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Mazina MY, Vorobyeva NE. Mechanisms of transcriptional regulation of ecdysone response. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The mechanisms of ecdysone-dependent expression have been studied for many decades. Initially, the activation of individual genes under the influence of ecdysone was studied on the model of polythene chromosomes from salivary glands of Drosophila melanogaster. These works helped to investigate the many aspects of the Drosophila development. They also revealed plenty of valuable information regarding the fundamental mechanisms controlling the genes’ work. Many years ago, a model describing the process of gene activation by ecdysone, named after the author – Ashburner model – was proposed. This model is still considered an excellent description of the ecdysone cascade, which is implemented in the salivary glands during the formation of the Drosophila pupa. However, these days there is an opinion that the response of cells to the hormone ecdysone can develop with significant differences, depending on the type of cells. The same genes can be activated or repressed under the influence of ecdysone in different tissues. Likely, certain DNA-binding transcription factors that are involved in the ecdysonedependent response together with the EcR/Usp heterodimer are responsible for cell-type specificity. A number of transcriptional regulators involved in the ecdysone response have been described. Among them are several complexes responsible for chromatin remodeling and modification. It has been shown by various methods that ecdysone-dependent activation/repression of gene transcription develops with significant structural changes of chromatin on regulatory elements. The description of the molecular mechanism of this process, in particular, the role of individual proteins in it, as well as structural interactions between various regulatory elements is a matter of the future. This review is aimed to discuss the available information regarding the main regulators that interact with the ecdysone receptor. We provide a brief description of the regulator’s participation in the ecdysone response and links to the corresponding study. We also discuss general aspects of the mechanism of ecdysone-dependent regulation and highlight the most promising points for further research.
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Affiliation(s)
- M. Yu. Mazina
- Institute of Gene Biology, RAS, Group of transcriptional complexes dynamics
| | - N. E. Vorobyeva
- Institute of Gene Biology, RAS, Group of transcriptional complexes dynamics
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Schöne S, Bothe M, Einfeldt E, Borschiwer M, Benner P, Vingron M, Thomas-Chollier M, Meijsing SH. Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise. PLoS Genet 2018; 14:e1007793. [PMID: 30427832 PMCID: PMC6261644 DOI: 10.1371/journal.pgen.1007793] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 11/28/2018] [Accepted: 10/26/2018] [Indexed: 12/29/2022] Open
Abstract
The binding of transcription factors to short recognition sequences plays a pivotal role in controlling the expression of genes. The sequence and shape characteristics of binding sites influence DNA binding specificity and have also been implicated in modulating the activity of transcription factors downstream of binding. To quantitatively assess the transcriptional activity of tens of thousands of designed synthetic sites in parallel, we developed a synthetic version of STARR-seq (synSTARR-seq). We used the approach to systematically analyze how variations in the recognition sequence of the glucocorticoid receptor (GR) affect transcriptional regulation. Our approach resulted in the identification of a novel highly active functional GR binding sequence and revealed that sequence variation both within and flanking GR’s core binding site can modulate GR activity without apparent changes in DNA binding affinity. Notably, we found that the sequence composition of variants with similar activity profiles was highly diverse. In contrast, groups of variants with similar activity profiles showed specific DNA shape characteristics indicating that DNA shape may be a better predictor of activity than DNA sequence. Finally, using single cell experiments with individual enhancer variants, we obtained clues indicating that the architecture of the response element can independently tune expression mean and cell-to cell variability in gene expression (noise). Together, our studies establish synSTARR as a powerful method to systematically study how DNA sequence and shape modulate transcriptional output and noise. The expression level of genes is controlled by transcription factors, which are proteins that bind to genomic response elements that contain their recognition DNA sequence. Importantly, genes are not simply turned on but need to be expressed at the right level. This is, at least in part, assured by the sequence composition of genomic response elements. Here, we studied how the recognition DNA sequence influences gene regulation by a transcription factor called the glucocorticoid receptor. Specifically, we developed a method to test the activity of variants in a highly parallelized setting where everything is kept identical except for the sequence of the binding site. The systematic analysis of tens of thousands of sequence variants facilitated the identification of a previously unknown sequence variant with high activity. Moreover, we report how sequence variation of the response element influences cell-to-cell variability in expression levels. Finally, we observe similar activity profiles for distinct sequence variants that share similar three-dimensional DNA shape characteristics arguing that the three-dimensional perception of DNA by the glucocorticoid receptor, modulates its activity towards individual target genes.
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Affiliation(s)
- Stefanie Schöne
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Melissa Bothe
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Edda Einfeldt
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Philipp Benner
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Morgane Thomas-Chollier
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
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53
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Cheng D, Cheng T, Yang X, Zhang Q, Fu J, Feng T, Gong J, Xia Q. The genome-wide transcriptional regulatory landscape of ecdysone in the silkworm. Epigenetics Chromatin 2018; 11:48. [PMID: 30149809 PMCID: PMC6109983 DOI: 10.1186/s13072-018-0216-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/10/2018] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The silkworm, Bombyx mori, a typical representative of metamorphic insects, is of great agricultural and economic importance. The steroid hormone ecdysone (20-hydroxyecdysone, 20E) is the central regulator of insect developmental transitions, and its nuclear receptors are crucial for numerous biological processes, including reproduction, metabolism, and immunity. However, genome-wide DNA regulatory elements and the ecdysone receptor (EcR) that control these programs of gene expression are not well defined. RESULTS In this study, we investigated the alterations in three types of histone modification in silkworm embryonic cells treated with 20E by chromatin immunoprecipitation sequencing (ChIP-seq). We identified enhancers using histone modifications and derived genome-wide ecdysone-dependent enhancer activity maps in the silkworm. We found enhancers enriched for monomethylation of histone H3 Lys4 (H3K4me1) that showed dynamic changes in acetylation of histone H3 Lys27 (H3K27ac) after 20E treatment and functioned to regulate the transcription of specific genes. EcR regulated transcription by binding not only to proximal promoters but also to the distal enhancers of target genes. Moreover, only 52.65% EcR peaks contained ecdysone response element (EcRE) motif, suggesting that EcR regulates the expression of target genes not only by binding directly to EcRE, but also by binding with other transcription factor. CONCLUSIONS Our findings provide novel insights into the complex regulatory landscape of hormone-responsive cell activity and a basis for understanding the complex transcriptional regulatory processes of ecdysone.
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Affiliation(s)
- Dong Cheng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Tingcai Cheng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China. .,Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, 2, Tiansheng Road, Beibei, Chongqing, 400715, China.
| | - Xi Yang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Quan Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Jianfeng Fu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Tieshan Feng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Jiao Gong
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China.,Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, 2, Tiansheng Road, Beibei, Chongqing, 400715, China
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54
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Zhou L, Lim MYT, Kaur P, Saj A, Bortolamiol-Becet D, Gopal V, Tolwinski N, Tucker-Kellogg G, Okamura K. Importance of miRNA stability and alternative primary miRNA isoforms in gene regulation during Drosophila development. eLife 2018; 7:e38389. [PMID: 30024380 PMCID: PMC6066331 DOI: 10.7554/elife.38389] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/04/2018] [Indexed: 12/19/2022] Open
Abstract
Mature microRNAs (miRNAs) are processed from primary transcripts (pri-miRNAs), and their expression is controlled at transcriptional and post-transcriptional levels. However, how regulation at multiple levels achieves precise control remains elusive. Using published and new datasets, we profile a time course of mature and pri-miRNAs in Drosophila embryos and reveal the dynamics of miRNA production and degradation as well as dynamic changes in pri-miRNA isoform selection. We found that 5' nucleotides influence stability of mature miRNAs. Furthermore, distinct half-lives of miRNAs from the mir-309 cluster shape their temporal expression patterns, and the importance of rapid degradation of the miRNAs in gene regulation is detected as distinct evolutionary signatures at the target sites in the transcriptome. Finally, we show that rapid degradation of miR-3/-309 may be important for regulation of the planar cell polarity pathway component Vang. Altogether, the results suggest that complex mechanisms regulate miRNA expression to support normal development.
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Affiliation(s)
- Li Zhou
- Temasek Life Sciences LaboratorySingaporeSingapore
- Department of Biological Sciences, Faculty of ScienceNational University of SingaporeSingaporeSingapore
| | - Mandy Yu Theng Lim
- Temasek Life Sciences LaboratorySingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Prameet Kaur
- Division of ScienceYale-NUS CollegeSingaporeSingapore
| | - Abil Saj
- Cancer Therapeutics and Stratified OncologyGenome Institute of SingaporeSingaporeSingapore
| | | | - Vikneswaran Gopal
- Department of Statistics and Applied Probability, Faculty of ScienceNational University of SingaporeSingaporeSingapore
| | - Nicholas Tolwinski
- Department of Biological Sciences, Faculty of ScienceNational University of SingaporeSingaporeSingapore
- Division of ScienceYale-NUS CollegeSingaporeSingapore
| | - Greg Tucker-Kellogg
- Department of Biological Sciences, Faculty of ScienceNational University of SingaporeSingaporeSingapore
| | - Katsutomo Okamura
- Temasek Life Sciences LaboratorySingaporeSingapore
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
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55
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Jefferson WN, Kinyamu HK, Wang T, Miranda AX, Padilla-Banks E, Suen AA, Williams CJ. Widespread enhancer activation via ERα mediates estrogen response in vivo during uterine development. Nucleic Acids Res 2018; 46:5487-5503. [PMID: 29648668 PMCID: PMC6009594 DOI: 10.1093/nar/gky260] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/16/2018] [Accepted: 03/27/2018] [Indexed: 01/07/2023] Open
Abstract
Little is known regarding how steroid hormone exposures impact the epigenetic landscape in a living organism. Here, we took a global approach to understanding how exposure to the estrogenic chemical, diethylstilbestrol (DES), affects the neonatal mouse uterine epigenome. Integration of RNA- and ChIP-sequencing data demonstrated that ∼80% of DES-altered genes had higher H3K4me1/H3K27ac signal in close proximity. Active enhancers, of which ∼3% were super-enhancers, had a high density of estrogen receptor alpha (ERα) binding sites and were correlated with alterations in nearby gene expression. Conditional uterine deletion of ERα, but not the pioneer transcription factors FOXA2 or FOXO1, prevented the majority of DES-mediated changes in gene expression and H3K27ac signal at target enhancers. An ERα dependent super-enhancer was located at the Padi gene locus and a topological connection to the Padi1 TSS was documented using 3C-PCR. Chromosome looping at this site was independent of ERα and DES exposure, indicating that the interaction is established prior to ligand signaling. However, enrichment of H3K27ac and transcriptional activation at this locus was both DES and ERα-dependent. These data suggest that DES alters uterine development and consequently adult reproductive function by modifying the enhancer landscape at ERα binding sites near estrogen-regulated genes.
