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Knüppel R, Kuttenberger C, Ferreira-Cerca S. Toward Time-Resolved Analysis of RNA Metabolism in Archaea Using 4-Thiouracil. Front Microbiol 2017; 8:286. [PMID: 28286499 PMCID: PMC5323407 DOI: 10.3389/fmicb.2017.00286] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/13/2017] [Indexed: 11/13/2022] Open
Abstract
Archaea are widespread organisms colonizing almost every habitat on Earth. However, the molecular biology of archaea still remains relatively uncharacterized. RNA metabolism is a central cellular process, which has been extensively analyzed in both bacteria and eukarya. In contrast, analysis of RNA metabolism dynamic in archaea has been limited to date. To facilitate analysis of the RNA metabolism dynamic at a system-wide scale in archaea, we have established non-radioactive pulse labeling of RNA, using the nucleotide analog 4-thiouracil (4TU) in two commonly used model archaea: the halophile Euryarchaeota Haloferax volcanii, and the thermo-acidophile Crenarchaeota Sulfolobus acidocaldarius. In this work, we show that 4TU pulse labeling can be efficiently performed in these two organisms in a dose- and time-dependent manner. In addition, our results suggest that uracil prototrophy had no critical impact on the overall 4TU incorporation in RNA molecules. Accordingly, our work suggests that 4TU incorporation can be widely performed in archaea, thereby expanding the molecular toolkit to analyze archaeal gene expression network dynamic in unprecedented detail.
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Affiliation(s)
- Robert Knüppel
- Biochemistry III, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg Regensburg, Germany
| | - Corinna Kuttenberger
- Biochemistry III, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Biochemistry III, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg Regensburg, Germany
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52
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Monte E, Rosa-Garrido M, Vondriska TM, Wang J. Undiscovered Physiology of Transcript and Protein Networks. Compr Physiol 2016; 6:1851-1872. [PMID: 27783861 PMCID: PMC10751805 DOI: 10.1002/cphy.c160003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The past two decades have witnessed a rapid evolution in our ability to measure RNA and protein from biological systems. As a result, new principles have arisen regarding how information is processed in cells, how decisions are made, and the role of networks in biology. This essay examines this technological evolution, reviewing (and critiquing) the conceptual framework that has emerged to explain how RNA and protein networks control cellular function. We identify how future investigations into transcriptomes, proteomes, and other cellular networks will enable development of more robust, quantitative models of cellular behavior whilst also providing new avenues to use knowledge of biological networks to improve human health. © 2016 American Physiological Society. Compr Physiol 6:1851-1872, 2016.
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Affiliation(s)
- Emma Monte
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Manuel Rosa-Garrido
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Thomas M. Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Jessica Wang
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, USA
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53
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Cohen BL, Pisera A. Crinoid phylogeny: new interpretation of the main Permo-Triassic divergence, comparisons with echinoids and brachiopods, and EvoDevo interpretations of major morphological variations. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bernard L. Cohen
- University of Glasgow; Wolfson Link Building; Glasgow G12 8QQ UK
| | - Andrzej Pisera
- Institute of Paleobiology; Polish Academy of Sciences; ul. Twarda 51/55 00-818 Warszawa Poland
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54
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Morrison ES, Badyaev AV. Structuring evolution: biochemical networks and metabolic diversification in birds. BMC Evol Biol 2016; 16:168. [PMID: 27561312 PMCID: PMC5000421 DOI: 10.1186/s12862-016-0731-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 08/01/2016] [Indexed: 12/17/2022] Open
Abstract
Background Recurrence and predictability of evolution are thought to reflect the correspondence between genomic and phenotypic dimensions of organisms, and the connectivity in deterministic networks within these dimensions. Direct examination of the correspondence between opportunities for diversification imbedded in such networks and realized diversity is illuminating, but is empirically challenging because both the deterministic networks and phenotypic diversity are modified in the course of evolution. Here we overcome this problem by directly comparing the structure of a “global” carotenoid network – comprising of all known enzymatic reactions among naturally occurring carotenoids – with the patterns of evolutionary diversification in carotenoid-producing metabolic networks utilized by birds. Results We found that phenotypic diversification in carotenoid networks across 250 species was closely associated with enzymatic connectivity of the underlying biochemical network – compounds with greater connectivity occurred the most frequently across species and were the hotspots of metabolic pathway diversification. In contrast, we found no evidence for diversification along the metabolic pathways, corroborating findings that the utilization of the global carotenoid network was not strongly influenced by history in avian evolution. Conclusions The finding that the diversification in species-specific carotenoid networks is qualitatively predictable from the connectivity of the underlying enzymatic network points to significant structural determinism in phenotypic evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0731-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erin S Morrison
