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Álvarez-Buylla Roces ME, Martínez-García JC, Dávila-Velderrain J, Domínguez-Hüttinger E, Martínez-Sánchez ME. Medical Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1069:1-33. [PMID: 30076565 DOI: 10.1007/978-3-319-89354-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The aim of this volume is to encourage the use of systems-level methodologies to contribute to the improvement of human-health . We intend to motivate biomedical researchers to complement their current theoretical and empirical practice with up-to-date systems biology conceptual approaches. Our perspective is based on the deep understanding of the key biomolecular regulatory mechanisms that underlie health, as well as the emergence and progression of human-disease . We strongly believe that the contemporary systems biology perspective opens the door to the effective development of novel methodologies to the improvement of prevention . This requires a deeper and integrative understanding of the involved underlying systems-level mechanisms. In order to explain our proposal in a simple way, in this chapter we privilege the conceptual exposition of our chosen framework over formal considerations. The formal exposition of our proposal will be expanded and discussed later in the next chapters.
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Campbell K, Lebreton G, Franch-Marro X, Casanova J. Differential roles of the Drosophila EMT-inducing transcription factors Snail and Serpent in driving primary tumour growth. PLoS Genet 2018; 14:e1007167. [PMID: 29420531 PMCID: PMC5821384 DOI: 10.1371/journal.pgen.1007167] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 02/21/2018] [Accepted: 12/25/2017] [Indexed: 02/06/2023] Open
Abstract
Several transcription factors have been identified that activate an epithelial-to-mesenchymal transition (EMT), which endows cells with the capacity to break through basement membranes and migrate away from their site of origin. A key program in development, in recent years it has been shown to be a crucial driver of tumour invasion and metastasis. However, several of these EMT-inducing transcription factors are often expressed long before the initiation of the invasion-metastasis cascade as well as in non-invasive tumours. Increasing evidence suggests that they may promote primary tumour growth, but their precise role in this process remains to be elucidated. To investigate this issue we have focused our studies on two Drosophila transcription factors, the classic EMT inducer Snail and the Drosophila orthologue of hGATAs4/6, Serpent, which drives an alternative mechanism of EMT; both Snail and GATA are specifically expressed in a number of human cancers, particularly at the invasive front and in metastasis. Thus, we recreated conditions of Snail and of Serpent high expression in the fly imaginal wing disc and analysed their effect. While either Snail or Serpent induced a profound loss of epithelial polarity and tissue organisation, Serpent but not Snail also induced an increase in the size of wing discs. Furthermore, the Serpent-induced tumour-like tissues were able to grow extensively when transplanted into the abdomen of adult hosts. We found the differences between Snail and Serpent to correlate with the genetic program they elicit; while activation of either results in an increase in the expression of Yorki target genes, Serpent additionally activates the Ras signalling pathway. These results provide insight into how transcription factors that induce EMT can also promote primary tumour growth, and how in some cases such as GATA factors a ‘multi hit’ effect may be achieved through the aberrant activation of just a single gene. Many cancer cells acquire abnormal motility behaviour leading to metastasis, the main cause of cancer related deaths. In many cancers, transcription factors capable of inducing motile migratory cell behaviours, so-called EMT transcription factors, are found highly expressed. However, the expression of these genes is not restricted to metastatic invasive cancers; they are often found in benign tumours, or in tumours long before they show any sign of metastasis. This observation motivated us to ask if they may play a role in driving primary tumour growth. Our results show that the Drosophila EMT-inducers Snail and Serpent are both capable of driving overproliferation. However, Snail overproliferation is accompanied by a decrease in cell size as well as cell death, and consequently the tissue does not increase in size. Serpent also drives cell proliferation but this occurs together with an increase in cell size, but not cell death, thus having a profound effect on the overall size of the tissue. We show that both Snail and Serpent trigger activation of the Yorki pathway and in addition Serpent, but not Snail, also triggers activation of the Ras pathway. These results provide insight into how activation of some EMT-inducing genes can also promote primary tumour growth.
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Affiliation(s)
- Kyra Campbell
- Institut de Biologia Molecular de Barcelona (CSIC), Barcelona, Catalonia, Spain
- Institut de Recerca Biomèdica de Barcelona, (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
- * E-mail: (KC); (JC)
| | - Gaëlle Lebreton
- Institut de Biologia Molecular de Barcelona (CSIC), Barcelona, Catalonia, Spain
- Institut de Recerca Biomèdica de Barcelona, (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Xavier Franch-Marro
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Functional Genomics and Evolution, Department Passeig Marítim de la Barceloneta, Barcelona, Spain
| | - Jordi Casanova
- Institut de Biologia Molecular de Barcelona (CSIC), Barcelona, Catalonia, Spain
- Institut de Recerca Biomèdica de Barcelona, (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain
- * E-mail: (KC); (JC)
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Wang D, Rai B, Qi F, Liu T, Wang J, Wang X, Ma B. Influence of the Twist gene on the invasion and metastasis of colon cancer. Oncol Rep 2018; 39:31-44. [PMID: 29115546 PMCID: PMC5783602 DOI: 10.3892/or.2017.6076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 09/14/2017] [Indexed: 12/19/2022] Open
Abstract
The present study investigated the role of the Twist gene in epithelial-mesenchymal transition (EMT) and its effects on the invasion and metastasis of malignant tumors. In vitro, we transfected SW480, HCT116 and HT29 cells with recombinant plasmids, pTracer-CMV/BSD-Twist and pGenesil1.2-Twist-shRNA, to influence expression of Twist. The transfection efficacy of the plasmids in the cell lines was confirmed by flow cytometry. The relative mRNA and protein expression levels of Twist, E-cadherin and vimentin in the transfected cells were detected by RT-PCR and western blotting, respectively. In addition, migration and invasion were assessed by Transwell assays. In vivo, we established a xenogenic liver metastasis mouse model by intrasplenic injection with transfected SW480, HCT116 or HT29 human colon cancer cells and used hematoxylin and eosin (H&E) staining to demonstrate the effective establishment of the model. The relative mRNA levels of Twist and vimentin were detected by RT-PCR. In vitro, RT-PCR and western blotting showed higher relative mRNA and protein expression levels of Twist and vimentin in cell lines transfected with the recombinant, highly expressed Twist plasmid than in non-transfected cell lines (P<0.05), while E-cadherin was inhibited (P<0.05). After transfection with the plasmid pGenesil1.2-Twist-shRNA, the relative mRNA and protein levels of Twist and vimentin were markedly inhibited in the HCT116 cells (P<0.05), and the levels of E-cadherin were not changed (P>0.05), along with inhibition of the migration and invasion abilities of the cell line (P<0.01). In vivo, relative mRNA levels of Twist and vimentin in both the liver and spleen of the mouse model were higher in the groups that were injected with one of the three cell lines transfected with pTracer-CMV/BSD-Twist than in the groups injected with cells transfected with pGenesil1.2-Twist-shRNA (P<0.05). In conclusion, upregulation of Twist gene expression can promote EMT molecular events. Interfering with the Twist gene can effectively silence Twist gene expression in HCT116 cells and consequently inhibit colon cancer cell migration and invasion.
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Affiliation(s)
- Duowei Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Bikash Rai
- Department of General Surgery, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Feng Qi
- Department of General Surgery, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Tong Liu
- Department of General Surgery, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Jinmiao Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Xiaodong Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
| | - Bozhao Ma
- Department of General Surgery, Tianjin Medical University General Hospital, Heping, Tianjin 300052, P.R. China
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54
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Taylor MV, Hughes SM. Mef2 and the skeletal muscle differentiation program. Semin Cell Dev Biol 2017; 72:33-44. [PMID: 29154822 DOI: 10.1016/j.semcdb.2017.11.020] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/11/2017] [Accepted: 11/13/2017] [Indexed: 02/06/2023]
Abstract
Mef2 is a conserved and significant transcription factor in the control of muscle gene expression. In cell culture Mef2 synergises with MyoD-family members in the activation of gene expression and in the conversion of fibroblasts into myoblasts. Amongst its in vivo roles, Mef2 is required for both Drosophila muscle development and mammalian muscle regeneration. Mef2 has functions in other cell-types too, but this review focuses on skeletal muscle and surveys key findings on Mef2 from its discovery, shortly after that of MyoD, up to the present day. In particular, in vivo functions, underpinning mechanisms and areas of uncertainty are highlighted. We describe how Mef2 sits at a nexus in the gene expression network that controls the muscle differentiation program, and how Mef2 activity must be regulated in time and space to orchestrate specific outputs within the different aspects of muscle development. A theme that emerges is that there is much to be learnt about the different Mef2 proteins (from different paralogous genes, spliced transcripts and species) and how the activity of these proteins is controlled.
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Affiliation(s)
- Michael V Taylor
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK.
| | - Simon M Hughes
- Randall Division of Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London SE1 1UL UK
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55
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Suresh J, Harmston N, Lim KK, Kaur P, Jin HJ, Lusk JB, Petretto E, Tolwinski NS. An embryonic system to assess direct and indirect Wnt transcriptional targets. Sci Rep 2017; 7:11092. [PMID: 28894169 PMCID: PMC5593962 DOI: 10.1038/s41598-017-11519-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/25/2017] [Indexed: 02/07/2023] Open
Abstract
During animal development, complex signals determine and organize a vast number of tissues using a very small number of signal transduction pathways. These developmental signaling pathways determine cell fates through a coordinated transcriptional response that remains poorly understood. The Wnt pathway is involved in a variety of these cellular functions, and its signals are transmitted in part through a β-catenin/TCF transcriptional complex. Here we report an in vivo Drosophila assay that can be used to distinguish between activation, de-repression and repression of transcriptional responses, separating upstream and downstream pathway activation and canonical/non-canonical Wnt signals in embryos. We find specific sets of genes downstream of both β-catenin and TCF with an additional group of genes regulated by Wnt, while the non-canonical Wnt4 regulates a separate cohort of genes. We correlate transcriptional changes with phenotypic outcomes of cell differentiation and embryo size, showing our model can be used to characterize developmental signaling compartmentalization in vivo.
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Affiliation(s)
- Jahnavi Suresh
- Yale-NUS College, 12 College Ave West, #01- 201, Singapore, 138610, Republic of Singapore
| | - Nathan Harmston
- Duke-NUS Medical School, 8 College Road, 169857, Singapore, Republic of Singapore
| | - Ka Keat Lim
- Duke-NUS Medical School, 8 College Road, 169857, Singapore, Republic of Singapore
| | - Prameet Kaur
- Yale-NUS College, 12 College Ave West, #01- 201, Singapore, 138610, Republic of Singapore
| | - Helen Jingshu Jin
- Yale-NUS College, 12 College Ave West, #01- 201, Singapore, 138610, Republic of Singapore
| | - Jay B Lusk
- Yale-NUS College, 12 College Ave West, #01- 201, Singapore, 138610, Republic of Singapore
| | - Enrico Petretto
- Duke-NUS Medical School, 8 College Road, 169857, Singapore, Republic of Singapore
| | - Nicholas S Tolwinski
- Yale-NUS College, 12 College Ave West, #01- 201, Singapore, 138610, Republic of Singapore. .,Department of Biological Sciences, National University of Singapore, Block MD6, Centre for Translational Medicine, Yong Loo Lin School of Medicine, 14 Medical Drive, Level 10 South, 10-02M, Singapore, 117599, Republic of Singapore.