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Affiliation(s)
- Wendy N Jefferson
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - H Karimi Kinyamu
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Tianyuan Wang
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Adam X Miranda
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Elizabeth Padilla-Banks
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Alisa A Suen
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Carmen J Williams
- Reproductive & Developmental Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
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56
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Bardales JA, Wieser E, Kawaji H, Murakawa Y, Darzacq X. Selective Activation of Alternative MYC Core Promoters by Wnt-Responsive Enhancers. Genes (Basel) 2018; 9:genes9060270. [PMID: 29882899 PMCID: PMC6027352 DOI: 10.3390/genes9060270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 11/16/2022] Open
Abstract
In Metazoans, transcription of most genes is driven by the use of multiple alternative promoters. Although the precise regulation of alternative promoters is important for proper gene expression, the mechanisms that mediates their differential utilization remains unclear. Here, we investigate how the two alternative promoters (P1, P2) that drive MYC expression are regulated. We find that P1 and P2 can be differentially regulated across cell-types and that their selective usage is largely mediated by distal regulatory sequences. Moreover, we show that in colon carcinoma cells, Wnt-responsive enhancers preferentially upregulate transcription from the P1 promoter using reporter assays and in the context of the endogenous Wnt induction. In addition, multiple enhancer deletions using CRISPR/Cas9 corroborate the regulatory specificity of P1. Finally, we show that preferential activation between Wnt-responsive enhancers and the P1 promoter is influenced by the distinct core promoter elements that are present in the MYC promoters. Taken together, our results provide new insight into how enhancers can specifically target alternative promoters and suggest that formation of these selective interactions could allow more precise combinatorial regulation of transcription initiation.
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Affiliation(s)
- Jorge A Bardales
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA.
| | - Evin Wieser
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama 230-0045, Japan.
- Preventive Medicine and Applied Genomics Unit, RIKEN Advanced Center for Computing and Communication, Yokohama 230-0045, Japan.
| | - Yasuhiro Murakawa
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Yokohama 230-0045, Japan.
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
- Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA 94720, USA.
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57
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Liu Y, Yu S, Dhiman VK, Brunetti T, Eckart H, White KP. Functional assessment of human enhancer activities using whole-genome STARR-sequencing. Genome Biol 2017; 18:219. [PMID: 29151363 DOI: 10.1186/s13059-017-1345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 10/11/2017] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Genome-wide quantification of enhancer activity in the human genome has proven to be a challenging problem. Recent efforts have led to the development of powerful tools for enhancer quantification. However, because of genome size and complexity, these tools have yet to be applied to the whole human genome. RESULTS In the current study, we use a human prostate cancer cell line, LNCaP as a model to perform whole human genome STARR-seq (WHG-STARR-seq) to reliably obtain an assessment of enhancer activity. This approach builds upon previously developed STARR-seq in the fly genome and CapSTARR-seq techniques in targeted human genomic regions. With an improved library preparation strategy, our approach greatly increases the library complexity per unit of starting material, which makes it feasible and cost-effective to explore the landscape of regulatory activity in the much larger human genome. In addition to our ability to identify active, accessible enhancers located in open chromatin regions, we can also detect sequences with the potential for enhancer activity that are located in inaccessible, closed chromatin regions. When treated with the histone deacetylase inhibitor, Trichostatin A, genes nearby this latter class of enhancers are up-regulated, demonstrating the potential for endogenous functionality of these regulatory elements. CONCLUSION WHG-STARR-seq provides an improved approach to current pipelines for analysis of high complexity genomes to gain a better understanding of the intricacies of transcriptional regulation.
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Affiliation(s)
- Yuwen Liu
- Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, IL, 60637, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Shan Yu
- Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, IL, 60637, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Vineet K Dhiman
- Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, IL, 60637, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Tonya Brunetti
- Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, IL, 60637, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Heather Eckart
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, IL, 60637, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
- Tempus Labs, 600 West Chicago Ave., Chicago, IL, 60654, USA.
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58
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Liu Y, Yu S, Dhiman VK, Brunetti T, Eckart H, White KP. Functional assessment of human enhancer activities using whole-genome STARR-sequencing. Genome Biol 2017; 18:219. [PMID: 29151363 PMCID: PMC5694901 DOI: 10.1186/s13059-017-1345-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 10/11/2017] [Indexed: 11/25/2022] Open
Abstract
Background Genome-wide quantification of enhancer activity in the human genome has proven to be a challenging problem. Recent efforts have led to the development of powerful tools for enhancer quantification. However, because of genome size and complexity, these tools have yet to be applied to the whole human genome. Results In the current study, we use a human prostate cancer cell line, LNCaP as a model to perform whole human genome STARR-seq (WHG-STARR-seq) to reliably obtain an assessment of enhancer activity. This approach builds upon previously developed STARR-seq in the fly genome and CapSTARR-seq techniques in targeted human genomic regions. With an improved library preparation strategy, our approach greatly increases the library complexity per unit of starting material, which makes it feasible and cost-effective to explore the landscape of regulatory activity in the much larger human genome. In addition to our ability to identify active, accessible enhancers located in open chromatin regions, we can also detect sequences with the potential for enhancer activity that are located in inaccessible, closed chromatin regions. When treated with the histone deacetylase inhibitor, Trichostatin A, genes nearby this latter class of enhancers are up-regulated, demonstrating the potential for endogenous functionality of these regulatory elements. Conclusion WHG-STARR-seq provides an improved approach to current pipelines for analysis of high complexity genomes to gain a better understanding of the intricacies of transcriptional regulation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1345-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuwen Liu
- Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, IL, 60637, USA.,Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Shan Yu
- Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, IL, 60637, USA.,Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Vineet K Dhiman
- Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, IL, 60637, USA.,Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Tonya Brunetti
- Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, IL, 60637, USA.,Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Heather Eckart
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, IL, 60637, USA. .,Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA. .,Tempus Labs, 600 West Chicago Ave., Chicago, IL, 60654, USA.
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59
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Saito T, Wang S, Ohkawa K, Ohara H, Ikeura H, Ogawa Y, Kondo S. Lipid droplet-associated gene expression and chromatin remodelling in LIPASE 5'-upstream region from beginning- to mid-endodormant bud in 'Fuji' apple. PLANT MOLECULAR BIOLOGY 2017; 95:441-449. [PMID: 29019094 DOI: 10.1007/s11103-017-0662-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 09/14/2017] [Indexed: 05/26/2023]
Abstract
We found that lipid accumulation in the meristem region and the expression of MdLIP2A, which appears to be regulated by chromatin remodeling, coincided with endodormancy induction in the 'Fuji' apple. In deciduous trees, including apples (Malus × domestica Borkh.), lipid accumulation in the meristem region towards endodormancy induction has been thought to be an important process for the acquisition of cold tolerance. In this study, we conducted histological staining of crude lipids in the meristem region of 'Fuji' apples and found that lipid accumulation coincided with endodormancy induction. Since a major component of lipid bodies (triacylglycerol) is esterified fatty acids, we analysed fatty acid-derived volatile compounds and genes encoding fatty acid-modifying enzymes (MdLOX1A and MdHPL2A); the reduction of lipid breakdown also coincided with endodormancy induction. We then characterised the expression patterns of lipid body-regulatory genes MdOLE1 and MdLIP2A during endodormancy induction and found that the expression of MdLIP2A correlated well with lipid accumulation towards endodormancy induction. Based on these results, we conducted chromatin remodelling studies and localized the cis-element in the 5'-upstream region of MdLIP2A to clarify its regulatory mechanism. Finally, we revealed that chromatin was concentrated - 764 to - 862 bp of the 5'-upstream region of MdLIP2A, which harbours the GARE [gibberellin responsive MYB transcription factor binding site] and CArG [MADS-box transcription factor binding site] motifs-meristem development-related protein-binding sites.
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Affiliation(s)
- Takanori Saito
- Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Japan
| | - Shanshan Wang
- Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Japan
| | - Katsuya Ohkawa
- Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Japan
| | - Hitoshi Ohara
- Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Japan
- Center for Environment, Health and Field Sciences, Chiba University, Kashiwa-no-ha, 277-0882, Japan
| | - Hiromi Ikeura
- Organization for the Strategic Coordination of Research and Intellectual Properties, Meiji University, Kawasaki, 214-8571, Japan
| | - Yukiharu Ogawa
- Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Japan
| | - Satoru Kondo
- Graduate School of Horticulture, Chiba University, Matsudo, 271-8510, Japan.
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60
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Genome-wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori. Sci Rep 2017; 7:12919. [PMID: 29018289 PMCID: PMC5635003 DOI: 10.1038/s41598-017-13186-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/19/2017] [Indexed: 11/15/2022] Open
Abstract
Nucleosome-depleted open chromatin regions (OCRs) often harbor transcription factor (TF) binding sites that are associated with active DNA regulatory elements. To investigate the regulation of silk-protein genes, DNA molecules isolated from the silk glands of third-day fifth-instar silkworm larvae and embryo-derived (BmE) cells were subjected to formal dehyde-assisted isolation of regulatory elements (FAIRE) and high-throughput sequencing. In total, 68,000 OCRs were identified, and a number of TF-binding motifs were predicted. In particular, OCRs located near silk-protein genes contained potential binding sites for functional TFs. Moreover, many TFs were found to bind to clusters of OCRs upstream of silk-protein genes, and to regulate the expression of these genes. The expression of silk protein genes may be related not only to regulating TFs (such as fkh, Bmdimm, and Bmsage), but also to developmental and hormone-induced TFs (such as zen, eve, Br, and eip74ef). Elucidation of genome-wide OCRs and their regulatory motifs in silk protein genes will provide valuable data and clues for characterizing the mechanisms of transcriptional control of silk protein genes.
