary: The αA-crystallin ranks amongst the most highly expressed tissue-specific genes. It is an advantageous model system to probe both promoter-enhancer looping and to identify distal enhancers and their temporal/spatial activities.
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Affiliation(s)
- Rebecca S McGreal-Estrada
- Departments Ophthalmology and Visual Sciences and Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Ullmann 123, Bronx, NY 10461, USA
| | - Louise V Wolf
- Departments Ophthalmology and Visual Sciences and Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Ullmann 123, Bronx, NY 10461, USA.,Office of Research Services (ORS), Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place - Box 1120, New York, NY 10029-6574
| | - Ales Cvekl
- Departments Ophthalmology and Visual Sciences and Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Ullmann 123, Bronx, NY 10461, USA
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138
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Urban EA, Johnston RJ. Buffering and Amplifying Transcriptional Noise During Cell Fate Specification. Front Genet 2018; 9:591. [PMID: 30555516 PMCID: PMC6282114 DOI: 10.3389/fgene.2018.00591] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/15/2018] [Indexed: 11/29/2022] Open
Abstract
The molecular processes that drive gene transcription are inherently noisy. This noise often manifests in the form of transcriptional bursts, producing fluctuations in gene activity over time. During cell fate specification, this noise is often buffered to ensure reproducible developmental outcomes. However, sometimes noise is utilized as a “bet-hedging” mechanism to diversify functional roles across a population of cells. Studies of bacteria, yeast, and cultured cells have provided insights into the nature and roles of noise in transcription, yet we are only beginning to understand the mechanisms by which noise influences the development of multicellular organisms. Here we discuss the sources of transcriptional noise and the mechanisms that either buffer noise to drive reproducible fate choices or amplify noise to randomly specify fates.
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Affiliation(s)
- Elizabeth A Urban
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
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139
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Yuan X, Song M, Devine P, Bruneau BG, Scott IC, Wilson MD. Heart enhancers with deeply conserved regulatory activity are established early in zebrafish development. Nat Commun 2018; 9:4977. [PMID: 30478328 PMCID: PMC6255839 DOI: 10.1038/s41467-018-07451-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/26/2018] [Indexed: 12/21/2022] Open
Abstract
During the phylotypic period, embryos from different genera show similar gene expression patterns, implying common regulatory mechanisms. Here we set out to identify enhancers involved in the initial events of cardiogenesis, which occurs during the phylotypic period. We isolate early cardiac progenitor cells from zebrafish embryos and characterize 3838 open chromatin regions specific to this cell population. Of these regions, 162 overlap with conserved non-coding elements (CNEs) that also map to open chromatin regions in human. Most of the zebrafish conserved open chromatin elements tested drive gene expression in the developing heart. Despite modest sequence identity, human orthologous open chromatin regions recapitulate the spatial temporal expression patterns of the zebrafish sequence, potentially providing a basis for phylotypic gene expression patterns. Genome-wide, we discover 5598 zebrafish-human conserved open chromatin regions, suggesting that a diverse repertoire of ancient enhancers is established prior to organogenesis and the phylotypic period. During early embryogenesis, critical cardiac specification events occur. Here the authors isolate cardiac progenitor cells from early zebrafish embryos and characterize accessible chromatin regions specific to this cell population, finding that many of these regions overlap with conserved non-coding elements that are ortholgous to accessible chromatin regions in human.