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56
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Pearson JC, McKay DJ, Lieb JD, Crews ST. Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers. Development 2017; 143:3723-3732. [PMID: 27802137 DOI: 10.1242/dev.136895] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 08/30/2016] [Indexed: 12/25/2022]
Abstract
One of the key issues in studying transcriptional regulation during development is how to employ genome-wide assays that reveals sites of open chromatin and transcription factor binding to efficiently identify biologically relevant genes and enhancers. Analysis of Drosophila CNS midline cell development provides a useful system for studying transcriptional regulation at the genomic level due to a large, well-characterized set of midline-expressed genes and in vivo validated enhancers. In this study, FAIRE-seq on FACS-purified midline cells was performed and the midline FAIRE data were compared with whole-embryo FAIRE data. We find that regions of the genome with a strong midline FAIRE peak and weak whole-embryo FAIRE peak overlap with known midline enhancers and provide a useful predictive tool for enhancer identification. In a complementary analysis, we compared a large dataset of fragments that drive midline expression in vivo with the FAIRE data. Midline enhancer fragments with a midline FAIRE peak tend to be near midline-expressed genes, whereas midline enhancers without a midline FAIRE peak were often distant from midline-expressed genes and unlikely to drive midline transcription in vivo.
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Affiliation(s)
- Joseph C Pearson
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Daniel J McKay
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA .,Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Jason D Lieb
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Stephen T Crews
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA .,Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
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57
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Khoueiry P, Girardot C, Ciglar L, Peng PC, Gustafson EH, Sinha S, Furlong EE. Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity. eLife 2017; 6. [PMID: 28792889 PMCID: PMC5550276 DOI: 10.7554/elife.28440] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/21/2017] [Indexed: 12/15/2022] Open
Abstract
Sequence variation within enhancers plays a major role in both evolution and disease, yet its functional impact on transcription factor (TF) occupancy and enhancer activity remains poorly understood. Here, we assayed the binding of five essential TFs over multiple stages of embryogenesis in two distant Drosophila species (with 1.4 substitutions per neutral site), identifying thousands of orthologous enhancers with conserved or diverged combinatorial occupancy. We used these binding signatures to dissect two properties of developmental enhancers: (1) potential TF cooperativity, using signatures of co-associations and co-divergence in TF occupancy. This revealed conserved combinatorial binding despite sequence divergence, suggesting protein-protein interactions sustain conserved collective occupancy. (2) Enhancer in-vivo activity, revealing orthologous enhancers with conserved activity despite divergence in TF occupancy. Taken together, we identify enhancers with diverged motifs yet conserved occupancy and others with diverged occupancy yet conserved activity, emphasising the need to functionally measure the effect of divergence on enhancer activity.
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Affiliation(s)
- Pierre Khoueiry
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Charles Girardot
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Lucia Ciglar
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Pei-Chen Peng
- Carl R. Woese Institute of Genomic Biology, University of Illinois, Champaign, United States
| | - E Hilary Gustafson
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Saurabh Sinha
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.,Carl R. Woese Institute of Genomic Biology, University of Illinois, Champaign, United States
| | - Eileen Em Furlong
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
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58
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Arredondo JJ, Vivar J, Laine-Menéndez S, Martínez-Morentin L, Cervera M. CF2 transcription factor is involved in the regulation of Mef2 RNA levels, nuclei number and muscle fiber size. PLoS One 2017; 12:e0179194. [PMID: 28617826 PMCID: PMC5472297 DOI: 10.1371/journal.pone.0179194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 05/25/2017] [Indexed: 11/26/2022] Open
Abstract
CF2 and Mef2 influence a variety of developmental muscle processes at distinct stages of development. Nevertheless, the exact nature of the CF2-Mef2 relationship and its effects on muscle building remain yet to be resolved. Here, we explored the regulatory role of CF2 in the Drosophila embryo muscle formation. To address this question and not having proper null CF2 mutants we exploited loss or gain of function strategies to study the contribution of CF2 to Mef2 transcription regulation and to muscle formation. Our data point to CF2 as a factor involved in the regulation of muscle final size and/or the number of nuclei present in each muscle. This function is independent of its role as a Mef2 collaborative factor in the transcriptional regulation of muscle-structural genes. Although Mef2 expression patterns do not change, reductions or increases in parallel in CF2 and Mef2 transcript abundance were observed in interfered and overexpressed CF2 embryos. Since CF2 expression variations yield altered Mef2 expression levels but with correct spatio-temporal Mef2 expression patterns, it can be concluded that only the mechanism controlling expression levels is de-regulated. Here, it is proposed that CF2 regulates Mef2 expression through a Feedforward Loop circuit.
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Affiliation(s)
- Juan J. Arredondo
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas “Alberto Sols” UAM-CSIC and Centro de Investigación Biomédica en Red (CIBERER), c/ Arzobispo Morcillo 4, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail: (JJA); (MC)
| | - Jorge Vivar
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas “Alberto Sols” UAM-CSIC and Centro de Investigación Biomédica en Red (CIBERER), c/ Arzobispo Morcillo 4, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sara Laine-Menéndez
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas “Alberto Sols” UAM-CSIC and Centro de Investigación Biomédica en Red (CIBERER), c/ Arzobispo Morcillo 4, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Leticia Martínez-Morentin
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas “Alberto Sols” UAM-CSIC and Centro de Investigación Biomédica en Red (CIBERER), c/ Arzobispo Morcillo 4, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Margarita Cervera
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas “Alberto Sols” UAM-CSIC and Centro de Investigación Biomédica en Red (CIBERER), c/ Arzobispo Morcillo 4, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail: (JJA); (MC)
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Chambers M, Turki-Judeh W, Kim MW, Chen K, Gallaher SD, Courey AJ. Mechanisms of Groucho-mediated repression revealed by genome-wide analysis of Groucho binding and activity. BMC Genomics 2017; 18:215. [PMID: 28245789 PMCID: PMC5331681 DOI: 10.1186/s12864-017-3589-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 02/13/2017] [Indexed: 12/24/2022] Open
Abstract
Background The transcriptional corepressor Groucho (Gro) is required for the function of many developmentally regulated DNA binding repressors, thus helping to define the gene expression profile of each cell during development. The ability of Gro to repress transcription at a distance together with its ability to oligomerize and bind to histones has led to the suggestion that Gro may spread along chromatin. However, much is unknown about the mechanism of Gro-mediated repression and about the dynamics of Gro targeting. Results Our chromatin immunoprecipitation sequencing analysis of temporally staged Drosophila embryos shows that Gro binds in a highly dynamic manner primarily to clusters of discrete (<1 kb) segments. Consistent with the idea that Gro may facilitate communication between silencers and promoters, Gro binding is enriched at both cis-regulatory modules, as well as within the promotors of potential target genes. While this Gro-recruitment is required for repression, our data show that it is not sufficient for repression. Integration of Gro binding data with transcriptomic analysis suggests that, contrary to what has been observed for another Gro family member, Drosophila Gro is probably a dedicated repressor. This analysis also allows us to define a set of high confidence Gro repression targets. Using publically available data regarding the physical and genetic interactions between these targets, we are able to place them in the regulatory network controlling development. Through analysis of chromatin associated pre-mRNA levels at these targets, we find that genes regulated by Gro in the embryo are enriched for characteristics of promoter proximal paused RNA polymerase II. Conclusions Our findings are inconsistent with a one-dimensional spreading model for long-range repression and suggest that Gro-mediated repression must be regulated at a post-recruitment step. They also show that Gro is likely a dedicated repressor that sits at a prominent highly interconnected regulatory hub in the developmental network. Furthermore, our findings suggest a role for RNA polymerase II pausing in Gro-mediated repression. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3589-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Chambers
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Wiam Turki-Judeh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
| | - Min Woo Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Kenny Chen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.,Department of Energy, Institute of Genomics and Proteomics, University of California, Los Angeles, CA, 90095, USA
| | - Albert J Courey
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA. .,Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
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60
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Hu Y, Comjean A, Perrimon N, Mohr SE. The Drosophila Gene Expression Tool (DGET) for expression analyses. BMC Bioinformatics 2017; 18:98. [PMID: 28187709 PMCID: PMC5303223 DOI: 10.1186/s12859-017-1509-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 01/31/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Next-generation sequencing technologies have greatly increased our ability to identify gene expression levels, including at specific developmental stages and in specific tissues. Gene expression data can help researchers understand the diverse functions of genes and gene networks, as well as help in the design of specific and efficient functional studies, such as by helping researchers choose the most appropriate tissue for a study of a group of genes, or conversely, by limiting a long list of gene candidates to the subset that are normally expressed at a given stage or in a given tissue. RESULTS We report DGET, a Drosophila Gene Expression Tool ( www.flyrnai.org/tools/dget/web/ ), which stores and facilitates search of RNA-Seq based expression profiles available from the modENCODE consortium and other public data sets. Using DGET, researchers are able to look up gene expression profiles, filter results based on threshold expression values, and compare expression data across different developmental stages, tissues and treatments. In addition, at DGET a researcher can analyze tissue or stage-specific enrichment for an inputted list of genes (e.g., 'hits' from a screen) and search for additional genes with similar expression patterns. We performed a number of analyses to demonstrate the quality and robustness of the resource. In particular, we show that evolutionary conserved genes expressed at high or moderate levels in both fly and human tend to be expressed in similar tissues. Using DGET, we compared whole tissue profile and sub-region/cell-type specific datasets and estimated a potential source of false positives in one dataset. We also demonstrated the usefulness of DGET for synexpression studies by querying genes with expression profile similar to the mesodermal master regulator Twist. CONCLUSION Altogether, DGET provides a flexible tool for expression data retrieval and analysis with short or long lists of Drosophila genes, which can help scientists to design stage- or tissue-specific in vivo studies and do other subsequent analyses.
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Affiliation(s)
- Yanhui Hu
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
| | - Aram Comjean
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Norbert Perrimon
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Stephanie E Mohr
- Drosophila RNAi Screening Center, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
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61
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Almamun M, Kholod O, Stuckel AJ, Levinson BT, Johnson NT, Arthur GL, Davis JW, Taylor KH. Inferring a role for methylation of intergenic DNA in the regulation of genes aberrantly expressed in precursor B-cell acute lymphoblastic leukemia. Leuk Lymphoma 2017; 58:1-12. [PMID: 28094574 DOI: 10.1080/10428194.2016.1272683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A complete understanding of the mechanisms involved in the development of pre-B ALL is lacking. In this study, we integrated DNA methylation data and gene expression data to elucidate the impact of aberrant intergenic DNA methylation on gene expression in pre-B ALL. We found a subset of differentially methylated intergenic loci that were associated with altered gene expression in pre-B ALL patients. Notably, 84% of these regions were also bound by transcription factors (TF) known to play roles in differentiation and B-cell development in a lymphoblastoid cell line. Further, an overall downregulation of eRNA transcripts was observed in pre-B ALL patients and these transcripts were associated with the downregulation of putative target genes involved in B-cell migration, proliferation, and apoptosis. The identification of novel putative regulatory regions highlights the significance of intergenic DNA sequences and may contribute to the identification of new therapeutic targets for the treatment of pre-B ALL.