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61
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Wei Y, Gokhale RH, Sonnenschein A, Montgomery KM, Ingersoll A, Arnosti DN. Complex cis-regulatory landscape of the insulin receptor gene underlies the broad expression of a central signaling regulator. Development 2017; 143:3591-3603. [PMID: 27702787 DOI: 10.1242/dev.138073] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/10/2016] [Indexed: 12/16/2022]
Abstract
Insulin signaling plays key roles in development, growth and metabolism through dynamic control of glucose uptake, global protein translation and transcriptional regulation. Altered levels of insulin signaling are known to play key roles in development and disease, yet the molecular basis of such differential signaling remains obscure. Expression of the insulin receptor (InR) gene itself appears to play an important role, but the nature of the molecular wiring controlling InR transcription has not been elucidated. We characterized the regulatory elements driving Drosophila InR expression and found that the generally broad expression of this gene is belied by complex individual switch elements, the dynamic regulation of which reflects direct and indirect contributions of FOXO, EcR, Rbf and additional transcription factors through redundant elements dispersed throughout ∼40 kb of non-coding regions. The control of InR transcription in response to nutritional and tissue-specific inputs represents an integration of multiple cis-regulatory elements, the structure and function of which may have been sculpted by evolutionary selection to provide a highly tailored set of signaling responses on developmental and tissue-specific levels.
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Affiliation(s)
- Yiliang Wei
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Rewatee H Gokhale
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Anne Sonnenschein
- Genetics Program, Michigan State University, East Lansing, MI 48824, USA
| | - Kelly Mone't Montgomery
- Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Andrew Ingersoll
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA Genetics Program, Michigan State University, East Lansing, MI 48824, USA
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62
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Cohen DM, Steger DJ. Nuclear Receptor Function through Genomics: Lessons from the Glucocorticoid Receptor. Trends Endocrinol Metab 2017; 28:531-540. [PMID: 28495406 PMCID: PMC5505657 DOI: 10.1016/j.tem.2017.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/14/2017] [Accepted: 04/18/2017] [Indexed: 12/20/2022]
Abstract
Unlocking the therapeutic potential of the glucocorticoid receptor (GR) has motivated a search for small molecules that selectively modulate its ability to activate or repress gene transcription. Recently, breakthrough studies in the field of genomics have reinvigorated debate over longstanding transcriptional models explaining how GR controls tissue-specific gene expression. Here, we highlight these genomic studies with the dual goals of advancing understanding of nuclear receptor-mediated transcription and stimulating thought on the development of anti-inflammatory and immunosuppressive ligands for GR that have reduced harmful effects on metabolism.
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Affiliation(s)
- Daniel M Cohen
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David J Steger
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, and The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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63
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Santiago-Algarra D, Dao LTM, Pradel L, España A, Spicuglia S. Recent advances in high-throughput approaches to dissect enhancer function. F1000Res 2017; 6:939. [PMID: 28690838 PMCID: PMC5482341 DOI: 10.12688/f1000research.11581.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/13/2017] [Indexed: 12/17/2022] Open
Abstract
The regulation of gene transcription in higher eukaryotes is accomplished through the involvement of transcription start site (TSS)-proximal (promoters) and -distal (enhancers) regulatory elements. It is now well acknowledged that enhancer elements play an essential role during development and cell differentiation, while genetic alterations in these elements are a major cause of human disease. Many strategies have been developed to identify and characterize enhancers. Here, we discuss recent advances in high-throughput approaches to assess enhancer activity, from the well-established massively parallel reporter assays to the recent clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based technologies. We highlight how these approaches contribute toward a better understanding of enhancer function, eventually leading to the discovery of new types of regulatory sequences, and how the alteration of enhancers can affect transcriptional regulation.
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Affiliation(s)
| | - Lan T M Dao
- Aix-Marseille University, TAGC, Marseille, France
| | - Lydie Pradel
- Aix-Marseille University, TAGC, Marseille, France
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64
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Uyehara CM, Nystrom SL, Niederhuber MJ, Leatham-Jensen M, Ma Y, Buttitta LA, McKay DJ. Hormone-dependent control of developmental timing through regulation of chromatin accessibility. Genes Dev 2017; 31:862-875. [PMID: 28536147 PMCID: PMC5458754 DOI: 10.1101/gad.298182.117] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/26/2017] [Indexed: 11/24/2022]
Abstract
Uyehara et al. show that hormone-induced transcription factors control temporal gene expression by regulating accessibility of DNA regulatory elements. Using the Drosophila wing, they demonstrate that temporal changes in gene expression are accompanied by genome-wide changes in chromatin accessibility at temporal-specific enhancers. Specification of tissue identity during development requires precise coordination of gene expression in both space and time. Spatially, master regulatory transcription factors are required to control tissue-specific gene expression programs. However, the mechanisms controlling how tissue-specific gene expression changes over time are less well understood. Here, we show that hormone-induced transcription factors control temporal gene expression by regulating the accessibility of DNA regulatory elements. Using the Drosophila wing, we demonstrate that temporal changes in gene expression are accompanied by genome-wide changes in chromatin accessibility at temporal-specific enhancers. We also uncover a temporal cascade of transcription factors following a pulse of the steroid hormone ecdysone such that different times in wing development can be defined by distinct combinations of hormone-induced transcription factors. Finally, we show that the ecdysone-induced transcription factor E93 controls temporal identity by directly regulating chromatin accessibility across the genome. Notably, we found that E93 controls enhancer activity through three different modalities, including promoting accessibility of late-acting enhancers and decreasing accessibility of early-acting enhancers. Together, this work supports a model in which an extrinsic signal triggers an intrinsic transcription factor cascade that drives development forward in time through regulation of chromatin accessibility.
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Affiliation(s)
- Christopher M Uyehara
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Spencer L Nystrom
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Matthew J Niederhuber
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Mary Leatham-Jensen
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Yiqin Ma
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Laura A Buttitta
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Daniel J McKay
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
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65
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Endocrine network essential for reproductive success in Drosophila melanogaster. Proc Natl Acad Sci U S A 2017; 114:E3849-E3858. [PMID: 28439025 DOI: 10.1073/pnas.1620760114] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Ecdysis-triggering hormone (ETH) was originally discovered and characterized as a molt termination signal in insects through its regulation of the ecdysis sequence. Here we report that ETH persists in adult Drosophila melanogaster, where it functions as an obligatory allatotropin to promote juvenile hormone (JH) production and reproduction. ETH signaling deficits lead to sharply reduced JH levels and consequent reductions of ovary size, egg production, and yolk deposition in mature oocytes. Expression of ETH and ETH receptor genes is in turn dependent on ecdysone (20E). Furthermore, 20E receptor knockdown specifically in Inka cells reduces fecundity. Our findings indicate that the canonical developmental roles of 20E, ETH, and JH during juvenile stages are repurposed to function as an endocrine network essential for reproductive success.
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66
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Kreher J, Kovač K, Bouazoune K, Mačinković I, Ernst AL, Engelen E, Pahl R, Finkernagel F, Murawska M, Ullah I, Brehm A. EcR recruits dMi-2 and increases efficiency of dMi-2-mediated remodelling to constrain transcription of hormone-regulated genes. Nat Commun 2017; 8:14806. [PMID: 28378812 PMCID: PMC5382322 DOI: 10.1038/ncomms14806] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 01/30/2017] [Indexed: 12/27/2022] Open
Abstract
Gene regulation by steroid hormones plays important roles in health and disease. In Drosophila, the hormone ecdysone governs transitions between key developmental stages. Ecdysone-regulated genes are bound by a heterodimer of ecdysone receptor (EcR) and Ultraspiracle. According to the bimodal switch model, steroid hormone receptors recruit corepressors in the absence of hormone and coactivators in its presence. Here we show that the nucleosome remodeller dMi-2 is recruited to ecdysone-regulated genes to limit transcription. Contrary to the prevalent model, recruitment of the dMi-2 corepressor increases upon hormone addition to constrain gene activation through chromatin remodelling. Furthermore, EcR and dMi-2 form a complex that is devoid of Ultraspiracle. Unexpectedly, EcR contacts the dMi-2 ATPase domain and increases the efficiency of dMi-2-mediated nucleosome remodelling. This study identifies a non-canonical EcR-corepressor complex with the potential for a direct regulation of ATP-dependent nucleosome remodelling by a nuclear hormone receptor.
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Affiliation(s)
- Judith Kreher
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Kristina Kovač
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Karim Bouazoune
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Igor Mačinković
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Anna Luise Ernst
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Erik Engelen
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Roman Pahl
- Institute of Medical Biometry and Epidemiology, Philipps University Marburg, Marburg 35037, Germany
| | - Florian Finkernagel
- Center for Tumour Biology and Immunology, Philipps University Marburg, Marburg 35043, Germany
| | - Magdalena Murawska
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Ikram Ullah
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
| | - Alexander Brehm
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35037, Germany
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67
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Franz A, Shlyueva D, Brunner E, Stark A, Basler K. Probing the canonicity of the Wnt/Wingless signaling pathway. PLoS Genet 2017; 13:e1006700. [PMID: 28369070 PMCID: PMC5393890 DOI: 10.1371/journal.pgen.1006700] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/17/2017] [Accepted: 03/15/2017] [Indexed: 02/02/2023] Open
Abstract
The hallmark of canonical Wnt signaling is the transcriptional induction of Wnt target genes by the beta-catenin/TCF complex. Several studies have proposed alternative interaction partners for beta-catenin or TCF, but the relevance of potential bifurcations in the distal Wnt pathway remains unclear. Here we study on a genome-wide scale the requirement for Armadillo (Arm, Drosophila beta-catenin) and Pangolin (Pan, Drosophila TCF) in the Wnt/Wingless(Wg)-induced transcriptional response of Drosophila Kc cells. Using somatic genetics, we demonstrate that both Arm and Pan are absolutely required for mediating activation and repression of target genes. Furthermore, by means of STARR-sequencing we identified Wnt/Wg-responsive enhancer elements and found that all responsive enhancers depend on Pan. Together, our results confirm the dogma of canonical Wnt/Wg signaling and argue against the existence of distal pathway branches in this system. Our manuscript addresses the question of whether either of the canonical transduction components, beta-catenin or TCF, can be bypassed when the Wnt pathway is activated. By using somatic cell genetics in Drosophila cells (via CRISPR/Cas9 editing) in combination with RNA-seq and STARR-seq (Self-transcribing-active-regulatory-region-sequencing) as functional read-outs, we provide firm evidence against the existence of distal branches in the Wnt pathway.