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Affiliation(s)
- Xuefei Yuan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Mengyi Song
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Patrick Devine
- Gladstone Institutes, San Francisco, CA, 94158, USA.,Department of Pathology, University of California, San Francisco, San Francisco, CA, 94143-0511, USA
| | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, 94158, USA.,Department of Pediatrics and Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ian C Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Michael D Wilson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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140
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Grover S, Williams ME, Kaiser R, Hughes JT, Gresham L, Rebeiz M, Williams TM. Augmentation of a wound response element accompanies the origin of a Hox-regulated Drosophila abdominal pigmentation trait. Dev Biol 2018; 441:159-175. [PMID: 29981311 PMCID: PMC6075670 DOI: 10.1016/j.ydbio.2018.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/29/2018] [Accepted: 07/01/2018] [Indexed: 11/16/2022]
Abstract
A challenge for evolutionary research is to uncover how new morphological traits evolve the coordinated spatial and temporal expression patterns of genes that govern their formation during development. Detailed studies are often limited to characterizing how one or a few genes contributed to a trait's emergence, and thus our knowledge of how entire GRNs evolve their coordinated expression of each gene remains unresolved. The melanic color patterns decorating the male abdominal tergites of Drosophila (D.) melanogaster evolved in part by novel expression patterns for genes acting at the terminus of a pigment metabolic pathway, driven by cis-regulatory elements (CREs) with distinct mechanisms of Hox regulation. Here, we examined the expression and evolutionary histories of two important enzymes in this pathway, encoded by the pale and Ddc genes. We found that while both genes exhibit dynamic patterns of expression, a robust pattern of Ddc expression specifically evolved in the lineage of fruit flies with pronounced melanic abdomens. Derived Ddc expression requires the activity of a CRE previously shown to activate expression in response to epidermal wounding. We show that a binding site for the Grainy head transcription factor that promotes the ancestral wound healing function of this CRE is also required for abdominal activity. Together with previous findings in this system, our work shows how the GRN for a novel trait emerged by assembling unique yet similarly functioning CREs from heterogeneous starting points.
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Affiliation(s)
- Sumant Grover
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Melissa E Williams
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Rebecca Kaiser
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Jesse T Hughes
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Lauren Gresham
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Thomas M Williams
- Department of Biology, University of Dayton, 300 College Park, Dayton, OH 45469, USA; The Integrative Science and Engineering Center, University of Dayton, 300 College Park, Dayton, OH 45469, USA.
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141
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Rogers JM, Bulyk ML. Diversification of transcription factor-DNA interactions and the evolution of gene regulatory networks. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2018; 10:e1423. [PMID: 29694718 PMCID: PMC6202284 DOI: 10.1002/wsbm.1423] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/23/2018] [Accepted: 03/11/2018] [Indexed: 01/17/2023]
Abstract
Sequence-specific transcription factors (TFs) bind short DNA sequences in the genome to regulate the expression of target genes. In the last decade, numerous technical advances have enabled the determination of the DNA-binding specificities of many of these factors. Large-scale screens of many TFs enabled the creation of databases of TF DNA-binding specificities, typically represented as position weight matrices (PWMs). Although great progress has been made in determining and predicting binding specificities systematically, there are still many surprises to be found when studying a particular TF's interactions with DNA in detail. Paralogous TFs' binding specificities can differ in subtle ways, in a manner that is not immediately apparent from looking at their PWMs. These differences affect gene regulatory outputs and enable TFs to rewire transcriptional networks over evolutionary time. This review discusses recent observations made in the study of TF-DNA interactions that highlight the importance of continued in-depth analysis of TF-DNA interactions and their inherent complexity. This article is categorized under: Biological Mechanisms > Regulatory Biology.
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Affiliation(s)
- Julia M. Rogers
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, 02138, USA
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA, 02138, USA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
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142
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Peng Y, Zhang Y. Enhancer and super-enhancer: Positive regulators in gene transcription. Animal Model Exp Med 2018; 1:169-179. [PMID: 30891562 PMCID: PMC6388056 DOI: 10.1002/ame2.12032] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/19/2018] [Accepted: 07/31/2018] [Indexed: 12/23/2022] Open
Abstract
Enhancer is a positive regulator for spatiotemporal development in eukaryotes. As a cluster, super-enhancer is closely related to cell identity- and fate-determined processes. Both of them function tightly depending on their targeted transcription factors, cofactors, and genes through distal genomic interactions. They have been recognized as critical components and played positive roles in transcriptional regulatory network or factory. Recent advances of next-generation sequencing have dramatically expanded our ability and knowledge to interrogate the molecular mechanism of enhancer and super-enhancer for transcription. Here, we review the history, importance, advances and challenges on enhancer and super-enhancer field. This will benefit our understanding of their function mechanism for transcription underlying precise gene expression.