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Affiliation(s)
- Md Almamun
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Olha Kholod
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Alexei J Stuckel
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Benjamin T Levinson
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Nathan T Johnson
- b Bioinformatics and Computational Biology , Worcester Polytechnic Institute , Worcester , MA , USA
| | - Gerald L Arthur
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - J Wade Davis
- c Department of Health Management and Informatics , University of Missouri-Columbia , Columbia , MO , USA
| | - Kristen H Taylor
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
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62
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Campbell K, Casanova J. A common framework for EMT and collective cell migration. Development 2016; 143:4291-4300. [DOI: 10.1242/dev.139071] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During development, cells often switch between static and migratory behaviours. Such transitions are fundamental events in development and are linked to harmful consequences in pathology. It has long been considered that epithelial cells either migrate collectively as epithelial cells, or undergo an epithelial-to-mesenchymal transition and migrate as individual mesenchymal cells. Here, we assess what is currently known about in vivo cell migratory phenomena and hypothesise that such migratory behaviours do not fit into alternative and mutually exclusive categories. Rather, we propose that these categories can be viewed as the most extreme cases of a general continuum of morphological variety, with cells harbouring different degrees or combinations of epithelial and mesenchymal features and displaying an array of migratory behaviours.
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Affiliation(s)
- Kyra Campbell
- Institut de Biologia Molecular de Barcelona (CSIC), C/Baldiri Reixac 10, Barcelona, Catalonia 08028, Spain
- Institut de Recerca Biomèdica de Barcelona, C/Baldiri Reixac 10, Barcelona, Catalonia 08028, Spain
| | - Jordi Casanova
- Institut de Biologia Molecular de Barcelona (CSIC), C/Baldiri Reixac 10, Barcelona, Catalonia 08028, Spain
- Institut de Recerca Biomèdica de Barcelona, C/Baldiri Reixac 10, Barcelona, Catalonia 08028, Spain
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63
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Koenecke N, Johnston J, He Q, Meier S, Zeitlinger J. Drosophila poised enhancers are generated during tissue patterning with the help of repression. Genome Res 2016; 27:64-74. [PMID: 27979994 PMCID: PMC5204345 DOI: 10.1101/gr.209486.116] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 11/08/2016] [Indexed: 12/18/2022]
Abstract
Histone modifications are frequently used as markers for enhancer states, but how to interpret enhancer states in the context of embryonic development is not clear. The poised enhancer signature, involving H3K4me1 and low levels of H3K27ac, has been reported to mark inactive enhancers that are poised for future activation. However, future activation is not always observed, and alternative reasons for the widespread occurrence of this enhancer signature have not been investigated. By analyzing enhancers during dorsal-ventral (DV) axis formation in the Drosophila embryo, we find that the poised enhancer signature is specifically generated during patterning in the tissue where the enhancers are not induced, including at enhancers that are known to be repressed by a transcriptional repressor. These results suggest that, rather than serving exclusively as an intermediate step before future activation, the poised enhancer state may be a mark for spatial regulation during tissue patterning. We discuss the possibility that the poised enhancer state is more generally the result of repression by transcriptional repressors.
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Affiliation(s)
- Nina Koenecke
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jeff Johnston
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Qiye He
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Samuel Meier
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,University of Kansas Medical Center, Department of Pathology, Kansas City, Kansas 66160, USA
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64
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Koenecke N, Johnston J, Gaertner B, Natarajan M, Zeitlinger J. Genome-wide identification of Drosophila dorso-ventral enhancers by differential histone acetylation analysis. Genome Biol 2016; 17:196. [PMID: 27678375 PMCID: PMC5037609 DOI: 10.1186/s13059-016-1057-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 09/05/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Drosophila dorso-ventral (DV) patterning is one of the best-understood regulatory networks to date, and illustrates the fundamental role of enhancers in controlling patterning, cell fate specification, and morphogenesis during development. Histone acetylation such as H3K27ac is an excellent marker for active enhancers, but it is challenging to obtain precise locations for enhancers as the highest levels of this modification flank the enhancer regions. How to best identify tissue-specific enhancers in a developmental system de novo with a minimal set of data is still unclear. RESULTS Using DV patterning as a test system, we develop a simple and effective method to identify tissue-specific enhancers de novo. We sample a broad set of candidate enhancer regions using data on CREB-binding protein co-factor binding or ATAC-seq chromatin accessibility, and then identify those regions with significant differences in histone acetylation between tissues. This method identifies hundreds of novel DV enhancers and outperforms ChIP-seq data of relevant transcription factors when benchmarked with mRNA expression data and transgenic reporter assays. These DV enhancers allow the de novo discovery of the relevant transcription factor motifs involved in DV patterning and contain additional motifs that are evolutionarily conserved and for which the corresponding transcription factors are expressed in a DV-biased fashion. Finally, we identify novel target genes of the regulatory network, implicating morphogenesis genes as early targets of DV patterning. CONCLUSIONS Taken together, our approach has expanded our knowledge of the DV patterning network even further and is a general method to identify enhancers in any developmental system, including mammalian development.
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Affiliation(s)
- Nina Koenecke
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Jeff Johnston
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Bjoern Gaertner
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.,Present address: Department of Pediatrics, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Malini Natarajan
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA. .,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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65
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Swift J, Coruzzi GM. A matter of time - How transient transcription factor interactions create dynamic gene regulatory networks. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:75-83. [PMID: 27546191 DOI: 10.1016/j.bbagrm.2016.08.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 08/06/2016] [Accepted: 08/10/2016] [Indexed: 12/16/2022]
Abstract
Dynamic reprogramming of transcriptional networks enables cells to adapt to a changing environment. Thus, it is crucial not only to understand what gene targets are regulated by a transcription factor (TF) but also when. This review explores the way TFs function with respect to time, paying particular attention to discoveries made in plants - where coordinated, genome-wide responses to environmental change is crucial to the survival of these sessile organisms. We investigate the molecular mechanisms that mediate transient TF-DNA binding, and assess how these rapid and dynamic interactions translate to long-term temporal regulation of genomes. We also discuss how current molecular techniques can catch, and sometimes miss, transient TF-target interactions that underlie dynamic cellular responses. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Joseph Swift
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York 10003, USA.
| | - Gloria M Coruzzi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York 10003, USA
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66
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Pers D, Buchta T, Özüak O, Wolff S, Pietsch JM, Memon MB, Roth S, Lynch JA. Global analysis of dorsoventral patterning in the wasp Nasonia reveals extensive incorporation of novelty in a regulatory network. BMC Biol 2016; 14:63. [PMID: 27480122 PMCID: PMC4968023 DOI: 10.1186/s12915-016-0285-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/18/2016] [Indexed: 01/23/2023] Open
Abstract
Background Gene regulatory networks (GRNs) underlie developmental patterning and morphogenetic processes, and changes in the interactions within the underlying GRNs are a major driver of evolutionary processes. In order to make meaningful comparisons that can provide significant insights into the evolution of regulatory networks, homologous networks from multiple taxa must be deeply characterized. One of the most thoroughly characterized GRNs is the dorsoventral (DV) patterning system of the Drosophila melanogaster embryo. We have developed the wasp Nasonia as a comparative DV patterning model because it has shown the convergent evolution of a mode of early embryonic patterning very similar to that of the fly, and it is of interest to know whether the similarity at the gross level also extends to the molecular level. Results We used RNAi to dorsalize and ventralize Nasonia embryos, RNAseq to quantify transcriptome-wide expression levels, and differential expression analysis to identify genes whose expression levels change in either RNAi case. This led to the identification of >100 genes differentially expressed and regulated along the DV axis. Only a handful of these genes are shared DV components in both fly and wasp. Many of those unique to Nasonia are cytoskeletal and adhesion molecules, which may be related to the divergent cell and tissue behavior observed at gastrulation. In addition, many transcription factors and signaling components are only DV regulated in Nasonia, likely reflecting the divergent upstream patterning mechanisms involved in producing the conserved pattern of cell fates observed at gastrulation. Finally, several genes that lack Drosophila orthologs show robust and distinct expression patterns. These include genes with vertebrate homologs that have been lost in the fly lineage, genes that are found only among Hymenoptera, and several genes that entered the Nasonia genome through lateral transfer from endosymbiotic bacteria. Conclusions Altogether, our results provide insights into how GRNs respond to new functional demands and how they can incorporate novel components. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0285-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Pers
- Department of Biological Sciences, University of Illinois at Chicago, MBRB 4020, 900 S. Ashland Avenue, Chicago, IL, 60402, USA
| | - Thomas Buchta
- Institute for Developmental Biology, University at Cologne, Cologne, Germany
| | - Orhan Özüak
- Institute for Developmental Biology, University at Cologne, Cologne, Germany
| | - Selma Wolff
- Institute for Developmental Biology, University at Cologne, Cologne, Germany
| | - Jessica M Pietsch
- Institute for Developmental Biology, University at Cologne, Cologne, Germany
| | - Mohammad Bilal Memon
- Department of Biological Sciences, University of Illinois at Chicago, MBRB 4020, 900 S. Ashland Avenue, Chicago, IL, 60402, USA
| | - Siegfried Roth
- Institute for Developmental Biology, University at Cologne, Cologne, Germany
| | - Jeremy A Lynch
- Department of Biological Sciences, University of Illinois at Chicago, MBRB 4020, 900 S. Ashland Avenue, Chicago, IL, 60402, USA.
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An Ectopic Network of Transcription Factors Regulated by Hippo Signaling Drives Growth and Invasion of a Malignant Tumor Model. Curr Biol 2016; 26:2101-13. [DOI: 10.1016/j.cub.2016.06.035] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 05/21/2016] [Accepted: 06/16/2016] [Indexed: 12/19/2022]
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68
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Su L, Luo Y, Yang Z, Yang J, Yao C, Cheng F, Shan J, Chen J, Li F, Liu L, Liu C, Xu Y, Jiang L, Guo D, Prieto J, Ávila MA, Shen J, Qian C. MEF2D Transduces Microenvironment Stimuli to ZEB1 to Promote Epithelial-Mesenchymal Transition and Metastasis in Colorectal Cancer. Cancer Res 2016; 76:5054-67. [PMID: 27364559 DOI: 10.1158/0008-5472.can-16-0246] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 06/03/2016] [Indexed: 11/16/2022]
Abstract
Epithelial-mesenchymal transition (EMT) is an essential mechanism of metastasis, including in colorectal cancer. Although EMT processes are often triggered in cancer cells by their surrounding microenvironment, how EMT-relevant genes control these processes is not well understood. In multiple types of cancers, the transcription factor MEF2D has been implicated in cell proliferation, but its contributions to metastasis have not been addressed. Here, we show MEF2D is overexpressed in clinical colorectal cancer tissues where its high expression correlates with metastatic process. Functional investigations showed that MEF2D promoted cancer cell invasion and EMT and that it was essential for certain microenvironment signals to induce EMT and metastasis in vivo Mechanistically, MEF2D directly regulated transcription of the EMT driver gene ZEB1 and facilitated histone acetylation at the ZEB1 promoter. More importantly, MEF2D responded to various tumor microenvironment signals and acted as a central integrator transducing multiple signals to activate ZEB1 transcription. Overall, our results define a critical function for MEF2D in upregulating EMT and the metastatic capacity of colorectal cancer cells. Further, they offer new insights into how microenvironment signals activate EMT-relevant genes and deepen the pathophysiologic significance of MEF2D, with potential implications for the prevention and treatment of metastatic colorectal cancer. Cancer Res; 76(17); 5054-67. ©2016 AACR.