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Affiliation(s)
- Alexandra Franz
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Daria Shlyueva
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Erich Brunner
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- * E-mail:
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68
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Pascual-Garcia P, Debo B, Aleman JR, Talamas JA, Lan Y, Nguyen NH, Won KJ, Capelson M. Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts. Mol Cell 2017; 66:63-76.e6. [PMID: 28366641 DOI: 10.1016/j.molcel.2017.02.020] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 01/19/2017] [Accepted: 02/17/2017] [Indexed: 01/09/2023]
Abstract
Nuclear pore complex components (Nups) have been implicated in transcriptional regulation, yet what regulatory steps are controlled by metazoan Nups remains unclear. We identified the presence of multiple Nups at promoters, enhancers, and insulators in the Drosophila genome. In line with this binding, we uncovered a functional role for Nup98 in mediating enhancer-promoter looping at ecdysone-inducible genes. These genes were found to be stably associated with nuclear pores before and after activation. Although changing levels of Nup98 disrupted enhancer-promoter contacts, it did not affect ongoing transcription but instead compromised subsequent transcriptional activation or transcriptional memory. In support of the enhancer-looping role, we found Nup98 to gain and retain physical interactions with architectural proteins upon stimulation with ecdysone. Together, our data identify Nups as a class of architectural proteins for enhancers and supports a model in which animal genomes use the nuclear pore as an organizing scaffold for inducible poised genes.
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Affiliation(s)
- Pau Pascual-Garcia
- Department of Cell and Developmental Biology, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brian Debo
- Department of Cell and Developmental Biology, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer R Aleman
- Department of Cell and Developmental Biology, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica A Talamas
- Department of Cell and Developmental Biology, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Department of Cell and Developmental Biology, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nha H Nguyen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyoung J Won
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maya Capelson
- Department of Cell and Developmental Biology, Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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69
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Wang X, Kültz D. Osmolality/salinity-responsive enhancers (OSREs) control induction of osmoprotective genes in euryhaline fish. Proc Natl Acad Sci U S A 2017; 114:E2729-E2738. [PMID: 28289196 PMCID: PMC5380061 DOI: 10.1073/pnas.1614712114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Fish respond to salinity stress by transcriptional induction of many genes, but the mechanism of their osmotic regulation is unknown. We developed a reporter assay using cells derived from the brain of the tilapia Oreochromis mossambicus (OmB cells) to identify osmolality/salinity-responsive enhancers (OSREs) in the genes of Omossambicus Genomic DNA comprising the regulatory regions of two strongly salinity-induced genes, inositol monophosphatase 1 (IMPA1.1) and myo-inositol phosphate synthase (MIPS), was isolated and analyzed with dual luciferase enhancer trap reporter assays. We identified five sequences (two in IMPA1.1 and three in MIPS) that share a common consensus element (DDKGGAAWWDWWYDNRB), which we named "OSRE1." Additional OSREs that were less effective in conferring salinity-induced trans-activation and do not match the OSRE1 consensus also were identified in both MIPS and IMPA1.1 Although OSRE1 shares homology with the mammalian osmotic-response element/tonicity-responsive enhancer (ORE/TonE) enhancer, the latter is insufficient to confer osmotic induction in fish. Like other enhancers, OSRE1 trans-activates genes independent of orientation. We conclude that OSRE1 is a cis-regulatory element (CRE) that enhances the hyperosmotic induction of osmoregulated genes in fish. Our study also shows that tailored reporter assays developed for OmB cells facilitate the identification of CREs in fish genomes. Knowledge of the OSRE1 motif allows affinity-purification of the corresponding transcription factor and computational approaches for enhancer screening of fish genomes. Moreover, our study enables targeted inactivation of OSRE1 enhancers, a method superior to gene knockout for functional characterization because it confines impairment of gene function to a specific context (salinity stress) and eliminates pitfalls of constitutive gene knockouts (embryonic lethality, developmental compensation).
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Affiliation(s)
- Xiaodan Wang
- Biochemical Evolution Laboratory, Department of Animal Science, University of California, Davis, CA, 95616
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Dietmar Kültz
- Biochemical Evolution Laboratory, Department of Animal Science, University of California, Davis, CA, 95616;
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70
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Ipe J, Swart M, Burgess KS, Skaar TC. High-Throughput Assays to Assess the Functional Impact of Genetic Variants: A Road Towards Genomic-Driven Medicine. Clin Transl Sci 2017; 10:67-77. [PMID: 28213901 PMCID: PMC5355973 DOI: 10.1111/cts.12440] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/03/2017] [Indexed: 01/08/2023] Open
Affiliation(s)
- J Ipe
- Indiana University School of MedicineDepartment of MedicineDivision of Clinical PharmacologyIndianapolisIndianaUSA
| | - M Swart
- Indiana University School of MedicineDepartment of MedicineDivision of Clinical PharmacologyIndianapolisIndianaUSA
| | - KS Burgess
- Indiana University School of MedicineDepartment of MedicineDivision of Clinical PharmacologyIndianapolisIndianaUSA
- Indiana University School of MedicineDepartment of Pharmacology and ToxicologyIndianapolisIndianaUSA
| | - TC Skaar
- Indiana University School of MedicineDepartment of MedicineDivision of Clinical PharmacologyIndianapolisIndianaUSA
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71
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Ables ET, Drummond-Barbosa D. Steroid Hormones and the Physiological Regulation of Tissue-Resident Stem Cells: Lessons from the Drosophila Ovary. CURRENT STEM CELL REPORTS 2017; 3:9-18. [PMID: 28458991 PMCID: PMC5407287 DOI: 10.1007/s40778-017-0070-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Stem cells respond to local paracrine signals; more recently, however, systemic hormones have also emerged as key regulators of stem cells. This review explores the role of steroid hormones in stem cells, using the Drosophila germline stem cell as a centerpiece for discussion. RECENT FINDINGS Stem cells sense and respond directly and indirectly to steroid hormones, which regulate diverse sets of target genes via interactions with nuclear hormone receptors. Hormone-regulated networks likely integrate the actions of multiple systemic signals to adjust the activity of stem cell lineages in response to changes in physiological status. SUMMARY Hormones are inextricably linked to animal physiology, and can control stem cells and their local niches. Elucidating the molecular mechanisms of hormone signaling in stem cells is essential for our understanding of the fundamental underpinnings of stem cell biology, and for informing new therapeutic interventions against cancers or for regenerative medicine.
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Affiliation(s)
- Elizabeth T. Ables
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Daniela Drummond-Barbosa
- Department of Biochemistry and Molecular Biology, Division of Reproductive Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
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72
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España AP, Santiago-Algarra D, Pradel L, Spicuglia S. [High-throughput approaches to study cis-regulating elements]. Biol Aujourdhui 2017; 211:271-280. [PMID: 29956654 DOI: 10.1051/jbio/2018015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Indexed: 12/22/2022]
Abstract
Gene expression in higher eukaryotes is regulated through the involvement of transcription start site (TSS)-proximal (promoters) and -distal (enhancers) regulatory elements. Enhancer elements play an essential role during development and cell differentiation, while genetic alterations in these elements are a major cause of human disease. Here, we discuss recent advances in high-throughput approaches to identify and characterize enhancer elements, from the well-established massively parallel reporter assays to the recent clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based technologies. We discuss how these approaches contribute toward a better understanding of enhancer function in normal and pathological conditions.
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Affiliation(s)
- Alexandre P España
- Aix-Marseille Université, INSERM, TAGC, UMR 1090, 13288 Marseille, France - Équipe Labellisée Ligue Contre le Cancer, Laboratoire TAGC, INSERM U1090, Aix-Marseille Université, Parc Scientifique de Luminy, 163 avenue de Luminy, 13288 Marseille Cedex 09, France
| | - David Santiago-Algarra
- Aix-Marseille Université, INSERM, TAGC, UMR 1090, 13288 Marseille, France - Équipe Labellisée Ligue Contre le Cancer, Laboratoire TAGC, INSERM U1090, Aix-Marseille Université, Parc Scientifique de Luminy, 163 avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Lydie Pradel
- Aix-Marseille Université, INSERM, TAGC, UMR 1090, 13288 Marseille, France - Équipe Labellisée Ligue Contre le Cancer, Laboratoire TAGC, INSERM U1090, Aix-Marseille Université, Parc Scientifique de Luminy, 163 avenue de Luminy, 13288 Marseille Cedex 09, France
| | - Salvatore Spicuglia
- Aix-Marseille Université, INSERM, TAGC, UMR 1090, 13288 Marseille, France - Équipe Labellisée Ligue Contre le Cancer, Laboratoire TAGC, INSERM U1090, Aix-Marseille Université, Parc Scientifique de Luminy, 163 avenue de Luminy, 13288 Marseille Cedex 09, France
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73
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Xiong XP, Kurthkoti K, Chang KY, Li JL, Ren X, Ni JQ, Rana TM, Zhou R. miR-34 Modulates Innate Immunity and Ecdysone Signaling in Drosophila. PLoS Pathog 2016; 12:e1006034. [PMID: 27893816 PMCID: PMC5125713 DOI: 10.1371/journal.ppat.1006034] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/31/2016] [Indexed: 12/31/2022] Open
Abstract
microRNAs are endogenous small regulatory RNAs that modulate myriad biological processes by repressing target gene expression in a sequence-specific manner. Here we show that the conserved miRNA miR-34 regulates innate immunity and ecdysone signaling in Drosophila. miR-34 over-expression activates antibacterial innate immunity signaling both in cultured cells and in vivo, and flies over-expressing miR-34 display improved survival and pathogen clearance upon Gram-negative bacterial infection; whereas miR-34 knockout animals are defective in antibacterial defense. In particular, miR-34 achieves its immune-stimulatory function, at least in part, by repressing the two novel target genes Dlg1 and Eip75B. In addition, our study reveals a mutual repression between miR-34 expression and ecdysone signaling, and identifies miR-34 as a node in the intricate interplay between ecdysone signaling and innate immunity. Lastly, we identify cis-regulatory genomic elements and trans-acting transcription factors required for optimal ecdysone-mediated repression of miR-34. Taken together, our study enriches the repertoire of immune-modulating miRNAs in animals, and provides new insights into the interplay between steroid hormone signaling and innate immunity.