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
| | - Alexander V Badyaev
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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55
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Tintori SC, Osborne Nishimura E, Golden P, Lieb JD, Goldstein B. A Transcriptional Lineage of the Early C. elegans Embryo. Dev Cell 2016; 38:430-44. [PMID: 27554860 PMCID: PMC4999266 DOI: 10.1016/j.devcel.2016.07.025] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/19/2016] [Accepted: 07/27/2016] [Indexed: 12/30/2022]
Abstract
During embryonic development, cells must establish fates, morphologies, and behaviors in coordination with one another to form a functional body. A prevalent hypothesis for how this coordination is achieved is that each cell's fate and behavior is determined by a defined mixture of RNAs. Only recently has it become possible to measure the full suite of transcripts in a single cell. Here we quantify genome-wide mRNA abundance in each cell of the Caenorhabditis elegans embryo up to the 16-cell stage. We describe spatially dynamic expression, quantify cell-specific differential activation of the zygotic genome, and identify genes that were previously unappreciated as being critical for development. We present an interactive data visualization tool that allows broad access to our dataset. This genome-wide single-cell map of mRNA abundance, alongside the well-studied life history and fate of each cell, describes at a cellular resolution the mRNA landscape that guides development.
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Affiliation(s)
- Sophia C Tintori
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Erin Osborne Nishimura
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Patrick Golden
- School of Information and Library Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason D Lieb
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bob Goldstein
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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56
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Jia Z, Liu Y, Guan N, Bo X, Luo Z, Barnes MR. Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery. BMC Genomics 2016; 17:414. [PMID: 27234029 PMCID: PMC4884357 DOI: 10.1186/s12864-016-2737-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/11/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Drug repositioning, finding new indications for existing drugs, has gained much recent attention as a potentially efficient and economical strategy for accelerating new therapies into the clinic. Although improvement in the sensitivity of computational drug repositioning methods has identified numerous credible repositioning opportunities, few have been progressed. Arguably the "black box" nature of drug action in a new indication is one of the main blocks to progression, highlighting the need for methods that inform on the broader target mechanism in the disease context. RESULTS We demonstrate that the analysis of co-expressed genes may be a critical first step towards illumination of both disease pathology and mode of drug action. We achieve this using a novel framework, co-expressed gene-set enrichment analysis (cogena) for co-expression analysis of gene expression signatures and gene set enrichment analysis of co-expressed genes. The cogena framework enables simultaneous, pathway driven, disease and drug repositioning analysis. Cogena can be used to illuminate coordinated changes within disease transcriptomes and identify drugs acting mechanistically within this framework. We illustrate this using a psoriatic skin transcriptome, as an exemplar, and recover two widely used Psoriasis drugs (Methotrexate and Ciclosporin) with distinct modes of action. Cogena out-performs the results of Connectivity Map and NFFinder webservers in similar disease transcriptome analyses. Furthermore, we investigated the literature support for the other top-ranked compounds to treat psoriasis and showed how the outputs of cogena analysis can contribute new insight to support the progression of drugs into the clinic. We have made cogena freely available within Bioconductor or https://github.com/zhilongjia/cogena . CONCLUSIONS In conclusion, by targeting co-expressed genes within disease transcriptomes, cogena offers novel biological insight, which can be effectively harnessed for drug discovery and repositioning, allowing the grouping and prioritisation of drug repositioning candidates on the basis of putative mode of action.
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Affiliation(s)
- Zhilong Jia
- Department of Chemistry and Biology, College of Science, National University of Defense Technology, Changsha, Hunan, 410073, People's Republic of China
- William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Ying Liu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, People's Republic of China
| | - Naiyang Guan
- College of Computer, National University of Defense Technology, Changsha, 410073, People's Republic of China
- National Laboratory for Parallel and Distributed Processing, National University of Defense Technology, Changsha, 410073, People's Republic of China
| | - Xiaochen Bo
- Beijing Institute of Radiation Medicine, Beijing, 100850, People's Republic of China
| | - Zhigang Luo
- College of Computer, National University of Defense Technology, Changsha, 410073, People's Republic of China.