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Affiliation(s)
- Yanling Peng
- Animal Functional Genomics GroupAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Yubo Zhang
- Animal Functional Genomics GroupAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
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143
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Guan D, Xiong Y, Borck PC, Jang C, Doulias PT, Papazyan R, Fang B, Jiang C, Zhang Y, Briggs ER, Hu W, Steger D, Ischiropoulos H, Rabinowitz JD, Lazar MA. Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes. Cell 2018; 174:831-842.e12. [PMID: 30057115 PMCID: PMC6086765 DOI: 10.1016/j.cell.2018.06.031] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/23/2018] [Accepted: 06/13/2018] [Indexed: 12/11/2022]
Abstract
Overnutrition disrupts circadian metabolic rhythms by mechanisms that are not well understood. Here, we show that diet-induced obesity (DIO) causes massive remodeling of circadian enhancer activity in mouse liver, triggering synchronous high-amplitude circadian rhythms of both fatty acid (FA) synthesis and oxidation. SREBP expression was rhythmically induced by DIO, leading to circadian FA synthesis and, surprisingly, FA oxidation (FAO). DIO similarly caused a high-amplitude circadian rhythm of PPARα, which was also required for FAO. Provision of a pharmacological activator of PPARα abrogated the requirement of SREBP for FAO (but not FA synthesis), suggesting that SREBP indirectly controls FAO via production of endogenous PPARα ligands. The high-amplitude rhythm of PPARα imparted time-of-day-dependent responsiveness to lipid-lowering drugs. Thus, acquisition of rhythmicity for non-core clock components PPARα and SREBP1 remodels metabolic gene transcription in response to overnutrition and enables a chronopharmacological approach to metabolic disorders.
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Affiliation(s)
- Dongyin Guan
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ying Xiong
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Patricia C Borck
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cholsoon Jang
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Paschalis-Thomas Doulias
- Children's Hospital of Philadelphia Research Institute and Departments of Pediatrics and Systems Pharmacology & Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Romeo Papazyan
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bin Fang
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chunjie Jiang
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuxiang Zhang
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erika R Briggs
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenxiang Hu
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David Steger
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Harry Ischiropoulos
- Children's Hospital of Philadelphia Research Institute and Departments of Pediatrics and Systems Pharmacology & Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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144
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Torbey P, Thierion E, Collombet S, de Cian A, Desmarquet-Trin-Dinh C, Dura M, Concordet JP, Charnay P, Gilardi-Hebenstreit P. Cooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation. PLoS Genet 2018; 14:e1007581. [PMID: 30080860 PMCID: PMC6095606 DOI: 10.1371/journal.pgen.1007581] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/16/2018] [Accepted: 07/20/2018] [Indexed: 12/13/2022] Open
Abstract
Cis-regulation plays an essential role in the control of gene expression, and is particularly complex and poorly understood for developmental genes, which are subject to multiple levels of modulation. In this study, we performed a global analysis of the cis-acting elements involved in the control of the zebrafish developmental gene krox20. krox20 encodes a transcription factor required for hindbrain segmentation and patterning, a morphogenetic process highly conserved during vertebrate evolution. Chromatin accessibility analysis reveals a cis-regulatory landscape that includes 6 elements participating in the control of initiation and autoregulatory aspects of krox20 hindbrain expression. Combining transgenic reporter analyses and CRISPR/Cas9-mediated mutagenesis, we assign precise functions to each of these 6 elements and provide a comprehensive view of krox20 cis-regulation. Three important features emerged. First, cooperation between multiple cis-elements plays a major role in the regulation. Cooperation can surprisingly combine synergy and redundancy, and is not restricted to transcriptional enhancer activity (for example, 4 distinct elements cooperate through different modes to maintain autoregulation). Second, several elements are unexpectedly versatile, which allows them to be involved in different aspects of control of gene expression. Third, comparative analysis of the elements and their activities in several vertebrate species reveals that this versatility is underlain by major plasticity across evolution, despite the high conservation of the gene expression pattern. These characteristics are likely to be of broad significance for developmental genes.