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Affiliation(s)
- Xiao-Peng Xiong
- Tumor Initiation and Maintenance Program; Sanford Burnham Prebys Medical Discovery Institute, California, United States of America
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, California, United States of America
| | - Krishna Kurthkoti
- Tumor Initiation and Maintenance Program; Sanford Burnham Prebys Medical Discovery Institute, California, United States of America
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, California, United States of America
| | - Kung-Yen Chang
- Tumor Initiation and Maintenance Program; Sanford Burnham Prebys Medical Discovery Institute, California, United States of America
- Department of Pediatrics, University of California San Diego School of Medicine, California, United States of America
| | - Jian-Liang Li
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida, United States of America
| | - Xingjie Ren
- Gene Regulatory Laboratory, School of Medicine, Tsinghua University, Beijing, China
| | - Jian-Quan Ni
- Gene Regulatory Laboratory, School of Medicine, Tsinghua University, Beijing, China
| | - Tariq M. Rana
- Tumor Initiation and Maintenance Program; Sanford Burnham Prebys Medical Discovery Institute, California, United States of America
- Department of Pediatrics, University of California San Diego School of Medicine, California, United States of America
| | - Rui Zhou
- Tumor Initiation and Maintenance Program; Sanford Burnham Prebys Medical Discovery Institute, California, United States of America
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, California, United States of America
- * E-mail:
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74
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Guo Y, Flegel K, Kumar J, McKay DJ, Buttitta LA. Ecdysone signaling induces two phases of cell cycle exit in Drosophila cells. Biol Open 2016; 5:1648-1661. [PMID: 27737823 PMCID: PMC5155522 DOI: 10.1242/bio.017525] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
During development, cell proliferation and differentiation must be tightly coordinated to ensure proper tissue morphogenesis. Because steroid hormones are central regulators of developmental timing, understanding the links between steroid hormone signaling and cell proliferation is crucial to understanding the molecular basis of morphogenesis. Here we examined the mechanism by which the steroid hormone ecdysone regulates the cell cycle in Drosophila. We find that a cell cycle arrest induced by ecdysone in Drosophila cell culture is analogous to a G2 cell cycle arrest observed in the early pupa wing. We show that in the wing, ecdysone signaling at the larva-to-puparium transition induces Broad which in turn represses the cdc25c phosphatase String. The repression of String generates a temporary G2 arrest that synchronizes the cell cycle in the wing epithelium during early pupa wing elongation and flattening. As ecdysone levels decline after the larva-to-puparium pulse during early metamorphosis, Broad expression plummets, allowing String to become re-activated, which promotes rapid G2/M progression and a subsequent synchronized final cell cycle in the wing. In this manner, pulses of ecdysone can both synchronize the final cell cycle and promote the coordinated acquisition of terminal differentiation characteristics in the wing. Summary: Pulsed ecdysone signaling remodels cell cycle dynamics, causing distinct primary and secondary cell cycle arrests in Drosophila cells, analogous to those observed in the wing during metamorphosis.
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Affiliation(s)
- Yongfeng Guo
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kerry Flegel
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jayashree Kumar
- Biology Department and Genetics Department, Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daniel J McKay
- Biology Department and Genetics Department, Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, Chapel Hill, NC 27599, USA
| | - Laura A Buttitta
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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75
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Mazina MY, Nikolenko JV, Fursova NA, Nedil'ko PN, Krasnov AN, Vorobyeva NE. Early-late genes of the ecdysone cascade as models for transcriptional studies. Cell Cycle 2016; 14:3593-601. [PMID: 26506480 DOI: 10.1080/15384101.2015.1100772] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The DHR3 and Hr4 early-late genes of the ecdysone cascade are described as models for transcriptional studies in Drosophila cells. In a set of experiments, it became clear that these genes are a convenient and versatile system for research into the physiological conditions upon 20-hydroxyecdysone induction. DHR3 and Hr4 gene transcription is characterized by fast activation kinetics, which enables transcriptional studies without the influence of indirect effects. A limited number of activated genes (only 73 genes are induced one hour after treatment) promote the selectivity of transcriptional studies via 20-hydroxyecdysone induction. DHR3 and Hr4 gene expression is dose dependent, is completely controlled by the hormone titer and decreases within hours of 20-hydroxyecdysone withdrawal. The DHR3 and Hr4 gene promoters become functional within 20 minutes after induction, which makes them useful tools for investigation if the early activation process. Their transcription is controlled by the RNA polymerase II pausing mechanism, which is widespread in the genome of Drosophila melanogaster but is still underinvestigated. Uniform expression activation of the DHR3 and Hr4 genes in a cell population was confirmed at both the RNA and protein levels. Homogeneity of the transcription response makes DHR3/Hr4 system valuable for investigation of the protein dynamics during transcription induction.
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Affiliation(s)
- Marina Yu Mazina
- a Department of Transcription Regulation and Chromatin Dynamic ; Institute of Gene Biology , Russian Academy of Sciences ; Moscow , Russia
| | - Julia V Nikolenko
- a Department of Transcription Regulation and Chromatin Dynamic ; Institute of Gene Biology , Russian Academy of Sciences ; Moscow , Russia
| | - Nadezda A Fursova
- a Department of Transcription Regulation and Chromatin Dynamic ; Institute of Gene Biology , Russian Academy of Sciences ; Moscow , Russia
| | - Petr N Nedil'ko
- a Department of Transcription Regulation and Chromatin Dynamic ; Institute of Gene Biology , Russian Academy of Sciences ; Moscow , Russia
| | - Aleksey N Krasnov
- a Department of Transcription Regulation and Chromatin Dynamic ; Institute of Gene Biology , Russian Academy of Sciences ; Moscow , Russia
| | - Nadezhda E Vorobyeva
- a Department of Transcription Regulation and Chromatin Dynamic ; Institute of Gene Biology , Russian Academy of Sciences ; Moscow , Russia
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76
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A Genetic Mosaic Screen Reveals Ecdysone-Responsive Genes Regulating Drosophila Oogenesis. G3-GENES GENOMES GENETICS 2016; 6:2629-42. [PMID: 27226164 PMCID: PMC4978916 DOI: 10.1534/g3.116.028951] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Multiple aspects of Drosophila oogenesis, including germline stem cell activity, germ cell differentiation, and follicle survival, are regulated by the steroid hormone ecdysone. While the transcriptional targets of ecdysone signaling during development have been studied extensively, targets in the ovary remain largely unknown. Early studies of salivary gland polytene chromosomes led to a model in which ecdysone stimulates a hierarchical transcriptional cascade, wherein a core group of ecdysone-sensitive transcription factors induce tissue-specific responses by activating secondary branches of transcriptional targets. More recently, genome-wide approaches have identified hundreds of putative ecdysone-responsive targets. Determining whether these putative targets represent bona fide targets in vivo, however, requires that they be tested via traditional mutant analysis in a cell-type specific fashion. To investigate the molecular mechanisms whereby ecdysone signaling regulates oogenesis, we used genetic mosaic analysis to screen putative ecdysone-responsive genes for novel roles in the control of the earliest steps of oogenesis. We identified a cohort of genes required for stem cell maintenance, stem and progenitor cell proliferation, and follicle encapsulation, growth, and survival. These genes encode transcription factors, chromatin modulators, and factors required for RNA transport, stability, and ribosome biogenesis, suggesting that ecdysone might control a wide range of molecular processes during oogenesis. Our results suggest that, although ecdysone target genes are known to have cell type-specific roles, many ecdysone response genes that control larval or pupal cell types at developmental transitions are used reiteratively in the adult ovary. These results provide novel insights into the molecular mechanisms by which ecdysone signaling controls oogenesis, laying new ground for future studies.
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77
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Abstract
There are thousands of known associations between genetic variants and complex human phenotypes, and the rate of novel discoveries is rapidly increasing. Translating those associations into knowledge of disease mechanisms remains a fundamental challenge because the associated variants are overwhelmingly in noncoding regions of the genome where we have few guiding principles to predict their function. Intersecting the compendium of identified genetic associations with maps of regulatory activity across the human genome has revealed that phenotype-associated variants are highly enriched in candidate regulatory elements. Allele-specific analyses of gene regulation can further prioritize variants that likely have a functional effect on disease mechanisms; and emerging high-throughput assays to quantify the activity of candidate regulatory elements are a promising next step in that direction. Together, these technologies have created the ability to systematically and empirically test hypotheses about the function of noncoding variants and haplotypes at the scale needed for comprehensive and systematic follow-up of genetic association studies. Major coordinated efforts to quantify regulatory mechanisms across genetically diverse populations in increasingly realistic cell models would be highly beneficial to realize that potential.
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Affiliation(s)
- William L Lowe
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University Medical School, Durham, North Carolina 27708, USA
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78
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Lopes R, Korkmaz G, Agami R. Applying CRISPR-Cas9 tools to identify and characterize transcriptional enhancers. Nat Rev Mol Cell Biol 2016; 17:597-604. [PMID: 27381243 DOI: 10.1038/nrm.2016.79] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of the CRISPR-Cas9 system triggered a revolution in the field of genome engineering. Initially, the use of this system was focused on the study of protein-coding genes but, recently, a number of CRISPR-Cas9-based tools have been developed to study non-coding transcriptional regulatory elements. These technological advances offer unprecedented opportunities for elucidating the functions of enhancers in their endogenous context. Here, we discuss the application, current limitations and future development of CRISPR-Cas9 systems to identify and characterize enhancer elements in a high-throughput manner.