- National Laboratory for Parallel and Distributed Processing, National University of Defense Technology, Changsha, 410073, People's Republic of China.
| | - Michael R Barnes
- William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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Morikawa M, Derynck R, Miyazono K. TGF-β and the TGF-β Family: Context-Dependent Roles in Cell and Tissue Physiology. Cold Spring Harb Perspect Biol 2016; 8:8/5/a021873. [PMID: 27141051 DOI: 10.1101/cshperspect.a021873] [Citation(s) in RCA: 842] [Impact Index Per Article: 105.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The transforming growth factor-β (TGF-β) is the prototype of the TGF-β family of growth and differentiation factors, which is encoded by 33 genes in mammals and comprises homo- and heterodimers. This review introduces the reader to the TGF-β family with its complexity of names and biological activities. It also introduces TGF-β as the best-studied factor among the TGF-β family proteins, with its diversity of roles in the control of cell proliferation and differentiation, wound healing and immune system, and its key roles in pathology, for example, skeletal diseases, fibrosis, and cancer.
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Affiliation(s)
- Masato Morikawa
- Ludwig Cancer Research, Science for Life Laboratory, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Rik Derynck
- Department of Cell and Tissue Biology, University of California at San Francisco, San Francisco, California 94143
| | - Kohei Miyazono
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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58
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Morales J, Kadota Y, Zipfel C, Molina A, Torres MA. The Arabidopsis NADPH oxidases RbohD and RbohF display differential expression patterns and contributions during plant immunity. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1663-76. [PMID: 26798024 DOI: 10.1093/jxb/erv558] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plant NADPH oxidases, also known as respiratory burst oxidase homologues (RBOHs), produce reactive oxygen species (ROS) that perform a wide range of functions. RbohD and RbohF, two of the 10 Rboh genes present in Arabidopsis, are pleiotropic and mediate diverse physiological processes including the response to pathogens. We hypothesized that the spatio-temporal control of RbohD and RbohF gene expression might be critical in determining their multiplicity of functions. Transgenic Arabidopsis plants with RbohD and RbohF promoter fusions to β-glucuronidase and Luciferase reporter genes were generated. Analysis of these plants revealed a differential expression pattern for RbohD and RbohF throughout plant development and during immune responses. RbohD and RbohF gene expression was differentially modulated by pathogen-associated molecular patterns. Histochemical stains and in vivo expression analysis showed a correlation between the level of RbohD and RbohF promoter activity, H2O2 accumulation and the amount of cell death in response to the pathogenic bacterium Pseudomonas syringae pv. tomato DC3000 and the necrotrophic fungus Plectosphaerella cucumerina. A promoter-swap strategy revealed that the promoter region of RbohD was required to drive production of ROS by this gene in response to pathogens. Moreover, RbohD promoter was activated during Arabidopsis interaction with a non-virulent P. cucumerina isolate, and susceptibility tests with the double mutant rbohD rbohF uncovered a new function for these oxidases in basal resistance. Altogether, our results suggest that differential spatio-temporal expression of the Rboh genes contributes to fine-tune RBOH/NADPH oxidase-dependent ROS production and signaling in Arabidopsis immunity.