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Affiliation(s)
- Li Su
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Yongli Luo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Zhi Yang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Jing Yang
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Chao Yao
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Feifei Cheng
- School of Life Science, Zhejiang Sci-Tech University, Hangzhou, China
| | - Juanjuan Shan
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Jun Chen
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Fangfang Li
- Medical Research Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Limei Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Chungang Liu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Yanmin Xu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Lupin Jiang
- Department of Obstetrics and Gynecology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Deyu Guo
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Jesus Prieto
- Center of Investigation for Applied Medicine, University of Navarra, Pamplona, Spain
| | - Matías A Ávila
- Center of Investigation for Applied Medicine, University of Navarra, Pamplona, Spain
| | - Junjie Shen
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China.
| | - Cheng Qian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China.
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69
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Li CW, Chen BS. Investigating core genetic-and-epigenetic cell cycle networks for stemness and carcinogenic mechanisms, and cancer drug design using big database mining and genome-wide next-generation sequencing data. Cell Cycle 2016; 15:2593-2607. [PMID: 27295129 PMCID: PMC5053590 DOI: 10.1080/15384101.2016.1198862] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recent studies have demonstrated that cell cycle plays a central role in development and carcinogenesis. Thus, the use of big databases and genome-wide high-throughput data to unravel the genetic and epigenetic mechanisms underlying cell cycle progression in stem cells and cancer cells is a matter of considerable interest. Real genetic-and-epigenetic cell cycle networks (GECNs) of embryonic stem cells (ESCs) and HeLa cancer cells were constructed by applying system modeling, system identification, and big database mining to genome-wide next-generation sequencing data. Real GECNs were then reduced to core GECNs of HeLa cells and ESCs by applying principal genome-wide network projection. In this study, we investigated potential carcinogenic and stemness mechanisms for systems cancer drug design by identifying common core and specific GECNs between HeLa cells and ESCs. Integrating drug database information with the specific GECNs of HeLa cells could lead to identification of multiple drugs for cervical cancer treatment with minimal side-effects on the genes in the common core. We found that dysregulation of miR-29C, miR-34A, miR-98, and miR-215; and methylation of ANKRD1, ARID5B, CDCA2, PIF1, STAMBPL1, TROAP, ZNF165, and HIST1H2AJ in HeLa cells could result in cell proliferation and anti-apoptosis through NFκB, TGF-β, and PI3K pathways. We also identified 3 drugs, methotrexate, quercetin, and mimosine, which repressed the activated cell cycle genes, ARID5B, STK17B, and CCL2, in HeLa cells with minimal side-effects.
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Affiliation(s)
- Cheng-Wei Li
- a Department of Electrical Engineering , National Tsing Hua University , Hsinchu , Taiwan
| | - Bor-Sen Chen
- a Department of Electrical Engineering , National Tsing Hua University , Hsinchu , Taiwan
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70
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Kozin VV, Kostyuchenko RP. Evolutionary conservation and variability of the mesoderm development in spiralia: A peculiar pattern of nereid polychaetes. BIOL BULL+ 2016. [DOI: 10.1134/s1062359016030079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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71
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Sandler JE, Stathopoulos A. Stepwise Progression of Embryonic Patterning. Trends Genet 2016; 32:432-443. [PMID: 27230753 DOI: 10.1016/j.tig.2016.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 01/23/2023]
Abstract
It is long established that the graded distribution of Dorsal transcription factor influences spatial domains of gene expression along the dorsoventral (DV) axis of Drosophila melanogaster embryos. However, the more recent realization that Dorsal levels also change with time raises the question of whether these dynamics are instructive. An overview of DV axis patterning is provided, focusing on new insights identified through quantitative analysis of temporal changes in Dorsal target gene expression from one nuclear cycle to the next ('steps'). Possible roles for the stepwise progression of this patterning program are discussed including (i) tight temporal regulation of signaling pathway activation, (ii) control of gene expression cohorts, and (iii) ensuring the irreversibility of the patterning and cell fate specification process.
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Affiliation(s)
- Jeremy E Sandler
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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72
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Kozin VV, Filimonova DA, Kupriashova EE, Kostyuchenko RP. Mesoderm patterning and morphogenesis in the polychaete Alitta virens (Spiralia, Annelida): Expression of mesodermal markers Twist, Mox, Evx and functional role for MAP kinase signaling. Mech Dev 2016; 140:1-11. [PMID: 27000638 DOI: 10.1016/j.mod.2016.03.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 12/11/2022]
Abstract
Mesoderm represents the evolutionary youngest germ layer and forms numerous novel tissues in bilaterian animals. Despite the established conservation of the gene regulatory networks that drive mesoderm differentiation (e.g. myogenesis), mechanisms of mesoderm specification are highly variable in distant model species. Thus, broader phylogenetic sampling is required to reveal common features of mesoderm formation across bilaterians. Here we focus on a representative of Spiralia, the marine annelid Alitta virens, whose mesoderm development is still poorly investigated on the molecular level. We characterize three novel early mesodermal markers for A. virens - Twist, Mox, and Evx - which are differentially expressed within the mesodermal lineages. The Twist mRNA is ubiquitously distributed in the fertilized egg and exhibits specific expression in endomesodermal- and ectomesodermal-founder cells at gastrulation. Twist is expressed around the blastopore and later in a segmental metameric pattern. We consider this expression to be ancestral, and in support of the enterocoelic hypothesis of mesoderm evolution. We also revealed an early pattern of the MAPK activation in A. virens that is different from the previously reported pattern in spiralians. Inhibition of the MAPK pathway by U0126 disrupts the metameric Twist and Mox expression, indicating an early requirement of the MAPK cascade for proper morphogenesis of endomesodermal tissues.
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Affiliation(s)
- Vitaly V Kozin
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia.
| | - Daria A Filimonova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia
| | - Ekaterina E Kupriashova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia
| | - Roman P Kostyuchenko
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia.
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73
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He B, Tan K. Understanding transcriptional regulatory networks using computational models. Curr Opin Genet Dev 2016; 37:101-108. [PMID: 26950762 DOI: 10.1016/j.gde.2016.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/29/2016] [Accepted: 02/08/2016] [Indexed: 01/06/2023]
Abstract
Transcriptional regulatory networks (TRNs) encode instructions for animal development and physiological responses. Recent advances in genomic technologies and computational modeling have revolutionized our ability to construct models of TRNs. Here, we survey current computational methods for inferring TRN models using genome-scale data. We discuss their advantages and limitations. We summarize representative TRNs constructed using genome-scale data in both normal and disease development. We discuss lessons learned about the structure/function relationship of TRNs, based on examining various large-scale TRN models. Finally, we outline some open questions regarding TRNs, including how to improve model accuracy by integrating complementary data types, how to infer condition-specific TRNs, and how to compare TRNs across conditions and species in order to understand their structure/function relationship.
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Affiliation(s)
- Bing He
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
| | - Kai Tan
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA.
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74
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Quantitative Single-Embryo Profile of Drosophila Genome Activation and the Dorsal-Ventral Patterning Network. Genetics 2016; 202:1575-84. [PMID: 26896327 DOI: 10.1534/genetics.116.186783] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/04/2016] [Indexed: 02/01/2023] Open
Abstract
During embryonic development of Drosophila melanogaster, the maternal-to-zygotic transition (MZT) marks a significant and rapid turning point when zygotic transcription begins and control of development is transferred from maternally deposited transcripts. Characterizing the sequential activation of the genome during the MZT requires precise timing and a sensitive assay to measure changes in expression. We utilized the NanoString nCounter instrument, which directly counts messenger RNA transcripts without reverse transcription or amplification, to study >70 genes expressed along the dorsal-ventral (DV) axis of early Drosophila embryos, dividing the MZT into 10 time points. Transcripts were quantified for every gene studied at all time points, providing the first dataset of absolute numbers of transcripts during Drosophila development. We found that gene expression changes quickly during the MZT, with early nuclear cycle 14 (NC14) the most dynamic time for the embryo. twist is one of the most abundant genes in the entire embryo and we use mutants to quantitatively demonstrate how it cooperates with Dorsal to activate transcription and is responsible for some of the rapid changes in transcription observed during early NC14. We also uncovered elements within the gene regulatory network that maintain precise transcript levels for sets of genes that are spatiotemporally cotranscribed within the presumptive mesoderm or dorsal ectoderm. Using these new data, we show that a fine-scale, quantitative analysis of temporal gene expression can provide new insights into developmental biology by uncovering trends in gene networks, including coregulation of target genes and specific temporal input by transcription factors.
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75
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A Clinical Indications Prediction Scale Based on TWIST1 for Human Mesenchymal Stem Cells. EBioMedicine 2015; 4:62-73. [PMID: 26981553 PMCID: PMC4776067 DOI: 10.1016/j.ebiom.2015.12.020] [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] [Received: 07/17/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 12/13/2022] Open
Abstract
In addition to their stem/progenitor properties, mesenchymal stem cells (MSCs) also exhibit potent effector (angiogenic, antiinflammatory, immuno-modulatory) functions that are largely paracrine in nature. It is widely believed that effector functions underlie most of the therapeutic potential of MSCs and are independent of their stem/progenitor properties. Here we demonstrate that stem/progenitor and effector functions are coordinately regulated at the cellular level by the transcription factor Twist1 and specified within populations according to a hierarchical model. We further show that manipulation of Twist1 levels by genetic approaches or by exposure to widely used culture supplements including fibroblast growth factor 2 (Ffg2) and interferon gamma (IFN-gamma) alters MSC efficacy in cell-based and in vivo assays in a predictable manner. Thus, by mechanistically linking stem/progenitor and effector functions our studies provide a unifying framework in the form of an MSC hierarchy that models the functional complexity of populations. Using this framework, we developed a CLinical Indications Prediction (CLIP) scale that predicts how donor-to-donor heterogeneity and culture conditions impact the therapeutic efficacy of MSC populations for different disease indications. Mesenchymal stem cells exhibit stem/progenitor and effector (angiogenic, anti-inflammatory, immuno-modulatory) functions. Twist1 coordinately regulates stem/progenitor and effector functions, which are specified hierarchically in populations. Twist1 levels predict inter-population differences in therapeutic efficacy of mesenchymal stem cells for different disease indications.