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Affiliation(s)
- Rui Lopes
- Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Gozde Korkmaz
- Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Reuven Agami
- Division of Biological Stress Response, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Department of Genetics, Erasmus University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
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79
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Maeshima K, Stanford SM, Hammaker D, Sacchetti C, Zeng LF, Ai R, Zhang V, Boyle DL, Aleman Muench GR, Feng GS, Whitaker JW, Zhang ZY, Wang W, Bottini N, Firestein GS. Abnormal PTPN11 enhancer methylation promotes rheumatoid arthritis fibroblast-like synoviocyte aggressiveness and joint inflammation. JCI Insight 2016; 1. [PMID: 27275015 DOI: 10.1172/jci.insight.86580] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The PTPN11 gene, encoding the tyrosine phosphatase SHP-2, is overexpressed in rheumatoid arthritis (RA) fibroblast-like synoviocytes (FLS) compared with osteoarthritis (OA) FLS and promotes RA FLS invasiveness. Here, we explored the molecular basis for PTPN11 overexpression in RA FLS and the role of SHP-2 in RA pathogenesis. Using computational methods, we identified a putative enhancer in PTPN11 intron 1, which contained a glucocorticoid receptor- binding (GR-binding) motif. This region displayed enhancer function in RA FLS and contained 2 hypermethylation sites in RA compared with OA FLS. RA FLS stimulation with the glucocorticoid dexamethasone induced GR binding to the enhancer and PTPN11 expression. Glucocorticoid responsiveness of PTPN11 was significantly higher in RA FLS than OA FLS and required the differentially methylated CpGs for full enhancer function. SHP-2 expression was enriched in the RA synovial lining, and heterozygous Ptpn11 deletion in radioresistant or innate immune cells attenuated K/BxN serum transfer arthritis in mice. Treatment with SHP-2 inhibitor 11a-1 reduced RA FLS migration and responsiveness to TNF and IL-1β stimulation and reduced arthritis severity in mice. Our findings demonstrate how abnormal epigenetic regulation of a pathogenic gene determines FLS behavior and demonstrate that targeting SHP-2 or the SHP-2 pathway could be a therapeutic strategy for RA.
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Affiliation(s)
- Keisuke Maeshima
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Stephanie M Stanford
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Deepa Hammaker
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Cristiano Sacchetti
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Li-Fan Zeng
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Rizi Ai
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Vida Zhang
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - David L Boyle
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - German R Aleman Muench
- Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Gen-Sheng Feng
- Department of Pathology and Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - John W Whitaker
- Janssen Pharmaceuticals Companies of Johnson and Johnson, La Jolla, California, USA
| | - Zhong-Yin Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Nunzio Bottini
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego School of Medicine, La Jolla, California, USA.; Division of Cellular Biology, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA
| | - Gary S Firestein
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego School of Medicine, La Jolla, California, USA
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80
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Duren RP, Boudreaux SP, Conneely OM. Genome Wide Mapping of NR4A Binding Reveals Cooperativity with ETS Factors to Promote Epigenetic Activation of Distal Enhancers in Acute Myeloid Leukemia Cells. PLoS One 2016; 11:e0150450. [PMID: 26938745 PMCID: PMC4777543 DOI: 10.1371/journal.pone.0150450] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/14/2016] [Indexed: 12/25/2022] Open
Abstract
Members of the NR4A subfamily of orphan nuclear receptors regulate cell fate decisions via both genomic and non-genomic mechanisms in a cell and tissue selective manner. NR4As play a key role in maintenance of hematopoietic stem cell homeostasis and are critical tumor suppressors of acute myeloid leukemia (AML). Expression of NR4As is broadly silenced in leukemia initiating cell enriched populations from human patients relative to normal hematopoietic stem/progenitor cells. Rescue of NR4A expression in human AML cells inhibits proliferation and reprograms AML gene signatures via transcriptional mechanisms that remain to be elucidated. By intersecting an acutely regulated NR4A1 dependent transcriptional profile with genome wide NR4A binding distribution, we now identify an NR4A targetome of 685 genes that are directly regulated by NR4A1. We show that NR4As regulate gene transcription primarily through interaction with distal enhancers that are co-enriched for NR4A1 and ETS transcription factor motifs. Using a subset of NR4A activated genes, we demonstrate that the ETS factors ERG and FLI-1 are required for activation of NR4A bound enhancers and NR4A target gene induction. NR4A1 dependent recruitment of ERG and FLI-1 promotes binding of p300 histone acetyltransferase to epigenetically activate NR4A bound enhancers via acetylation at histone H3K27. These findings disclose novel epigenetic mechanisms by which NR4As and ETS factors cooperate to drive NR4A dependent gene transcription in human AML cells.
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Affiliation(s)
- Ryan P. Duren
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas, United States of America
| | - Seth P. Boudreaux
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas, United States of America
| | - Orla M. Conneely
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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81
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Abstract
Steroid hormones induce cascades of gene activation and repression with transformative effects on cell fate . Steroid transduction plays a major role in the development and physiology of nearly all metazoan species, and in the progression of the most common forms of cancer. Despite the paramount importance of steroids in developmental and translational biology, a complete map of transcriptional response has not been developed for any hormone . In the case of 20-hydroxyecdysone (ecdysone) in Drosophila melanogaster, these trajectories range from apoptosis to immortalization. We mapped the ecdysone transduction network in a cohort of 41 cell lines, the largest such atlas yet assembled. We found that the early transcriptional response mirrors the distinctiveness of physiological origins: genes respond in restricted patterns, conditional on the expression levels of dozens of transcription factors. Only a small cohort of genes is constitutively modulated independent of initial cell state. Ecdysone-responsive genes tend to organize into directional same-stranded units, with consecutive genes induced from the same strand. Here, we identify half of the ecdysone receptor heterodimer as the primary rate-limiting step in the response, and find that initial receptor isoform levels modulate the activated cohort of target transcription factors. This atlas of steroid response reveals organizing principles of gene regulation by a model type II nuclear receptor and lays the foundation for comprehensive and predictive understanding of the ecdysone transduction network in the fruit fly.
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82
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Abstract
Nuclear receptors (NR) act as an integrated conduit for environmental and hormonal signals to govern genomic responses, which relate to cell fate decisions. We review how their integrated actions with each other, shared co-factors and other transcription factors are disrupted in cancer. Steroid hormone nuclear receptors are oncogenic drivers in breast and prostate cancer and blockade of signaling is a major therapeutic goal. By contrast to blockade of receptors, in other cancers enhanced receptor function is attractive, as illustrated initially with targeting of retinoic acid receptors in leukemia. In the post-genomic era large consortia, such as The Cancer Genome Atlas, have developed a remarkable volume of genomic data with which to examine multiple aspects of nuclear receptor status in a pan-cancer manner. Therefore to extend the review of NR function we have also undertaken bioinformatics analyses of NR expression in over 3000 tumors, spread across six different tumor types (bladder, breast, colon, head and neck, liver and prostate). Specifically, to ask how the NR expression was distorted (altered expression, mutation and CNV) we have applied bootstrapping approaches to simulate data for comparison, and also compared these NR findings to 12 other transcription factor families. Nuclear receptors were uniquely and uniformly downregulated across all six tumor types, more than predicted by chance. These approaches also revealed that each tumor type had a specific NR expression profile but these were most similar between breast and prostate cancer. Some NRs were down-regulated in at least five tumor types (e.g. NR3C2/MR and NR5A2/LRH-1)) whereas others were uniquely down-regulated in one tumor (e.g. NR1B3/RARG). The downregulation was not driven by copy number variation or mutation and epigenetic mechanisms maybe responsible for the altered nuclear receptor expression.
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Affiliation(s)
- Mark D Long
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
| | - Moray J Campbell
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY 14263, USA
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83
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Stampfel G, Kazmar T, Frank O, Wienerroither S, Reiter F, Stark A. Transcriptional regulators form diverse groups with context-dependent regulatory functions. Nature 2015; 528:147-51. [PMID: 26550828 DOI: 10.1038/nature15545] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 09/02/2015] [Indexed: 12/25/2022]
Abstract
One of the most important questions in biology is how transcription factors (TFs) and cofactors control enhancer function and thus gene expression. Enhancer activation usually requires combinations of several TFs, indicating that TFs function synergistically and combinatorially. However, while TF binding has been extensively studied, little is known about how combinations of TFs and cofactors control enhancer function once they are bound. It is typically unclear which TFs participate in combinatorial enhancer activation, whether different TFs form functionally distinct groups, or if certain TFs might substitute for each other in defined enhancer contexts. Here we assess the potential regulatory contributions of TFs and cofactors to combinatorial enhancer control with enhancer complementation assays. We recruited GAL4-DNA-binding-domain fusions of 812 Drosophila TFs and cofactors to 24 enhancer contexts and measured enhancer activities by 82,752 luciferase assays in S2 cells. Most factors were functional in at least one context, yet their contributions differed between contexts and varied from repression to activation (up to 289-fold) for individual factors. Based on functional similarities across contexts, we define 15 groups of TFs that differ in developmental functions and protein sequence features. Similar TFs can substitute for each other, enabling enhancer re-engineering by exchanging TF motifs, and TF-cofactor pairs cooperate during enhancer control and interact physically. Overall, we show that activators and repressors can have diverse regulatory functions that typically depend on the enhancer context. The systematic functional characterization of TFs and cofactors should further our understanding of combinatorial enhancer control and gene regulation.
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Affiliation(s)
- Gerald Stampfel
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Tomáš Kazmar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Olga Frank
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Sebastian Wienerroither
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Franziska Reiter
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Dr. Bohr-Gasse 7, 1030 Vienna, Austria
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84
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Yao L, Berman BP, Farnham PJ. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol 2015; 50:550-73. [PMID: 26446758 PMCID: PMC4666684 DOI: 10.3109/10409238.2015.1087961] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Enhancers are short regulatory sequences bound by sequence-specific transcription factors and play a major role in the spatiotemporal specificity of gene expression patterns in development and disease. While it is now possible to identify enhancer regions genomewide in both cultured cells and primary tissues using epigenomic approaches, it has been more challenging to develop methods to understand the function of individual enhancers because enhancers are located far from the gene(s) that they regulate. However, it is essential to identify target genes of enhancers not only so that we can understand the role of enhancers in disease but also because this information will assist in the development of future therapeutic options. After reviewing models of enhancer function, we discuss recent methods for identifying target genes of enhancers. First, we describe chromatin structure-based approaches for directly mapping interactions between enhancers and promoters. Second, we describe the use of correlation-based approaches to link enhancer state with the activity of nearby promoters and/or gene expression. Third, we describe how to test the function of specific enhancers experimentally by perturbing enhancer–target relationships using high-throughput reporter assays and genome editing. Finally, we conclude by discussing as yet unanswered questions concerning how enhancers function, how target genes can be identified, and how to distinguish direct from indirect changes in gene expression mediated by individual enhancers.