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Affiliation(s)
- Jorge Morales
- Centro de Biotecnología y Genómica de Plantas (UPM, INIA), Escuela Superior Técnica de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus Montegancedo, Autopista M40 Km 38, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Yasuhiro Kadota
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK RIKEN Center for Sustainable Resource Science, Plant Immunity Research Group, Suehiro-cho 1-7-22 Tsurumi-ku, Yokohama 230-0045, Japan
| | - Cyril Zipfel
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Antonio Molina
- Centro de Biotecnología y Genómica de Plantas (UPM, INIA), Escuela Superior Técnica de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus Montegancedo, Autopista M40 Km 38, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Miguel-Angel Torres
- Centro de Biotecnología y Genómica de Plantas (UPM, INIA), Escuela Superior Técnica de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus Montegancedo, Autopista M40 Km 38, Pozuelo de Alarcón, 28223, Madrid, Spain
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59
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Owens NDL, Blitz IL, Lane MA, Patrushev I, Overton JD, Gilchrist MJ, Cho KWY, Khokha MK. Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development. Cell Rep 2016; 14:632-647. [PMID: 26774488 PMCID: PMC4731879 DOI: 10.1016/j.celrep.2015.12.050] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/02/2015] [Accepted: 12/07/2015] [Indexed: 01/19/2023] Open
Abstract
Transcript regulation is essential for cell function, and misregulation can lead to disease. Despite technologies to survey the transcriptome, we lack a comprehensive understanding of transcript kinetics, which limits quantitative biology. This is an acute challenge in embryonic development, where rapid changes in gene expression dictate cell fate decisions. By ultra-high-frequency sampling of Xenopus embryos and absolute normalization of sequence reads, we present smooth gene expression trajectories in absolute transcript numbers. During a developmental period approximating the first 8 weeks of human gestation, transcript kinetics vary by eight orders of magnitude. Ordering genes by expression dynamics, we find that "temporal synexpression" predicts common gene function. Remarkably, a single parameter, the characteristic timescale, can classify transcript kinetics globally and distinguish genes regulating development from those involved in cellular metabolism. Overall, our analysis provides unprecedented insight into the reorganization of maternal and embryonic transcripts and redefines our ability to perform quantitative biology.
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Affiliation(s)
- Nick D L Owens
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK
| | - Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697 USA
| | - Maura A Lane
- Program in Vertebrate Developmental Biology, Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Ilya Patrushev
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK
| | - John D Overton
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Yale Center for Genome Analysis , Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Michael J Gilchrist
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK.
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697 USA.
| | - Mustafa K Khokha
- Program in Vertebrate Developmental Biology, Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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60
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Dequéant ML, Fagegaltier D, Hu Y, Spirohn K, Simcox A, Hannon GJ, Perrimon N. Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization. Proc Natl Acad Sci U S A 2015; 112:12974-9. [PMID: 26438832 PMCID: PMC4620889 DOI: 10.1073/pnas.1517729112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The use of time series profiling to identify groups of functionally related genes (synexpression groups) is a powerful approach for the discovery of gene function. Here we apply this strategy during Ras(V12) immortalization of Drosophila embryonic cells, a phenomenon not well characterized. Using high-resolution transcriptional time-series datasets, we generated a gene network based on temporal expression profile similarities. This analysis revealed that common immortalized cells are related to adult muscle precursors (AMPs), a stem cell-like population contributing to adult muscles and sharing properties with vertebrate satellite cells. Remarkably, the immortalized cells retained the capacity for myogenic differentiation when treated with the steroid hormone ecdysone. Further, we validated in vivo the transcription factor CG9650, the ortholog of mammalian Bcl11a/b, as a regulator of AMP proliferation predicted by our analysis. Our study demonstrates the power of time series synexpression analysis to characterize Drosophila embryonic progenitor lines and identify stem/progenitor cell regulators.
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Affiliation(s)
| | | | - Yanhui Hu
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Kerstin Spirohn
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Amanda Simcox
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
| | - Gregory J Hannon
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
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61
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ELABELA Is an Endogenous Growth Factor that Sustains hESC Self-Renewal via the PI3K/AKT Pathway. Cell Stem Cell 2015; 17:435-47. [DOI: 10.1016/j.stem.2015.08.010] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 05/12/2015] [Accepted: 08/12/2015] [Indexed: 12/17/2022]
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62
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Frades I, Andreasson E, Mato JM, Alexandersson E, Matthiesen R, Martínez-Chantar ML. Integrative genomic signatures of hepatocellular carcinoma derived from nonalcoholic Fatty liver disease. PLoS One 2015; 10:e0124544. [PMID: 25993042 PMCID: PMC4439034 DOI: 10.1371/journal.pone.0124544] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 03/05/2015] [Indexed: 12/11/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a risk factor for Hepatocellular carcinoma (HCC), but he transition from NAFLD to HCC is poorly understood. Feature selection algorithms in human and genetically modified mice NAFLD and HCC microarray data were applied to generate signatures of NAFLD progression and HCC differential survival. These signatures were used to study the pathogenesis of NAFLD derived HCC and explore which subtypes of cancers that can be investigated using mouse models. Our findings show that: (I) HNF4 is a common potential transcription factor mediating the transcription of NAFLD progression genes (II) mice HCC derived from NAFLD co-cluster with a less aggressive human HCC subtype of differential prognosis and mixed etiology (III) the HCC survival signature is able to correctly classify 95% of the samples and gives Fgf20 and Tgfb1i1 as the most robust genes for prediction (IV) the expression values of genes composing the signature in an independent human HCC dataset revealed different HCC subtypes showing differences in survival time by a Logrank test. In summary, we present marker signatures for NAFLD derived HCC molecular pathogenesis both at the gene and pathway level.