Mesenchymal stem cells are being evaluated in human clinical trials for treating ischemic, inflammatory, and immunological diseases. However, most completed trials have yielded suboptimal outcomes due to the inability to predict the potency of different donor populations, which are functionally heterogeneous. We demonstrate that clinically relevant biological activities of MSCs are coordinately regulated by the transcription factor Twist1. Furthermore, we showed that TWIST1 levels reliably predict differences in the angiogenic, anti-inflammatory, and immuno-modulatory activity of populations and as such used it to develop a Clinical Indications Prediction (CLIP) scale. By predicting potency of MSC populations for different disease indications the CLIP scale is expected to dramatically improve MSC-based clinical trial outcomes.
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Shi J, Cao J, Zhou BP. Twist-BRD4 complex: potential drug target for basal-like breast cancer. Curr Pharm Des 2015; 21:1256-61. [PMID: 25506891 DOI: 10.2174/1381612821666141211153853] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 12/05/2014] [Indexed: 01/02/2023]
Abstract
As an important basic helix-loop-helix (bHLH) transcription factor, Twist associates with several physiological processes such as mesodermal development, and pathological processes such as Saethre-Chotzen syndrome. During cancer progression, Twist induces epithelial-mesenchymal transition (EMT), potentiating cancer cell invasion and metastasis. Although many studies have revealed its multiple biological roles, it remained unclear how Twist transcriptionally activates targeted genes. Recently we discovered tip60-mediated Twist di-acetylation in the ''histone H4-mimic'' GK-X-GK motif. The di-acetylated Twist recruits BRD4 and related transcriptional components to super-enhancer of its targeted genes during progression of basal-like breast cancer (BLBC). Here, we review this new advance of regulation and functional mechanism of Twist.
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77
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Lin S, Ewen-Campen B, Ni X, Housden BE, Perrimon N. In Vivo Transcriptional Activation Using CRISPR/Cas9 in Drosophila. Genetics 2015; 201:433-42. [PMID: 26245833 PMCID: PMC4596659 DOI: 10.1534/genetics.115.181065] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/04/2015] [Indexed: 12/30/2022] Open
Abstract
A number of approaches for Cas9-mediated transcriptional activation have recently been developed, allowing target genes to be overexpressed from their endogenous genomic loci. However, these approaches have thus far been limited to cell culture, and this technique has not been demonstrated in vivo in any animal. The technique involving the fewest separate components, and therefore the most amenable to in vivo applications, is the dCas9-VPR system, where a nuclease-dead Cas9 is fused to a highly active chimeric activator domain. In this study, we characterize the dCas9-VPR system in Drosophila cells and in vivo. We show that this system can be used in cell culture to upregulate a range of target genes, singly and in multiplex, and that a single guide RNA upstream of the transcription start site can activate high levels of target transcription. We observe marked heterogeneity in guide RNA efficacy for any given gene, and we confirm that transcription is inhibited by guide RNAs binding downstream of the transcription start site. To demonstrate one application of this technique in cells, we used dCas9-VPR to identify target genes for Twist and Snail, two highly conserved transcription factors that cooperate during Drosophila mesoderm development. In addition, we simultaneously activated both Twist and Snail to identify synergistic responses to this physiologically relevant combination. Finally, we show that dCas9-VPR can activate target genes and cause dominant phenotypes in vivo, providing the first demonstration of dCas9 activation in a multicellular animal. Transcriptional activation using dCas9-VPR thus offers a simple and broadly applicable technique for a variety of overexpression studies.
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Affiliation(s)
- Shuailiang Lin
- Tsinghua-Peking-National Institute of Biological Sciences Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China Department of Genetics
| | | | | | | | - Norbert Perrimon
- Department of Genetics Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115
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78
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Abstract
Immune responses and metabolic regulation are tightly coupled in all animals, but the underlying mechanistic connections are nowhere completely clear. In flies and in humans, prolonged or excessive immune activation can drive metabolic disruption and cause loss of metabolic stores. Conversely, disruptions of metabolic homeostasis, such as periods of malnutrition, can have significant impacts on immune function. We have recently identified the transcription factor MEF2 as a critical switch between anabolic and immune function in the adult Drosophila fat body. A conserved phosphorylation determines the affinity of MEF2 for the TATA-binding protein, effecting a choice between energy storage and immune function. The goal of this review is to place this molecular event in the broader context of metabolic-immune interaction in Drosophila, exploring what is and is not known about the ties between these 2 critical physiological functions.
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Affiliation(s)
- Marc Dionne
- a Centre for the Molecular and Cellular Biology of Inflammation; King's College London School of Medicine; London, United Kingdom
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79
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Bertin B, Renaud Y, Aradhya R, Jagla K, Junion G. TRAP-rc, Translating Ribosome Affinity Purification from Rare Cell Populations of Drosophila Embryos. J Vis Exp 2015. [PMID: 26381166 PMCID: PMC4692598 DOI: 10.3791/52985] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Measuring levels of mRNAs in the process of translation in individual cells provides information on the proteins involved in cellular functions at a given point in time. The protocol dubbed Translating Ribosome Affinity Purification (TRAP) is able to capture this mRNA translation process in a cell-type-specific manner. Based on the affinity purification of polysomes carrying a tagged ribosomal subunit, TRAP can be applied to translatome analyses in individual cells, making it possible to compare cell types during the course of developmental processes or to track disease development progress and the impact of potential therapies at molecular level. Here we report an optimized version of the TRAP protocol, called TRAP-rc (rare cells), dedicated to identifying engaged-in-translation RNAs from rare cell populations. TRAP-rc was validated using the Gal4/UAS targeting system in a restricted population of muscle cells in Drosophila embryos. This novel protocol allows the recovery of cell-type-specific RNA in sufficient quantities for global gene expression analytics such as microarrays or RNA-seq. The robustness of the protocol and the large collections of Gal4 drivers make TRAP-rc a highly versatile approach with potential applications in cell-specific genome-wide studies.
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80
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Hallier B, Hoffmann J, Roeder T, Tögel M, Meyer H, Paululat A. The bHLH Transcription Factor Hand Regulates the Expression of Genes Critical to Heart and Muscle Function in Drosophila melanogaster. PLoS One 2015; 10:e0134204. [PMID: 26252215 PMCID: PMC4529270 DOI: 10.1371/journal.pone.0134204] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 07/08/2015] [Indexed: 11/29/2022] Open
Abstract
Hand proteins belong to the highly conserved family of basic Helix-Loop-Helix transcription factors and are critical to distinct developmental processes, including cardiogenesis and neurogenesis in vertebrates. In Drosophila melanogaster a single orthologous hand gene is expressed with absence of the respective protein causing semilethality during early larval instars. Surviving adult animals suffer from shortened lifespan associated with a disorganized myofibrillar structure being apparent in the dorsal vessel, the wing hearts and in midgut tissue. Based on these data, the major biological significance of Hand seems to be related to muscle development, maintenance or function; however, up to now the physiological basis for Hand functionality remains elusive. Thus, the identification of genes whose expression is, directly or indirectly, regulated by Hand has considerable relevance with respect to understanding its biological functionality in flies and vertebrates. Beneficially, hand mutants are viable and exhibit affected tissues, which renders Drosophila an ideal model to investigate up- or downregulated target genes by a comparative microarray approach focusing on the respective tissues from mutant specimens. Our present work reveals for the first time that Drosophila Hand regulates the expression of numerous genes of diverse physiological relevancy, including distinct factors required for proper muscle development and function such as Zasp52 or Msp-300. These results relate Hand activity to muscle integrity and functionality and may thus be highly beneficial to the evaluation of corresponding hand phenotypes.
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Affiliation(s)
- Benjamin Hallier
- Department of Zoology/Developmental Biology, University of Osnabrück, 49069 Osnabrück, Germany
| | - Julia Hoffmann
- Department of Animal Physiology, University of Kiel, 24098 Kiel, Germany
| | - Thomas Roeder
- Department of Animal Physiology, University of Kiel, 24098 Kiel, Germany
| | - Markus Tögel
- Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Heiko Meyer
- Department of Zoology/Developmental Biology, University of Osnabrück, 49069 Osnabrück, Germany
| | - Achim Paululat
- Department of Zoology/Developmental Biology, University of Osnabrück, 49069 Osnabrück, Germany
- * E-mail:
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81
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Doggett K, Turkel N, Willoughby LF, Ellul J, Murray MJ, Richardson HE, Brumby AM. BTB-Zinc Finger Oncogenes Are Required for Ras and Notch-Driven Tumorigenesis in Drosophila. PLoS One 2015. [PMID: 26207831 PMCID: PMC4514741 DOI: 10.1371/journal.pone.0132987] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
During tumorigenesis, pathways that promote the epithelial-to-mesenchymal transition (EMT) can both facilitate metastasis and endow tumor cells with cancer stem cell properties. To gain a greater understanding of how these properties are interlinked in cancers we used Drosophila epithelial tumor models, which are driven by orthologues of human oncogenes (activated alleles of Ras and Notch) in cooperation with the loss of the cell polarity regulator, scribbled (scrib). Within these tumors, both invasive, mesenchymal-like cell morphology and continual tumor overgrowth, are dependent upon Jun N-terminal kinase (JNK) activity. To identify JNK-dependent changes within the tumors we used a comparative microarray analysis to define a JNK gene signature common to both Ras and Notch-driven tumors. Amongst the JNK-dependent changes was a significant enrichment for BTB-Zinc Finger (ZF) domain genes, including chronologically inappropriate morphogenesis (chinmo). chinmo was upregulated by JNK within the tumors, and overexpression of chinmo with either RasV12 or Nintra was sufficient to promote JNK-independent epithelial tumor formation in the eye/antennal disc, and, in cooperation with RasV12, promote tumor formation in the adult midgut epithelium. Chinmo primes cells for oncogene-mediated transformation through blocking differentiation in the eye disc, and promoting an escargot-expressing stem or enteroblast cell state in the adult midgut. BTB-ZF genes are also required for Ras and Notch-driven overgrowth of scrib mutant tissue, since, although loss of chinmo alone did not significantly impede tumor development, when loss of chinmo was combined with loss of a functionally related BTB-ZF gene, abrupt, tumor overgrowth was significantly reduced. abrupt is not a JNK-induced gene, however, Abrupt is present in JNK-positive tumor cells, consistent with a JNK-associated oncogenic role. As some mammalian BTB-ZF proteins are also highly oncogenic, our work suggests that EMT-promoting signals in human cancers could similarly utilize networks of these proteins to promote cancer stem cell states.