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Affiliation(s)
- Lijing Yao
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
| | - Benjamin P Berman
- b Department of Biomedical Sciences , Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Peggy J Farnham
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
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85
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Waszak SM, Delaneau O, Gschwind AR, Kilpinen H, Raghav SK, Witwicki RM, Orioli A, Wiederkehr M, Panousis NI, Yurovsky A, Romano-Palumbo L, Planchon A, Bielser D, Padioleau I, Udin G, Thurnheer S, Hacker D, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Cell 2015; 162:1039-50. [PMID: 26300124 DOI: 10.1016/j.cell.2015.08.001] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 03/17/2015] [Accepted: 07/29/2015] [Indexed: 12/12/2022]
Abstract
Chromatin state variation at gene regulatory elements is abundant across individuals, yet we understand little about the genetic basis of this variability. Here, we profiled several histone modifications, the transcription factor (TF) PU.1, RNA polymerase II, and gene expression in lymphoblastoid cell lines from 47 whole-genome sequenced individuals. We observed that distinct cis-regulatory elements exhibit coordinated chromatin variation across individuals in the form of variable chromatin modules (VCMs) at sub-Mb scale. VCMs were associated with thousands of genes and preferentially cluster within chromosomal contact domains. We mapped strong proximal and weak, yet more ubiquitous, distal-acting chromatin quantitative trait loci (cQTL) that frequently explain this variation. cQTLs were associated with molecular activity at clusters of cis-regulatory elements and mapped preferentially within TF-bound regions. We propose that local, sequence-independent chromatin variation emerges as a result of genetic perturbations in cooperative interactions between cis-regulatory elements that are located within the same genomic domain.
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Affiliation(s)
- Sebastian M Waszak
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Olivier Delaneau
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland; Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva 1211, Switzerland
| | - Andreas R Gschwind
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne 1015, Switzerland
| | - Helena Kilpinen
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland; Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva 1211, Switzerland
| | - Sunil K Raghav
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Robert M Witwicki
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne 1015, Switzerland
| | - Andrea Orioli
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne 1015, Switzerland
| | - Michael Wiederkehr
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne 1015, Switzerland
| | - Nikolaos I Panousis
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland; Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva 1211, Switzerland
| | - Alisa Yurovsky
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland; Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva 1211, Switzerland
| | - Luciana Romano-Palumbo
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
| | - Alexandra Planchon
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
| | - Deborah Bielser
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
| | - Ismael Padioleau
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland; Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva 1211, Switzerland
| | - Gilles Udin
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Sarah Thurnheer
- Protein Expression Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - David Hacker
- Protein Expression Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne 1015, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne 1015, Switzerland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland.
| | - Emmanouil T Dermitzakis
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland; Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva 1211, Switzerland.
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86
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Pindyurin AV, de Jong J, Akhtar W. TRIP through the chromatin: a high throughput exploration of enhancer regulatory landscapes. Genomics 2015; 106:171-177. [PMID: 26080039 DOI: 10.1016/j.ygeno.2015.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/01/2015] [Accepted: 06/09/2015] [Indexed: 11/25/2022]
Abstract
Enhancers are regulatory elements that promote gene expression in a spatio-temporal way and are involved in a wide range of developmental and disease processes. Both the identification and subsequent functional dissection of enhancers are key steps in understanding these processes. Several high-throughput approaches were recently developed for these purposes; however, in almost all cases enhancers are being tested outside their native chromatin context. Until recently, the analysis of enhancer activities at their native genomic locations was low throughput, laborious and time-consuming. Here, we discuss the potential of a powerful approach, TRIP, to study the functioning of enhancers in their native chromatin environments by introducing sensor constructs directly in the genome. TRIP allows for simultaneously analyzing the quantitative readout of numerous sensor constructs integrated at random locations in the genome. The high-throughput and flexible nature of TRIP opens up potential to study different aspects of enhancer biology at an unprecedented level.
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Affiliation(s)
- Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Johann de Jong
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Waseem Akhtar
- Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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87
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Vockley CM, Guo C, Majoros WH, Nodzenski M, Scholtens DM, Hayes MG, Lowe WL, Reddy TE. Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort. Genome Res 2015; 25:1206-14. [PMID: 26084464 PMCID: PMC4510004 DOI: 10.1101/gr.190090.115] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 06/15/2015] [Indexed: 12/30/2022]
Abstract
We report a novel high-throughput method to empirically quantify individual-specific regulatory element activity at the population scale. The approach combines targeted DNA capture with a high-throughput reporter gene expression assay. As demonstration, we measured the activity of more than 100 putative regulatory elements from 95 individuals in a single experiment. In agreement with previous reports, we found that most genetic variants have weak effects on distal regulatory element activity. Because haplotypes are typically maintained within but not between assayed regulatory elements, the approach can be used to identify causal regulatory haplotypes that likely contribute to human phenotypes. Finally, we demonstrate the utility of the method to functionally fine map causal regulatory variants in regions of high linkage disequilibrium identified by expression quantitative trait loci (eQTL) analyses.
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Affiliation(s)
- Christopher M Vockley
- Department of Cell Biology, Duke University Medical School, Durham, North Carolina 27710, USA; Center for Genomic and Computational Biology, Duke University Medical School, Durham, North Carolina 27710, USA
| | - Cong Guo
- Center for Genomic and Computational Biology, Duke University Medical School, Durham, North Carolina 27710, USA; University Program in Genetics and Genomics, Duke University, Durham, North Carolina 27710, USA
| | - William H Majoros
- Center for Genomic and Computational Biology, Duke University Medical School, Durham, North Carolina 27710, USA; Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27710, USA
| | - Michael Nodzenski
- Department of Preventive Medicine, Division of Biostatistics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Denise M Scholtens
- Department of Preventive Medicine, Division of Biostatistics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - William L Lowe
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Timothy E Reddy
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27710, USA; Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, North Carolina 27710, USA
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88
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STARR-seq - principles and applications. Genomics 2015; 106:145-150. [PMID: 26072434 DOI: 10.1016/j.ygeno.2015.06.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/19/2015] [Accepted: 06/08/2015] [Indexed: 12/21/2022]
Abstract
Differential gene expression is the basis for cell type diversity in multicellular organisms and the driving force of development and differentiation. It is achieved by cell type-specific transcriptional enhancers, which are genomic DNA sequences that activate the transcription of their target genes. Their identification and characterization is fundamental to our understanding of gene regulation. Features that are associated with enhancer activity, such as regulatory factor binding or histone modifications can predict the location of enhancers. Nonetheless, enhancer activity can only be assessed by transcriptional reporter assays. Over the past years massively parallel reporter assays have been developed for large scale testing of enhancers. In this review we focus on the principles and applications of STARR-seq, a functional assay that quantifies enhancer strengths in complex candidate libraries and thus allows activity-based enhancer identification in entire genomes. We explain how STARR-seq works, discuss current uses and give an outlook to future applications.
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89
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Skalska L, Stojnic R, Li J, Fischer B, Cerda-Moya G, Sakai H, Tajbakhsh S, Russell S, Adryan B, Bray SJ. Chromatin signatures at Notch-regulated enhancers reveal large-scale changes in H3K56ac upon activation. EMBO J 2015; 34:1889-904. [PMID: 26069324 DOI: 10.15252/embj.201489923] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 05/13/2015] [Indexed: 12/23/2022] Open
Abstract
The conserved Notch pathway functions in diverse developmental and disease-related processes, requiring mechanisms to ensure appropriate target selection and gene activation in each context. To investigate the influence of chromatin organisation and dynamics on the response to Notch signalling, we partitioned Drosophila chromatin using histone modifications and established the preferred chromatin conditions for binding of Su(H), the Notch pathway transcription factor. By manipulating activity of a co-operating factor, Lozenge/Runx, we showed that it can help facilitate these conditions. While many histone modifications were unchanged by Su(H) binding or Notch activation, we detected rapid changes in acetylation of H3K56 at Notch-regulated enhancers. This modification extended over large regions, required the histone acetyl-transferase CBP and was independent of transcription. Such rapid changes in H3K56 acetylation appear to be a conserved indicator of enhancer activation as they also occurred at the mammalian Notch-regulated Hey1 gene and at Drosophila ecdysone-regulated genes. This intriguing example of a core histone modification increasing over short timescales may therefore underpin changes in chromatin accessibility needed to promote transcription following signalling activation.
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Affiliation(s)
- Lenka Skalska
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Robert Stojnic
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Jinghua Li
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Bettina Fischer
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK Department of Genetics, University of Cambridge, Cambridge, UK
| | - Gustavo Cerda-Moya
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Hiroshi Sakai
- Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris, France
| | - Shahragim Tajbakhsh
- Department of Developmental & Stem Cell Biology, Institut Pasteur, Paris, France
| | - Steven Russell
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK Department of Genetics, University of Cambridge, Cambridge, UK
| | - Boris Adryan
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK Department of Genetics, University of Cambridge, Cambridge, UK
| | - Sarah J Bray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
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90
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Inoue F, Ahituv N. Decoding enhancers using massively parallel reporter assays. Genomics 2015; 106:159-164. [PMID: 26072433 DOI: 10.1016/j.ygeno.2015.06.005] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/22/2015] [Accepted: 06/08/2015] [Indexed: 10/23/2022]
Abstract
Enhancers control the timing, location and expression levels of their target genes. Nucleotide variation in enhancers has been shown to lead to numerous phenotypes, including human disease. While putative enhancer sequences and nucleotide variation within them can now be detected in a rapid manner using various genomic technologies, the understanding of the functional consequences of these variants still remains largely unknown. Massively parallel reporter assays (MPRAs) can overcome this hurdle by providing the ability to test thousands of sequences and nucleotide variants within them for enhancer activity en masse. Here, we describe this technology and specifically focus on how it is being used to obtain an increased understanding of enhancer regulatory code and grammar.
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Affiliation(s)
- Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA.