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Affiliation(s)
- Itziar Frades
- Metabolomics Unit, CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Bizkaia Technology Park, Derio, Bizkaia, Spain
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Jose Maria Mato
- Metabolomics Unit, CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Bizkaia Technology Park, Derio, Bizkaia, Spain
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Rune Matthiesen
- Department of Human genetics, National Health Institute Doutor Ricardo Jorge, Lisboa, Portugal
| | - Mª Luz Martínez-Chantar
- Metabolomics Unit, CIC bioGUNE, Centro de Investigación Cooperativa en Biociencias, Bizkaia Technology Park, Derio, Bizkaia, Spain
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63
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Murn J, Zarnack K, Yang YJ, Durak O, Murphy EA, Cheloufi S, Gonzalez DM, Teplova M, Curk T, Zuber J, Patel DJ, Ule J, Luscombe NM, Tsai LH, Walsh CA, Shi Y. Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes Dev 2015; 29:501-12. [PMID: 25737280 PMCID: PMC4358403 DOI: 10.1101/gad.258483.115] [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: 01/09/2015] [Accepted: 02/06/2015] [Indexed: 12/14/2022]
Abstract
Cellular morphology is an essential determinant of cellular function in all kingdoms of life, yet little is known about how cell shape is controlled. Here we describe a molecular program that controls the early morphology of neurons through a metazoan-specific zinc finger protein, Unkempt. Depletion of Unkempt in mouse embryos disrupts the shape of migrating neurons, while ectopic expression confers neuronal-like morphology to cells of different nonneuronal lineages. We found that Unkempt is a sequence-specific RNA-binding protein and identified its precise binding sites within coding regions of mRNAs linked to protein metabolism and trafficking. RNA binding is required for Unkempt-induced remodeling of cellular shape and is directly coupled to a reduced production of the encoded proteins. These findings link post-transcriptional regulation of gene expression with cellular shape and have general implications for the development and disease of multicellular organisms.
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Affiliation(s)
- Jernej Murn
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA;
| | - Kathi Zarnack
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Yawei J Yang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA;
| | - Omer Durak
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Elisabeth A Murphy
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Sihem Cheloufi
- Cancer Center, Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Dilenny M Gonzalez
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Marianna Teplova
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Johannes Zuber
- The Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Jernej Ule
- Department of Molecular Neuroscience, University College London Institute of Neurology, London WC1N 3BG, United Kingdom
| | - Nicholas M Luscombe
- European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom; UCL Genetics Institute, Department of Genetics, Environment, and Evolution, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom; Okinawa Institute for Science and Technology Graduate University, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts 02115, USA; Department of Pediatrics, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Yang Shi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA;
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Diotel N, Rodriguez Viales R, Armant O, März M, Ferg M, Rastegar S, Strähle U. Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches. J Comp Neurol 2015; 523:1202-21. [PMID: 25556858 PMCID: PMC4418305 DOI: 10.1002/cne.23733] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 12/17/2014] [Accepted: 12/17/2014] [Indexed: 12/19/2022]
Abstract
The zebrafish has become a model to study adult vertebrate neurogenesis. In particular, the adult telencephalon has been an intensely studied structure in the zebrafish brain. Differential expression of transcriptional regulators (TRs) is a key feature of development and tissue homeostasis. Here we report an expression map of 1,202 TR genes in the telencephalon of adult zebrafish. Our results are summarized in a database with search and clustering functions to identify genes expressed in particular regions of the telencephalon. We classified 562 genes into 13 distinct patterns, including genes expressed in the proliferative zone. The remaining 640 genes displayed unique and complex patterns of expression and could thus not be grouped into distinct classes. The neurogenic ventricular regions express overlapping but distinct sets of TR genes, suggesting regional differences in the neurogenic niches in the telencephalon. In summary, the small telencephalon of the zebrafish shows a remarkable complexity in TR gene expression. The adult zebrafish telencephalon has become a model to study neurogenesis. We established the expression pattern of more than 1200 transcription regulators (TR) in the adult telencephalon. The neurogenic regions express overlapping but distinct sets of TR genes suggesting regional differences in the neurogenic potential. J. Comp. Neurol. 523:1202–1221, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Nicolas Diotel
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Campus Nord, Karlsruhe, Germany
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65
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Bitner MA, Cohen BL. Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12217] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Maria Aleksandra Bitner
- Institute of Paleobiology; Polish Academy of Sciences; ul. Twarda 51/55 00-818 Warsaw Poland