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Affiliation(s)
- Patrick Torbey
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
| | - Elodie Thierion
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
| | - Samuel Collombet
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
| | - Anne de Cian
- Sorbonne Universités, Muséum National d’Histoire Naturelle, CNRS UMR 7196, INSERM U1154, Paris, France
| | - Carole Desmarquet-Trin-Dinh
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
| | - Mathilde Dura
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
| | - Jean-Paul Concordet
- Sorbonne Universités, Muséum National d’Histoire Naturelle, CNRS UMR 7196, INSERM U1154, Paris, France
| | - Patrick Charnay
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
- * E-mail: (PC); (PGH)
| | - Pascale Gilardi-Hebenstreit
- Institut de Biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, Inserm, PSL Université, Paris, France
- * E-mail: (PC); (PGH)
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145
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Bao R, Dia SE, Issa HA, Alhusein D, Friedrich M. Comparative Evidence of an Exceptional Impact of Gene Duplication on the Developmental Evolution of Drosophila and the Higher Diptera. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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146
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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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147
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Eksi SE, Barmina O, McCallough CL, Kopp A, Orenic TV. A Distalless-responsive enhancer of the Hox gene Sex combs reduced is required for segment- and sex-specific sensory organ development in Drosophila. PLoS Genet 2018; 14:e1007320. [PMID: 29634724 PMCID: PMC5909922 DOI: 10.1371/journal.pgen.1007320] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 04/20/2018] [Accepted: 03/19/2018] [Indexed: 11/18/2022] Open
Abstract
Hox genes are involved in the patterning of animal body parts at multiple levels of regulatory hierarchies. Early expression of Hox genes in different domains along the embryonic anterior-posterior (A/P) axis in insects, vertebrates, and other animals establishes segmental or regional identity. However, Hox gene function is also required later in development for the patterning and morphogenesis of limbs and other organs. In Drosophila, spatiotemporal modulation of Sex combs reduced (Scr) expression within the first thoracic (T1) leg underlies the generation of segment- and sex-specific sense organ patterns. High Scr expression in defined domains of the T1 leg is required for the development of T1-specific transverse bristle rows in both sexes and sex combs in males, implying that the patterning of segment-specific sense organs involves incorporation of Scr into the leg development and sex determination gene networks. We sought to gain insight into this process by identifying the cis-and trans-regulatory factors that direct Scr expression during leg development. We have identified two cis-regulatory elements that control spatially modulated Scr expression within T1 legs. One of these enhancers directs sexually dimorphic expression and is required for the formation of T1-specific bristle patterns. We show that the Distalless and Engrailed homeodomain transcription factors act through sequences in this enhancer to establish elevated Scr expression in spatially defined domains. This enhancer functions to integrate Scr into the intrasegmental gene regulatory network, such that Scr serves as a link between leg patterning, sex determination, and sensory organ development.
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Affiliation(s)
- Sebnem Ece Eksi
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Olga Barmina
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, United States of America
| | - Christopher L. McCallough
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, United States of America
- * E-mail: (AK); (TVO)
| | - Teresa Vales Orenic
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States of America
- * E-mail: (AK); (TVO)
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148
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Sarro R, Kocher AA, Emera D, Uebbing S, Dutrow EV, Weatherbee SD, Nottoli T, Noonan JP. Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development. Development 2018; 145:dev158550. [PMID: 29549111 PMCID: PMC5963865 DOI: 10.1242/dev.158550] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 03/09/2018] [Indexed: 12/28/2022]
Abstract
Developmental gene expression patterns are orchestrated by thousands of distant-acting transcriptional enhancers. However, identifying enhancers essential for the expression of their target genes has proven challenging. Maps of long-range regulatory interactions may provide the means to identify enhancers crucial for developmental gene expression. To investigate this hypothesis, we used circular chromosome conformation capture coupled with interaction maps in the mouse limb to characterize the regulatory topology of Pitx1, which is essential for hindlimb development. We identified a robust hindlimb-specific interaction between Pitx1 and a putative hindlimb-specific enhancer. To interrogate the role of this interaction in Pitx1 regulation, we used genome editing to delete this enhancer in mouse. Although deletion of the enhancer completely disrupts the interaction, Pitx1 expression in the hindlimb is only mildly affected, without any detectable compensatory interactions between the Pitx1 promoter and potentially redundant enhancers. Pitx1 enhancer null mice did not exhibit any of the characteristic morphological defects of the Pitx1-/- mutant. Our results suggest that robust, tissue-specific physical interactions at essential developmental genes have limited predictive value for identifying enhancer mutations with strong loss-of-function phenotypes.