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Affiliation(s)
- Karen Doggett
- Cell Cycle and Development Laboratory, Research Division, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
- * E-mail:
| | - Nezaket Turkel
- Cell Cycle and Development Laboratory, Research Division, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
| | - Lee F. Willoughby
- Cell Cycle and Development Laboratory, Research Division, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
| | - Jason Ellul
- Bioinformatics Core Facility, Research Division, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
| | - Michael J. Murray
- School of Biosciences, University of Melbourne, 1–100 Grattan Street, Parkville, Melbourne, Victoria, Australia
| | - Helena E. Richardson
- Cell Cycle and Development Laboratory, Research Division, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, 1–100 Grattan Street, Parkville, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, 1–100 Grattan Street, Parkville, Melbourne, Victoria, Australia
- School of Molecular Sciences, La Trobe University, Victoria, Australia
| | - Anthony M. Brumby
- Cell Cycle and Development Laboratory, Research Division, Peter MacCallum Cancer Centre, 7 St Andrew’s Place, East Melbourne, Melbourne, Victoria, Australia
- School of Biosciences, University of Melbourne, 1–100 Grattan Street, Parkville, Melbourne, Victoria, Australia
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de Taffin M, Carrier Y, Dubois L, Bataillé L, Painset A, Le Gras S, Jost B, Crozatier M, Vincent A. Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory Networks. PLoS One 2015. [PMID: 26204530 PMCID: PMC4512700 DOI: 10.1371/journal.pone.0133387] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Collier, the single Drosophila COE (Collier/EBF/Olf-1) transcription factor, is required in several developmental processes, including head patterning and specification of muscle and neuron identity during embryogenesis. To identify direct Collier (Col) targets in different cell types, we used ChIP-seq to map Col binding sites throughout the genome, at mid-embryogenesis. In vivo Col binding peaks were associated to 415 potential direct target genes. Gene Ontology analysis revealed a strong enrichment in proteins with DNA binding and/or transcription-regulatory properties. Characterization of a selection of candidates, using transgenic CRM-reporter assays, identified direct Col targets in dorso-lateral somatic muscles and specific neuron types in the central nervous system. These data brought new evidence that Col direct control of the expression of the transcription regulators apterous and eyes-absent (eya) is critical to specifying neuronal identities. They also showed that cross-regulation between col and eya in muscle progenitor cells is required for specification of muscle identity, revealing a new parallel between the myogenic regulatory networks operating in Drosophila and vertebrates. Col regulation of eya, both in specific muscle and neuronal lineages, may illustrate one mechanism behind the evolutionary diversification of Col biological roles.
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Affiliation(s)
- Mathilde de Taffin
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
| | - Yannick Carrier
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
| | - Laurence Dubois
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
| | - Laetitia Bataillé
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
| | - Anaïs Painset
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
- Plate-forme bio-informatique Genotoul/MIA-T, INRA, Borde Rouge, 31326, Castanet-Tolosan, France
| | - Stéphanie Le Gras
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université de Strasbourg, 67404, Illkirch, France
| | - Bernard Jost
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université de Strasbourg, 67404, Illkirch, France
| | - Michèle Crozatier
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
| | - Alain Vincent
- Centre de Biologie du Développement, UMR 5547 CNRS Université de Toulouse 3, 118 route de Narbonne, F-31062, Toulouse cedex 09, France
- * E-mail:
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83
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Dobi KC, Schulman VK, Baylies MK. Specification of the somatic musculature in Drosophila. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2015; 4:357-75. [PMID: 25728002 PMCID: PMC4456285 DOI: 10.1002/wdev.182] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/16/2015] [Accepted: 02/04/2015] [Indexed: 11/09/2022]
Abstract
The somatic muscle system formed during Drosophila embryogenesis is required for larvae to hatch, feed, and crawl. This system is replaced in the pupa by a new adult muscle set, responsible for activities such as feeding, walking, and flight. Both the larval and adult muscle systems are comprised of distinct muscle fibers to serve these specific motor functions. In this way, the Drosophila musculature is a valuable model for patterning within a single tissue: while all muscle cells share properties such as the contractile apparatus, properties such as size, position, and number of nuclei are unique for a particular muscle. In the embryo, diversification of muscle fibers relies first on signaling cascades that pattern the mesoderm. Subsequently, the combinatorial expression of specific transcription factors leads muscle fibers to adopt particular sizes, shapes, and orientations. Adult muscle precursors (AMPs), set aside during embryonic development, proliferate during the larval phases and seed the formation of the abdominal, leg, and flight muscles in the adult fly. Adult muscle fibers may either be formed de novo from the fusion of the AMPs, or are created by the binding of AMPs to an existing larval muscle. While less is known about adult muscle specification compared to the larva, expression of specific transcription factors is also important for its diversification. Increasingly, the mechanisms required for the diversification of fly muscle have found parallels in vertebrate systems and mark Drosophila as a robust model system to examine questions about how diverse cell types are generated within an organism.
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Affiliation(s)
- Krista C. Dobi
- Program in Developmental Biology, Sloan Kettering Institute, New York, NY, USA
| | - Victoria K. Schulman
- Program in Developmental Biology, Sloan Kettering Institute, New York, NY, USA
- Cell and Developmental Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Mary K. Baylies
- Program in Developmental Biology, Sloan Kettering Institute, New York, NY, USA
- Cell and Developmental Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
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84
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Using transgenic reporter assays to functionally characterize enhancers in animals. Genomics 2015; 106:185-192. [PMID: 26072435 DOI: 10.1016/j.ygeno.2015.06.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 05/11/2015] [Accepted: 06/09/2015] [Indexed: 11/21/2022]
Abstract
Enhancers or cis-regulatory modules play an instructive role in regulating gene expression during animal development and in response to the environment. Despite their importance, we only have an incomplete map of enhancers in the genome and our understanding of the mechanisms governing their function is still limited. Recent advances in genomics provided powerful tools to generate genome-wide maps of potential enhancers. However, most of these methods are based on indirect measures of enhancer activity and have to be followed by functional testing. Animal transgenesis has been a valuable method to functionally test and characterize enhancers in vivo. In this review I discuss how different transgenic strategies are utilized to characterize enhancers in model organisms focusing on studies in Drosophila and mouse. I will further discuss recent large-scale transgenic efforts to systematically identify and catalog enhancers as well as highlight the challenges and future directions in the field.
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85
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Brunetti TM, Fremin BJ, Cripps RM. Identification of singles bar as a direct transcriptional target of Drosophila Myocyte enhancer factor-2 and a regulator of adult myoblast fusion. Dev Biol 2015; 401:299-309. [PMID: 25797154 PMCID: PMC4424145 DOI: 10.1016/j.ydbio.2015.02.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 01/29/2015] [Accepted: 02/14/2015] [Indexed: 11/17/2022]
Abstract
In Drosophila, myoblast fusion is a conserved process in which founder cells (FCs) and fusion competent myoblasts (FCMs) fuse to form a syncytial muscle fiber. Mutants for the myogenic regulator Myocyte enhancer factor-2 (MEF2) show a failure of myoblast fusion, indicating that MEF2 regulates the fusion process. Indeed, chromatin immunoprecipitation studies show that several genes involved in myoblast fusion are bound by MEF2 during embryogenesis. Of these, the MARVEL domain gene singles bar (sing), is down-regulated in MEF2 knockdown pupae, and has five consensus MEF2 binding sites within a 9000-bp region. To determine if MEF2 is an essential and direct regulator of sing during pupal muscle development, we identified a 315-bp myoblast enhancer of sing. This enhancer was active during myoblast fusion, and mutation of two MEF2 sites significantly decreased enhancer activity. We show that lack of sing expression resulted in adult lethality and muscle loss, due to a failure of fusion during the pupal stage. Additionally, we sought to determine if sing was required in either FCs or FCMs to support fusion. Interestingly, knockdown of sing in either population did not significantly affect fusion, however, knockdown in both FCs and FCMs resulted in muscles with significantly reduced nuclei numbers, provisionally indicating that sing function is required in either cell type, but not both. Finally, we found that MEF2 regulated sing expression at the embryonic stage through the same 315-bp enhancer, indicating that sing is a MEF2 target at both critical stages of myoblast fusion. Our studies define for the first time how MEF2 directly controls fusion at multiple stages of the life cycle, and provide further evidence that the mechanisms of fusion characterized in Drosophila embryos is also used in the formation of the more complex adult muscles.
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Affiliation(s)
- Tonya M Brunetti
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Brayon J Fremin
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Richard M Cripps
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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86
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Sachs L, Chen YT, Drechsler A, Lynch JA, Panfilio KA, Lässig M, Berg J, Roth S. Dynamic BMP signaling polarized by Toll patterns the dorsoventral axis in a hemimetabolous insect. eLife 2015; 4:e05502. [PMID: 25962855 PMCID: PMC4423117 DOI: 10.7554/elife.05502] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 04/12/2015] [Indexed: 11/13/2022] Open
Abstract
Toll-dependent patterning of the dorsoventral axis in Drosophila represents one of the best understood gene regulatory networks. However, its evolutionary origin has remained elusive. Outside the insects Toll is not known for a patterning function, but rather for a role in pathogen defense. Here, we show that in the milkweed bug Oncopeltus fasciatus, whose lineage split from Drosophila's more than 350 million years ago, Toll is only required to polarize a dynamic BMP signaling network. A theoretical model reveals that this network has self-regulatory properties and that shallow Toll signaling gradients are sufficient to initiate axis formation. Such gradients can account for the experimentally observed twinning of insect embryos upon egg fragmentation and might have evolved from a state of uniform Toll activity associated with protecting insect eggs against pathogens.
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Affiliation(s)
- Lena Sachs
- Institute for Developmental Biology, University of Cologne, Köln, Germany
| | - Yen-Ta Chen
- Institute for Developmental Biology, University of Cologne, Köln, Germany
| | - Axel Drechsler
- Institute for Developmental Biology, University of Cologne, Köln, Germany
- Bundesministerium für Umwelt, Naturschutz, Bau und Reaktorsicherheit, Bonn, Germany
| | - Jeremy A Lynch
- Institute for Developmental Biology, University of Cologne, Köln, Germany
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, United States
| | - Kristen A Panfilio
- Institute for Developmental Biology, University of Cologne, Köln, Germany
| | - Michael Lässig
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany
| | - Johannes Berg
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany
| | - Siegfried Roth
- Institute for Developmental Biology, University of Cologne, Köln, Germany
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87
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O’Connell MD, Reeves GT. The presence of nuclear cactus in the early Drosophila embryo may extend the dynamic range of the dorsal gradient. PLoS Comput Biol 2015; 11:e1004159. [PMID: 25879657 PMCID: PMC4400154 DOI: 10.1371/journal.pcbi.1004159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/28/2015] [Indexed: 11/18/2022] Open
Abstract
In a developing embryo, the spatial distribution of a signaling molecule, or a morphogen gradient, has been hypothesized to carry positional information to pattern tissues. Recent measurements of morphogen distribution have allowed us to subject this hypothesis to rigorous physical testing. In the early Drosophila embryo, measurements of the morphogen Dorsal, which is a transcription factor responsible for initiating the earliest zygotic patterns along the dorsal-ventral axis, have revealed a gradient that is too narrow to pattern the entire axis. In this study, we use a mathematical model of Dorsal dynamics, fit to experimental data, to determine the ability of the Dorsal gradient to regulate gene expression across the entire dorsal-ventral axis. We found that two assumptions are required for the model to match experimental data in both Dorsal distribution and gene expression patterns. First, we assume that Cactus, an inhibitor that binds to Dorsal and prevents it from entering the nuclei, must itself be present in the nuclei. And second, we assume that fluorescence measurements of Dorsal reflect both free Dorsal and Cactus-bound Dorsal. Our model explains the dynamic behavior of the Dorsal gradient at lateral and dorsal positions of the embryo, the ability of Dorsal to regulate gene expression across the entire dorsal-ventral axis, and the robustness of gene expression to stochastic effects. Our results have a general implication for interpreting fluorescence-based measurements of signaling molecules.