| | - Bernard L. Cohen
- University of Glasgow; MVLS; Wolfson Link Building Glasgow G12 8QQ UK
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66
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Thomas P, Durek P, Solt I, Klinger B, Witzel F, Schulthess P, Mayer Y, Tikk D, Blüthgen N, Leser U. Computer-assisted curation of a human regulatory core network from the biological literature. Bioinformatics 2014; 31:1258-66. [DOI: 10.1093/bioinformatics/btu795] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 11/26/2014] [Indexed: 12/20/2022] Open
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67
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Castro-González C, Luengo-Oroz MA, Duloquin L, Savy T, Rizzi B, Desnoulez S, Doursat R, Kergosien YL, Ledesma-Carbayo MJ, Bourgine P, Peyriéras N, Santos A. A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis. PLoS Comput Biol 2014; 10:e1003670. [PMID: 24945246 PMCID: PMC4063669 DOI: 10.1371/journal.pcbi.1003670] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 04/28/2014] [Indexed: 01/30/2023] Open
Abstract
A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages. We propose a workflow to map the expression domains of multiple genes onto a series of 3D templates, or “atlas”, during early embryogenesis. It was applied to the zebrafish at different stages between 4 and 6.3 hpf, generating 6 templates. Our system overcomes the lack of significant morphological landmarks in early development by relying on the expression of a reference gene (goosecoid, gsc) and nuclear staining to guide the registration of the analyzed genes. The proposed method also successfully maps gene domains from partially imaged embryos, thus allowing greater microscope magnification and cellular resolution. By using the workflow to construct a spatiotemporal database of zebrafish, we opened the way to a systematic analysis of vertebrate embryogenesis. The atlas database, together with the mapping software (Match-IT), a custom-made visualization platform (Atlas-IT), and step-by-step user guides are available from the Supplementary Material. We expect that this will encourage other laboratories to generate, map, visualize and analyze new gene expression datasets.
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Affiliation(s)
- Carlos Castro-González
- Biomedical Image Technologies, ETSIT, Universidad Politécnica de Madrid, CEIMoncloa, Madrid, Spain
- Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
- Madrid-MIT M+Visión Consortium, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Miguel A. Luengo-Oroz
- Biomedical Image Technologies, ETSIT, Universidad Politécnica de Madrid, CEIMoncloa, Madrid, Spain
- Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Louise Duloquin
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- Institut des Systèmes Complexes, Paris, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
| | - Thierry Savy
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- Institut des Systèmes Complexes, Paris, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
| | - Barbara Rizzi
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- Institut des Systèmes Complexes, Paris, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
| | - Sophie Desnoulez
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
| | - René Doursat
- Institut des Systèmes Complexes, Paris, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Yannick L. Kergosien
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- LIMICS-INSERM UMR 1142, UFR SMBH, Université Paris 13, Bobigny, France
| | - María J. Ledesma-Carbayo
- Biomedical Image Technologies, ETSIT, Universidad Politécnica de Madrid, CEIMoncloa, Madrid, Spain
- Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Paul Bourgine
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- Institut des Systèmes Complexes, Paris, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
| | - Nadine Peyriéras
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- Institut des Systèmes Complexes, Paris, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- * E-mail: (NP); (AS)
| | - Andrés Santos
- Biomedical Image Technologies, ETSIT, Universidad Politécnica de Madrid, CEIMoncloa, Madrid, Spain
- Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
- * E-mail: (NP); (AS)
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68
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Guo Z, Maki M, Ding R, Yang Y, Zhang B, Xiong L. Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues. Sci Rep 2014; 4:5150. [PMID: 24889152 PMCID: PMC5381490 DOI: 10.1038/srep05150] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 05/08/2014] [Indexed: 12/18/2022] Open
Abstract
Tissue-specific miRNAs (TS miRNA) specifically expressed in particular tissues play an important role in tissue identity, differentiation and function. However, transcription factor (TF) and TS miRNA regulatory networks across multiple tissues have not been systematically studied. Here, we manually extracted 116 TS miRNAs and systematically investigated the regulatory network of TF-TS miRNA in 12 human tissues. We identified 2,347 TF-TS miRNA regulatory relations and revealed that most TF binding sites tend to enrich close to the transcription start site of TS miRNAs. Furthermore, we found TS miRNAs were regulated widely by non-tissue specific TFs and the tissue-specific expression level of TF have a close relationship with TF-genes regulation. Finally, we describe TSmiR (http://bioeng.swjtu.edu.cn/TSmiR), a novel and web-searchable database that houses interaction maps of TF-TS miRNA in 12 tissues. Taken together, these observations provide a new suggestion to better understand the regulatory network and mechanisms of TF-TS miRNAs underlying different tissues.