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91
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High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq. Nat Commun 2015; 6:6905. [PMID: 25872643 DOI: 10.1038/ncomms7905] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 03/12/2015] [Indexed: 01/19/2023] Open
Abstract
Cell-type specific regulation of gene expression requires the activation of promoters by distal genomic elements defined as enhancers. The identification and the characterization of enhancers are challenging in mammals due to their genome complexity. Here we develop CapStarr-Seq, a novel high-throughput strategy to quantitatively assess enhancer activity in mammals. This approach couples capture of regions of interest to previously developed Starr-seq technique. Extensive assessment of CapStarr-seq demonstrates accurate quantification of enhancer activity. Furthermore, we find that enhancer strength is associated with binding complexity of tissue-specific transcription factors and super-enhancers, while additive enhancer activity isolates key genes involved in cell identity and function. The CapStarr-Seq thus provides a fast and cost-effective approach to assess the activity of potential enhancers for a given cell type and will be helpful in decrypting transcription regulation mechanisms.
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92
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Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol 2015; 16:144-54. [PMID: 25650801 PMCID: PMC4517609 DOI: 10.1038/nrm3949] [Citation(s) in RCA: 670] [Impact Index Per Article: 74.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The human body contains several hundred cell types, all of which share the same genome. In metazoans, much of the regulatory code that drives cell type-specific gene expression is located in distal elements called enhancers. Although mammalian genomes contain millions of potential enhancers, only a small subset of them is active in a given cell type. Cell type-specific enhancer selection involves the binding of lineage-determining transcription factors that prime enhancers. Signal-dependent transcription factors bind to primed enhancers, which enables these broadly expressed factors to regulate gene expression in a cell type-specific manner. The expression of genes that specify cell type identity and function is associated with densely spaced clusters of active enhancers known as super-enhancers. The functions of enhancers and super-enhancers are influenced by, and affect, higher-order genomic organization.
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Affiliation(s)
| | | | | | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, UC San Diego
- Department of Medicine, UC San Diego
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93
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Org-1-dependent lineage reprogramming generates the ventral longitudinal musculature of the Drosophila heart. Curr Biol 2015; 25:488-94. [PMID: 25660543 DOI: 10.1016/j.cub.2014.12.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 12/01/2014] [Accepted: 12/03/2014] [Indexed: 01/27/2023]
Abstract
Only few examples of transdifferentiation, which denotes the conversion of one differentiated cell type to another, are known to occur during normal development, and more often, it is associated with regeneration processes. With respect to muscles, dedifferentiation/redifferentiation processes have been documented during post-traumatic muscle regeneration in blastema of newts as well as during myocardial regeneration. As shown herein, the ventral longitudinal muscles of the adult Drosophila heart arise from specific larval alary muscles in a process that represents the first known example of syncytial muscle transdifferentiation via dedifferentiation into mononucleate myoblasts during normal development. We demonstrate that this unique process depends on the reinitiation of a transcriptional program previously employed for embryonic alary muscle development, in which the factors Org-1 (Drosophila Tbx1) and Tailup (Drosophila Islet1) are key components. During metamorphosis, the action of these factors is combined with cell-autonomous inputs from the ecdysone steroid and the Hox gene Ultrabithorax, which provide temporal and spatial specificity to the transdifferentiation events. Following muscle dedifferentiation, inductive cues, particularly from the remodeling heart tube, are required for the redifferentiation of myoblasts into ventral longitudinal muscles. Our results provide new insights into mechanisms of lineage commitment and cell-fate plasticity during development.
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94
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Zabidi MA, Arnold CD, Schernhuber K, Pagani M, Rath M, Frank O, Stark A. Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation. Nature 2014; 518:556-9. [PMID: 25517091 DOI: 10.1038/nature13994] [Citation(s) in RCA: 302] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/20/2014] [Indexed: 12/13/2022]
Abstract
Gene transcription in animals involves the assembly of RNA polymerase II at core promoters and its cell-type-specific activation by enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has been less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different core promoters might exhibit an intrinsic specificity to certain enhancers. This is conceivable, as various core promoter sequence elements are differentially distributed between genes of different functions, including elements that are predominantly found at either developmentally regulated or at housekeeping genes. Here we show that thousands of enhancers in Drosophila melanogaster S2 and ovarian somatic cells (OSCs) exhibit a marked specificity to one of two core promoters--one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor--and confirm the existence of these two classes for five additional core promoters from genes with diverse functions. Housekeeping enhancers are active across the two cell types, while developmental enhancers exhibit strong cell-type specificity. Both enhancer classes differ in their genomic distribution, the functions of neighbouring genes, and the core promoter elements of these neighbouring genes. In addition, we identify two transcription factors--Dref and Trl--that bind and activate housekeeping versus developmental enhancers, respectively. Our results provide evidence for a sequence-encoded enhancer-core-promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome.
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Affiliation(s)
- Muhammad A Zabidi
- Research Institute of Molecular Pathology IMP, Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria
| | - Cosmas D Arnold
- Research Institute of Molecular Pathology IMP, Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria
| | - Katharina Schernhuber
- Research Institute of Molecular Pathology IMP, Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria
| | - Michaela Pagani
- Research Institute of Molecular Pathology IMP, Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria
| | - Martina Rath
- Research Institute of Molecular Pathology IMP, Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria
| | - Olga Frank
- Research Institute of Molecular Pathology IMP, Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology IMP, Vienna Biocenter VBC, Dr Bohr-Gasse 7, 1030 Vienna, Austria
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95
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Pri peptides are mediators of ecdysone for the temporal control of development. Nat Cell Biol 2014; 16:1035-44. [DOI: 10.1038/ncb3052] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 09/15/2014] [Indexed: 02/08/2023]
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96
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Abstract
Although it was originally believed that enhancers activate only the nearest promoter, recent global analyses enabled by high-throughput technology suggest that the network of enhancer-promoter interactions is far more complex. The mechanisms that determine the specificity of enhancer-promoter interactions are still poorly understood, but they are thought to include biochemical compatibility, constraints imposed by the three-dimensional architecture of chromosomes, insulator elements, and possibly the effects of local chromatin composition. In this review, we assess the current insights into these determinants, and highlight the functional genomic approaches that will lead the way towards better mechanistic understanding.
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97
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van Arensbergen J, van Steensel B, Bussemaker HJ. In search of the determinants of enhancer-promoter interaction specificity. Trends Cell Biol 2014; 24:695-702. [PMID: 25160912 DOI: 10.1016/j.tcb.2014.07.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/15/2014] [Accepted: 07/21/2014] [Indexed: 02/07/2023]
Abstract
Although it was originally believed that enhancers activate only the nearest promoter, recent global analyses enabled by high-throughput technology suggest that the network of enhancer-promoter interactions is far more complex. The mechanisms that determine the specificity of enhancer-promoter interactions are still poorly understood, but they are thought to include biochemical compatibility, constraints imposed by the three-dimensional architecture of chromosomes, insulator elements, and possibly the effects of local chromatin composition. In this review, we assess the current insights into these determinants, and highlight the functional genomic approaches that will lead the way towards better mechanistic understanding.
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Affiliation(s)
- Joris van Arensbergen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.
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98
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Slattery M, Zhou T, Yang L, Dantas Machado AC, Gordân R, Rohs R. Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci 2014; 39:381-99. [PMID: 25129887 DOI: 10.1016/j.tibs.2014.07.002] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/21/2022]
Abstract
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a genome. TFs recognize DNA in a specific manner; the mechanisms underlying this specificity have been identified for many TFs based on 3D structures of protein-DNA complexes. More recently, structural views have been complemented with data from high-throughput in vitro and in vivo explorations of the DNA-binding preferences of many TFs. Together, these approaches have greatly expanded our understanding of TF-DNA interactions. However, the mechanisms by which TFs select in vivo binding sites and alter gene expression remain unclear. Recent work has highlighted the many variables that influence TF-DNA binding, while demonstrating that a biophysical understanding of these many factors will be central to understanding TF function.
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Affiliation(s)
- Matthew Slattery
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA; Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Tianyin Zhou
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Lin Yang
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Ana Carolina Dantas Machado
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Departments of Biostatistics and Bioinformatics, Computer Science, and Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA.
| | - Remo Rohs
- Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
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99
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Van Bortle K, Corces VG. Lost in transition: dynamic enhancer organization across naive and primed stem cell states. Cell Stem Cell 2014; 14:693-4. [PMID: 24905156 PMCID: PMC4115280 DOI: 10.1016/j.stem.2014.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pluripotent stem cells transition between distinct naive and primed states that are controlled by overlapping sets of master regulatory transcription factors. In this issue of Cell Stem Cell, Buecker et al. (2014) and Factor et al. (2014) demonstrate that alternate enhancer usage, regulated by state-specific binding partners of master regulators, defines these pluripotent state transitions.
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Affiliation(s)
| | - Victor G Corces
- Department of Biology, Emory University, Atlanta, GA 30322, USA.
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100
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Drouin J. Minireview: pioneer transcription factors in cell fate specification. Mol Endocrinol 2014; 28:989-98. [PMID: 24825399 DOI: 10.1210/me.2014-1084] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The specification of cell fate is critical for proper cell differentiation and organogenesis. In endocrine tissues, this process leads to the differentiation, often a multistep process, of hormone-producing cells. This process is driven by a combination of transcription factors (TFs) that includes general factor, tissue-restricted, and/or cell-restricted factors. The last 2 decades have seen the discovery of many TFs of restricted expression and function in endocrine tissues. These factors are typically critical for expression of hormone-coding genes as well as for differentiation and proper function of hormone-producing cells. Further, genes encoding these tissue-restricted TFs are themselves subject to mutations that cause hormone deficiencies. Although the model that emerged from these 2 decades is one in which a specific combination of TFs drives a unique cell specification and genetic program, recent findings have led to the discovery of TFs that have the unique property of being able to remodel chromatin and thus modify the epigenome. Most importantly, such factors, known as pioneer TFs, appear to play critical roles in programming the epigenome during the successive steps involved in cell specification. This review summarizes our current understanding of the mechanisms for pioneer TF remodeling of chromatin. Currently, very few TFs that have proven pioneer activity are known, but it will be critical to identify these factors and understand their mechanisms of action if we are to harness the potential of regenerative therapies in endocrinology.
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Affiliation(s)
- Jacques Drouin
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montréal, Quebec, H2W 1R7 Canada
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