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Affiliation(s)
- Michael D. O’Connell
- North Carolina State University Department of Chemical and Biomolecular Engineering, Raleigh, North Carolina, United States of America
| | - Gregory T. Reeves
- North Carolina State University Department of Chemical and Biomolecular Engineering, Raleigh, North Carolina, United States of America
- * E-mail:
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88
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Chang AT, Liu Y, Ayyanathan K, Benner C, Jiang Y, Prokop JW, Paz H, Wang D, Li HR, Fu XD, Rauscher FJ, Yang J. An evolutionarily conserved DNA architecture determines target specificity of the TWIST family bHLH transcription factors. Genes Dev 2015; 29:603-16. [PMID: 25762439 PMCID: PMC4378193 DOI: 10.1101/gad.242842.114] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Basic helix-loop-helix (bHLH) transcription factors recognize the canonical E-box (CANNTG) to regulate gene transcription; however, given the prevalence of E-boxes in a genome, it has been puzzling how individual bHLH proteins selectively recognize E-box sequences on their targets. TWIST is a bHLH transcription factor that promotes epithelial-mesenchymal transition (EMT) during development and tumor metastasis. High-resolution mapping of TWIST occupancy in human and Drosophila genomes reveals that TWIST, but not other bHLH proteins, recognizes a unique double E-box motif with two E-boxes spaced preferentially by 5 nucleotides. Using molecular modeling and binding kinetic analyses, we found that the strict spatial configuration in the double E-box motif aligns two TWIST-E47 dimers on the same face of DNA, thus providing a high-affinity site for a highly stable intramolecular tetramer. Biochemical analyses showed that the WR domain of TWIST dimerizes to mediate tetramer formation, which is functionally required for TWIST-induced EMT. These results uncover a novel mechanism for a bHLH transcription factor to recognize a unique spatial configuration of E-boxes to achieve target specificity. The WR-WR domain interaction uncovered here sets an example of target gene specificity of a bHLH protein being controlled allosterically by a domain outside of the bHLH region.
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Affiliation(s)
- Andrew T Chang
- Department of Pharmacology, University of California at San Diego, La Jolla, California, 92093, USA; The Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, California, 92093, USA
| | - Yuanjie Liu
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | | | - Chris Benner
- Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Yike Jiang
- Department of Pharmacology, University of California at San Diego, La Jolla, California, 92093, USA; The Biological Science Graduate Program, University of California at San Diego, La Jolla, California, 92093, USA
| | - Jeremy W Prokop
- Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
| | - Helicia Paz
- Department of Pharmacology, University of California at San Diego, La Jolla, California, 92093, USA
| | - Dong Wang
- Department of Cell and Molecular Medicine, University of California at San Diego, La Jolla, California, 92093, USA
| | - Hai-Ri Li
- Department of Cell and Molecular Medicine, University of California at San Diego, La Jolla, California, 92093, USA
| | - Xiang-Dong Fu
- Department of Cell and Molecular Medicine, University of California at San Diego, La Jolla, California, 92093, USA
| | | | - Jing Yang
- Department of Pharmacology, University of California at San Diego, La Jolla, California, 92093, USA; Department of Pediatrics, University of California at San Diego, La Jolla, California, 92093, USA
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89
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He Q, Johnston J, Zeitlinger J. ChIP-nexus enables improved detection of in vivo transcription factor binding footprints. Nat Biotechnol 2015; 33:395-401. [PMID: 25751057 PMCID: PMC4390430 DOI: 10.1038/nbt.3121] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 12/08/2014] [Indexed: 11/13/2022]
Abstract
Understanding how eukaryotic enhancers are bound and regulated by specific combinations of transcription factors is still a major challenge. To better map transcription factor binding genome-wide at nucleotide resolution in vivo, we have developed a robust ChIP-exo protocol called ChIP experiments with nucleotide resolution through exonuclease, unique barcode and single ligation (ChIP-nexus), which utilizes an efficient DNA self-circularization step during library preparation. Application of ChIP-nexus to four proteins—human TBP and Drosophila NFkB, Twist and Max— demonstrates that it outperforms existing ChIP protocols in resolution and specificity, pinpoints relevant binding sites within enhancers containing multiple binding motifs and allows the analysis of in vivo binding specificities. Notably, we show that Max frequently interacts with DNA sequences next to its motif, and that this binding pattern correlates with local DNA sequence features such as DNA shape. ChIP-nexus will be broadly applicable to studying in vivo transcription factor binding specificity and its relationship to cis-regulatory changes in humans and model organisms.
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Affiliation(s)
- Qiye He
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Jeff Johnston
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
| | - Julia Zeitlinger
- 1] Stowers Institute for Medical Research, Kansas City, Missouri, USA. [2] Department of Pathology, Kansas University Medical Center, Kansas City, Kansas, USA
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90
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Elwell JA, Lovato TL, Adams MM, Baca EM, Lee T, Cripps RM. The myogenic repressor gene Holes in muscles is a direct transcriptional target of Twist and Tinman in the Drosophila embryonic mesoderm. Dev Biol 2015; 400:266-76. [PMID: 25704510 DOI: 10.1016/j.ydbio.2015.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 01/14/2015] [Accepted: 02/10/2015] [Indexed: 11/19/2022]
Abstract
Understanding the regulatory circuitry controlling myogenesis is critical to understanding developmental mechanisms and developmentally-derived diseases. We analyzed the transcriptional regulation of a Drosophila myogenic repressor gene, Holes in muscles (Him). Previously, Him was shown to inhibit Myocyte enhancer factor-2 (MEF2) activity, and is expressed in myoblasts but not differentiating myotubes. We demonstrate that different phases of Him embryonic expression arises through the actions of different enhancers, and we characterize the enhancer required for its early mesoderm expression. This Him early mesoderm enhancer contains two conserved binding sites for the basic helix-loop-helix regulator Twist, and one binding site for the NK homeodomain protein Tinman. The sites for both proteins are required for enhancer activity in early embryos. Twist and Tinman activate the enhancer in tissue culture assays, and ectopic expression of either factor is sufficient to direct ectopic expression of a Him-lacZ reporter, or of the endogenous Him gene. Moreover, sustained expression of twist in the mesoderm up-regulates mesodermal Him expression in late embryos. Our findings provide a model to define mechanistically how Twist can both promotes myogenesis through direct activation of Mef2, and can place a brake on myogenesis, through direct activation of Him.
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Affiliation(s)
- Jennifer A Elwell
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - TyAnna L Lovato
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Melanie M Adams
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Erica M Baca
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Thai Lee
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Richard M Cripps
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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91
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Meganathan K, Sotiriadou I, Natarajan K, Hescheler J, Sachinidis A. Signaling molecules, transcription growth factors and other regulators revealed from in-vivo and in-vitro models for the regulation of cardiac development. Int J Cardiol 2015; 183:117-28. [PMID: 25662074 DOI: 10.1016/j.ijcard.2015.01.049] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/19/2014] [Accepted: 01/25/2015] [Indexed: 02/08/2023]
Abstract
Several in-vivo heart developmental models have been applied to decipher the cardiac developmental patterning encompassing early, dorsal, cardiac and visceral mesoderm as well as various transcription factors such as Gata, Hand, Tin, Dpp, Pnr. The expression of cardiac specific transcription factors, such as Gata4, Tbx5, Tbx20, Tbx2, Tbx3, Mef2c, Hey1 and Hand1 are of fundamental significance for the in-vivo cardiac development. Not only the transcription factors, but also the signaling molecules involved in cardiac development were conserved among various species. Enrichment of the bone morphogenic proteins (BMPs) in the anterior lateral plate mesoderm is essential for the initiation of myocardial differentiation and the cardiac developmental process. Moreover, the expression of a number of cardiac transcription factors and structural genes initiate cardiac differentiation in the medial mesoderm. Other signaling molecules such as TGF-beta, IGF-1/2 and the fibroblast growth factor (FGF) play a significant role in cardiac repair/regeneration, ventricular heart development and specification of early cardiac mesoderm, respectively. The role of the Wnt signaling in cardiac development is still controversial discussed, as in-vitro results differ dramatically in relation to the animal models. Embryonic stem cells (ESC) were utilized as an important in-vitro model for the elucidation of the cardiac developmental processes since they can be easily manipulated by numerous signaling molecules, growth factors, small molecules and genetic manipulation. Finally, in the present review the dynamic role of the long noncoding RNA and miRNAs in the regulation of cardiac development are summarized and discussed.
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Affiliation(s)
- Kesavan Meganathan
- Center of Physiology and Pathophysiology, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Isaia Sotiriadou
- Center of Physiology and Pathophysiology, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Karthick Natarajan
- Center of Physiology and Pathophysiology, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Jürgen Hescheler
- Center of Physiology and Pathophysiology, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany
| | - Agapios Sachinidis
- Center of Physiology and Pathophysiology, Institute of Neurophysiology and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Germany.
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92
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Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference. Cell Rep 2014; 9:2290-303. [DOI: 10.1016/j.celrep.2014.11.038] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/24/2014] [Accepted: 11/22/2014] [Indexed: 11/20/2022] Open
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93
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Özüak O, Buchta T, Roth S, Lynch JA. Dorsoventral polarity of the Nasonia embryo primarily relies on a BMP gradient formed without input from Toll. Curr Biol 2014; 24:2393-8. [PMID: 25308075 DOI: 10.1016/j.cub.2014.08.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/12/2014] [Accepted: 08/14/2014] [Indexed: 10/24/2022]
Abstract
In Drosophila, Toll signaling leads to a gradient of nuclear uptake of Dorsal with a peak at the ventral egg pole and is the source for dorsoventral (DV) patterning and polarity of the embryo. In contrast, Toll signaling plays no role in embryonic patterning in most animals, while BMP signaling plays the major role. In order to understand the origin of the novelty of the Drosophila system, we have examined DV patterning in Nasonia vitripennis (Nv), a representative of the Hymenoptera and thus the most ancient branch points within the Holometabola. We have previously shown that while the expression of several conserved DV patterning genes is almost identical in Nasonia and Drosophila embryos at the onset of gastrulation, the ways these patterns evolve in early embryogenesis are very different from what is seen in Drosophila or the beetle Tribolium. In contrast to Drosophila or Tribolium, we find that wasp Toll has a very limited ventral role, whereas BMP is required for almost all DV polarity of the embryo, and these two signaling systems act independently of each other to generate DV polarity. This result gives insights into how the Toll pathway could have usurped a BMP-based DV patterning system in insects. In addition, our work strongly suggests that a novel system for BMP activity gradient formation must be employed in the wasp, since orthologs of crucial components of the fly system are either missing entirely or lack function in the embryo.