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Affiliation(s)
- Zhiyun Guo
- School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, 610031, P.R. China
| | - Miranda Maki
- Department of Biology, Lakehead University, Oliver Road, Thunder Bay, Ontario
| | - Ruofan Ding
- School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, 610031, P.R. China
| | - Yalan Yang
- School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, 610031, P.R. China
| | - Bao Zhang
- School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, 610031, P.R. China
| | - Lili Xiong
- School of Life Sciences and Bioengineering, Southwest Jiaotong University, Chengdu, 610031, P.R. China
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69
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Thiru P, Kern DM, McKinley KL, Monda JK, Rago F, Su KC, Tsinman T, Yarar D, Bell GW, Cheeseman IM. Kinetochore genes are coordinately up-regulated in human tumors as part of a FoxM1-related cell division program. Mol Biol Cell 2014; 25:1983-94. [PMID: 24829384 PMCID: PMC4072572 DOI: 10.1091/mbc.e14-03-0837] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The key player in directing proper chromosome segregation is the macromolecular kinetochore complex, which mediates DNA-microtubule interactions. Previous studies testing individual kinetochore genes documented examples of their overexpression in tumors relative to normal tissue, leading to proposals that up-regulation of specific kinetochore genes may promote tumor progression. However, kinetochore components do not function in isolation, and previous studies did not comprehensively compare the expression behavior of kinetochore components. Here we analyze the expression behavior of the full range of human kinetochore components in diverse published expression compendia, including normal tissues and tumor samples. Our results demonstrate that kinetochore genes are rarely overexpressed individually. Instead, we find that core kinetochore genes are coordinately regulated with other cell division genes under virtually all conditions. This expression pattern is strongly correlated with the expression of the forkhead transcription factor FoxM1, which binds to the majority of cell division promoters. These observations suggest that kinetochore gene up-regulation in cancer reflects a general activation of the cell division program and that altered expression of individual kinetochore genes is unlikely to play a causal role in tumorigenesis.