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Affiliation(s)
- Richard Sarro
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Acadia A Kocher
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Deena Emera
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Emily V Dutrow
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Scott D Weatherbee
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Timothy Nottoli
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Genome Editing Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
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149
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Lai YT, Deem KD, Borràs-Castells F, Sambrani N, Rudolf H, Suryamohan K, El-Sherif E, Halfon MS, McKay DJ, Tomoyasu Y. Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum. Development 2018. [PMID: 29540499 DOI: 10.1242/dev.160663] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evolution of cis-regulatory elements (such as enhancers) plays an important role in the production of diverse morphology. However, a mechanistic understanding is often limited by the absence of methods for studying enhancers in species other than established model systems. Here, we sought to establish methods to identify and test enhancer activity in the red flour beetle, Tribolium castaneum To identify possible enhancer regions, we first obtained genome-wide chromatin profiles from various tissues and stages of Tribolium using FAIRE (formaldehyde-assisted isolation of regulatory elements)-sequencing. Comparison of these profiles revealed a distinct set of open chromatin regions in each tissue and at each stage. In addition, comparison of the FAIRE data with sets of computationally predicted (i.e. supervised cis-regulatory module-predicted) enhancers revealed a very high overlap between the two datasets. Second, using nubbin in the wing and hunchback in the embryo as case studies, we established the first universal reporter assay system that works in various contexts in Tribolium, and in a cross-species context. Together, these advances will facilitate investigation of cis-evolution and morphological diversity in Tribolium and other insects.
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Affiliation(s)
- Yi-Ting Lai
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Kevin D Deem
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | | | - Nagraj Sambrani
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Heike Rudolf
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91058, Germany
| | - Kushal Suryamohan
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14214, USA
| | - Ezzat El-Sherif
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91058, Germany
| | - Marc S Halfon
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14214, USA
| | - Daniel J McKay
- Department of Biology, Department of Genetics, Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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150
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Evolutionary emergence of the rac3b/ rfng/ sgca regulatory cluster refined mechanisms for hindbrain boundaries formation. Proc Natl Acad Sci U S A 2018; 115:E3731-E3740. [PMID: 29610331 DOI: 10.1073/pnas.1719885115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Developmental programs often rely on parallel morphogenetic mechanisms that guarantee precise tissue architecture. While redundancy constitutes an obvious selective advantage, little is known on how novel morphogenetic mechanisms emerge during evolution. In zebrafish, rhombomeric boundaries behave as an elastic barrier, preventing cell intermingling between adjacent compartments. Here, we identify the fundamental role of the small-GTPase Rac3b in actomyosin cable assembly at hindbrain boundaries. We show that the novel rac3b/rfng/sgca regulatory cluster, which is specifically expressed at the boundaries, emerged in the Ostariophysi superorder by chromosomal rearrangement that generated new cis-regulatory interactions. By combining 4C-seq, ATAC-seq, transgenesis, and CRISPR-induced deletions, we characterized this regulatory domain, identifying hindbrain boundary-specific cis-regulatory elements. Our results suggest that the capacity of boundaries to act as an elastic mesh for segregating rhombomeric cells evolved by cooption of critical genes to a novel regulatory block, refining the mechanisms for hindbrain segmentation.
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