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Affiliation(s)
- Orhan Özüak
- Institute for Developmental Biology, University of Cologne, 50674 Cologne, Germany
| | - Thomas Buchta
- Institute for Developmental Biology, University of Cologne, 50674 Cologne, Germany
| | - Siegfried Roth
- Institute for Developmental Biology, University of Cologne, 50674 Cologne, Germany.
| | - Jeremy A Lynch
- Institute for Developmental Biology, University of Cologne, 50674 Cologne, Germany.
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94
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Harwood BN, Draper I, Kopin AS. Targeted inactivation of the rickets receptor in muscle compromises Drosophila viability. ACTA ACUST UNITED AC 2014; 217:4091-8. [PMID: 25278473 DOI: 10.1242/jeb.110098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Bursicon is a hormone that modulates wing expansion, cuticle hardening and melanization in Drosophila melanogaster. Bursicon activity is mediated through its cognate G protein-coupled receptor (GPCR), rickets. We have developed a membrane-tethered bursicon construct that enables spatial modulation of rickets-mediated physiology in transgenic flies. Ubiquitous expression of tethered bursicon throughout development results in arrest at the pupal stage. The few organisms that eclose fail to undergo wing expansion. These phenotypes suggest that expression of tethered bursicon inhibits rickets-mediated function. Consistent with this hypothesis, we show in vitro that sustained stimulation of rickets by tethered bursicon leads to receptor desensitization. Furthermore, tissue-specific expression of the tethered bursicon inhibitor unraveled a critical role for rickets in a subset of adult muscles. Taken together, our findings highlight the utility of membrane-tethered inhibitors as important genetic/pharmacological tools to dissect the tissue-specific roles of GPCRs in vivo.
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Affiliation(s)
- Benjamin N Harwood
- Tufts Medical Center, Molecular Cardiology Research Institute, Molecular Pharmacology Research Center, 800 Washington St, Box 7703, Boston, MA 02111, USA Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, 145 Harrison Avenue, Boston, MA 02111, USA
| | - Isabelle Draper
- Tufts Medical Center, Molecular Cardiology Research Institute, Molecular Pharmacology Research Center, 800 Washington St, Box 7703, Boston, MA 02111, USA
| | - Alan S Kopin
- Tufts Medical Center, Molecular Cardiology Research Institute, Molecular Pharmacology Research Center, 800 Washington St, Box 7703, Boston, MA 02111, USA Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, 145 Harrison Avenue, Boston, MA 02111, USA
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95
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Boukhatmi H, Schaub C, Bataillé L, Reim I, Frendo JL, Frasch M, Vincent A. An Org-1-Tup transcriptional cascade reveals different types of alary muscles connecting internal organs in Drosophila. Development 2014; 141:3761-71. [PMID: 25209244 DOI: 10.1242/dev.111005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The T-box transcription factor Tbx1 and the LIM-homeodomain transcription factor Islet1 are key components in regulatory circuits that generate myogenic and cardiogenic lineage diversity in chordates. We show here that Org-1 and Tup, the Drosophila orthologs of Tbx1 and Islet1, are co-expressed and required for formation of the heart-associated alary muscles (AMs) in the abdomen. The same holds true for lineage-related muscles in the thorax that have not been described previously, which we name thoracic alary-related muscles (TARMs). Lineage analyses identified the progenitor cell for each AM and TARM. Three-dimensional high-resolution analyses indicate that AMs and TARMs connect the exoskeleton to the aorta/heart and to different regions of the midgut, respectively, and surround-specific tracheal branches, pointing to an architectural role in the internal anatomy of the larva. Org-1 controls tup expression in the AM/TARM lineage by direct binding to two regulatory sites within an AM/TARM-specific cis-regulatory module, tupAME. The contributions of Org-1 and Tup to the specification of Drosophila AMs and TARMs provide new insights into the transcriptional control of Drosophila larval muscle diversification and highlight new parallels with gene regulatory networks involved in the specification of cardiopharyngeal mesodermal derivatives in chordates.
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Affiliation(s)
- Hadi Boukhatmi
- Université de Toulouse 3, Centre de Biologie du Développement, UMR 5547 CNRS and FRBT, 118 route de Narbonne, Toulouse F-31062, Cedex 09, France
| | - Christoph Schaub
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Biology, Division of Developmental Biology, Staudtstraβe 5, Erlangen 91058, Germany
| | - Laetitia Bataillé
- Université de Toulouse 3, Centre de Biologie du Développement, UMR 5547 CNRS and FRBT, 118 route de Narbonne, Toulouse F-31062, Cedex 09, France
| | - Ingolf Reim
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Biology, Division of Developmental Biology, Staudtstraβe 5, Erlangen 91058, Germany
| | - Jean-Louis Frendo
- Université de Toulouse 3, Centre de Biologie du Développement, UMR 5547 CNRS and FRBT, 118 route de Narbonne, Toulouse F-31062, Cedex 09, France
| | - Manfred Frasch
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Biology, Division of Developmental Biology, Staudtstraβe 5, Erlangen 91058, Germany
| | - Alain Vincent
- Université de Toulouse 3, Centre de Biologie du Développement, UMR 5547 CNRS and FRBT, 118 route de Narbonne, Toulouse F-31062, Cedex 09, France
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96
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Ciglar L, Girardot C, Wilczyński B, Braun M, Furlong EEM. Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis. Development 2014; 141:2633-43. [PMID: 24961800 PMCID: PMC4146391 DOI: 10.1242/dev.101956] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Molecular models of cell fate specification typically focus on the activation of specific lineage programs. However, the concurrent repression of unwanted transcriptional networks is also essential to stabilize certain cellular identities, as shown in a number of diverse systems and phyla. Here, we demonstrate that this dual requirement also holds true in the context of Drosophila myogenesis. By integrating genetics and genomics, we identified a new role for the pleiotropic transcriptional repressor Tramtrack69 in myoblast specification. Drosophila muscles are formed through the fusion of two discrete cell types: founder cells (FCs) and fusion-competent myoblasts (FCMs). When tramtrack69 is removed, FCMs appear to adopt an alternative muscle FC-like fate. Conversely, ectopic expression of this repressor phenocopies muscle defects seen in loss-of-function lame duck mutants, a transcription factor specific to FCMs. This occurs through Tramtrack69-mediated repression in FCMs, whereas Lame duck activates a largely distinct transcriptional program in the same cells. Lineage-specific factors are therefore not sufficient to maintain FCM identity. Instead, their identity appears more plastic, requiring the combination of instructive repressive and activating programs to stabilize cell fate.
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Affiliation(s)
- Lucia Ciglar
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany
| | - Charles Girardot
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany
| | - Bartek Wilczyński
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany
| | - Martina Braun
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany
| | - Eileen E M Furlong
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany
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97
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Zhang W, Li R, Feng D, Chernikov A, Chrisochoides N, Osgood C, Ji S. Evolutionary soft co-clustering: formulations, algorithms, and applications. Data Min Knowl Discov 2014. [DOI: 10.1007/s10618-014-0375-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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98
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Zhang X, Ma W, Cui J, Yao H, Zhou H, Ge Y, Xiao L, Hu X, Liu BH, Yang J, Li YY, Chen S, Eaves CJ, Wu D, Zhao Y. Regulation of p21 by TWIST2 contributes to its tumor-suppressor function in human acute myeloid leukemia. Oncogene 2014; 34:3000-10. [DOI: 10.1038/onc.2014.241] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 06/08/2014] [Accepted: 06/15/2014] [Indexed: 12/18/2022]
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99
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Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification. Nat Commun 2014; 5:4322. [PMID: 25005894 DOI: 10.1038/ncomms5322] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 06/06/2014] [Indexed: 12/11/2022] Open
Abstract
Head specification by the head-selector gene, orthodenticle (otx), is highly conserved among bilaterian lineages. However, the molecular mechanisms by which Otx and other transcription factors (TFs) interact with the genome to direct head formation are largely unknown. Here we employ ChIP-seq and RNA-seq approaches in Xenopus tropicalis gastrulae and find that occupancy of the corepressor, TLE/Groucho, is a better indicator of tissue-specific cis-regulatory modules (CRMs) than the coactivator p300, during early embryonic stages. On the basis of TLE binding and comprehensive CRM profiling, we define two distinct types of Otx2- and TLE-occupied CRMs. Using these devices, Otx2 and other head organizer TFs (for example, Lim1/Lhx1 (activator) or Goosecoid (repressor)) are able to upregulate or downregulate a large battery of target genes in the head organizer. An underlying principle is that Otx marks target genes for head specification to be regulated positively or negatively by partner TFs through specific types of CRMs.
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100
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Potier D, Seyres D, Guichard C, Iche-Torres M, Aerts S, Herrmann C, Perrin L. Identification of cis-regulatory modules encoding temporal dynamics during development. BMC Genomics 2014; 15:534. [PMID: 24972496 PMCID: PMC4097164 DOI: 10.1186/1471-2164-15-534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/13/2014] [Indexed: 12/02/2022] Open
Abstract
Background Developmental transcriptional regulatory networks are circuits of transcription factors (TFs) and cis-acting DNA elements (Cis Regulatory Modules, CRMs) that dynamically control expression of downstream genes. Comprehensive knowledge of these networks is an essential step towards our understanding of developmental processes. However, this knowledge is mostly based on genome-wide mapping of transcription factor binding sites, and therefore requires prior knowledge regarding the TFs involved in the network. Results Focusing on how temporal control of gene expression is integrated within a developmental network, we applied an in silico approach to discover regulatory motifs and CRMs of co-expressed genes, with no prior knowledge about the involved TFs. Our aim was to identify regulatory motifs and potential trans-acting factors which regulate the temporal expression of co-expressed gene sets during a particular process of organogenesis, namely adult heart formation in Drosophila. Starting from whole genome tissue specific expression dynamics, we used an in silico method, cisTargetX, to predict TF binding motifs and CRMs. Potential Nuclear Receptor (NR) binding motifs were predicted to control the temporal expression profile of a gene set with increased expression levels during mid metamorphosis. The predicted CRMs and NR motifs were validated in vivo by reporter gene essays. In addition, we provide evidence that three NRs modulate CRM activity and behave as temporal regulators of target enhancers. Conclusions Our approach was successful in identifying CRMs and potential TFs acting on the temporal regulation of target genes. In addition, our results suggest a modular architecture of the regulatory machinery, in which the temporal and spatial regulation can be uncoupled and encoded by distinct CRMs. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-534) contains supplementary material, which is available to authorized users.
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