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Affiliation(s)
- Prathapan Thiru
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - David M Kern
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Kara L McKinley
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Julie K Monda
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Florencia Rago
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Kuan-Chung Su
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Tonia Tsinman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Defne Yarar
- Merrimack Pharmaceuticals, Cambridge, MA 02139
| | - George W Bell
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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70
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Roy S, Kundu TK. Gene regulatory networks and epigenetic modifications in cell differentiation. IUBMB Life 2014; 66:100-9. [DOI: 10.1002/iub.1249] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/19/2014] [Accepted: 01/31/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Siddhartha Roy
- CSIR-Indian Institute of Chemical Biology; Kolkata 700 032 West Bengal India
| | - Tapas K. Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research; Bangalore 560064 Karnataka India
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71
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Hammonds AS, Bristow CA, Fisher WW, Weiszmann R, Wu S, Hartenstein V, Kellis M, Yu B, Frise E, Celniker SE. Spatial expression of transcription factors in Drosophila embryonic organ development. Genome Biol 2013; 14:R140. [PMID: 24359758 PMCID: PMC4053779 DOI: 10.1186/gb-2013-14-12-r140] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/20/2013] [Indexed: 11/29/2022] Open
Abstract
Background Site-specific transcription factors (TFs) bind DNA regulatory elements to control expression of target genes, forming the core of gene regulatory networks. Despite decades of research, most studies focus on only a small number of TFs and the roles of many remain unknown. Results We present a systematic characterization of spatiotemporal gene expression patterns for all known or predicted Drosophila TFs throughout embryogenesis, the first such comprehensive study for any metazoan animal. We generated RNA expression patterns for all 708 TFs by in situ hybridization, annotated the patterns using an anatomical controlled vocabulary, and analyzed TF expression in the context of organ system development. Nearly all TFs are expressed during embryogenesis and more than half are specifically expressed in the central nervous system. Compared to other genes, TFs are enriched early in the development of most organ systems, and throughout the development of the nervous system. Of the 535 TFs with spatially restricted expression, 79% are dynamically expressed in multiple organ systems while 21% show single-organ specificity. Of those expressed in multiple organ systems, 77 TFs are restricted to a single organ system either early or late in development. Expression patterns for 354 TFs are characterized for the first time in this study. Conclusions We produced a reference TF dataset for the investigation of gene regulatory networks in embryogenesis, and gained insight into the expression dynamics of the full complement of TFs controlling the development of each organ system.
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72
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Jeschke M, Baumgärtner S, Legewie S. Determinants of cell-to-cell variability in protein kinase signaling. PLoS Comput Biol 2013; 9:e1003357. [PMID: 24339758 PMCID: PMC3854479 DOI: 10.1371/journal.pcbi.1003357] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 10/06/2013] [Indexed: 12/28/2022] Open
Abstract
Cells reliably sense environmental changes despite internal and external fluctuations, but the mechanisms underlying robustness remain unclear. We analyzed how fluctuations in signaling protein concentrations give rise to cell-to-cell variability in protein kinase signaling using analytical theory and numerical simulations. We characterized the dose-response behavior of signaling cascades by calculating the stimulus level at which a pathway responds (‘pathway sensitivity’) and the maximal activation level upon strong stimulation. Minimal kinase cascades with gradual dose-response behavior show strong variability, because the pathway sensitivity and the maximal activation level cannot be simultaneously invariant. Negative feedback regulation resolves this trade-off and coordinately reduces fluctuations in the pathway sensitivity and maximal activation. Feedbacks acting at different levels in the cascade control different aspects of the dose-response curve, thereby synergistically reducing the variability. We also investigated more complex, ultrasensitive signaling cascades capable of switch-like decision making, and found that these can be inherently robust to protein concentration fluctuations. We describe how the cell-to-cell variability of ultrasensitive signaling systems can be actively regulated, e.g., by altering the expression of phosphatase(s) or by feedback/feedforward loops. Our calculations reveal that slow transcriptional negative feedback loops allow for variability suppression while maintaining switch-like decision making. Taken together, we describe design principles of signaling cascades that promote robustness. Our results may explain why certain signaling cascades like the yeast pheromone pathway show switch-like decision making with little cell-to-cell variability. Cells sense their surroundings and respond to soluble factors in the extracellular space. Extracellular factors frequently induce heterogeneous responses, thereby restricting the biological outcome to a fraction of the cell population. However, the question arises how such cell-to-cell variability can be controlled, because some cellular systems show a very homogenous response at a defined level of an extracellular stimulus. We derived an analytical framework to systematically characterize the cell-to-cell variability of intracellular signaling pathways which transduce external signals. We analyzed how heterogeneity arises from fluctuations in the total concentrations of signaling proteins because this is the main source of variability in eukaryotic systems. We find that signaling pathways can be highly variable or inherently invariant, depending on the kinetic parameters and the structural features of the cascade. Our results indicate that the cell-to-cell variability can be reduced by negative feedback in the cascade or by signaling crosstalk between parallel pathways. We precisely define the role of negative feedback loops in variability suppression, and show that different aspects of the dose-response curve can be controlled, depending on the feedback kinetics and site of action in the cascade. This work constitutes a first step towards a systematic understanding of cell-to-cell variability in signal transduction.
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Affiliation(s)
| | | | - Stefan Legewie
- Institute of Molecular Biology (IMB), Mainz, Germany
- * E-mail:
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73
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Nitanda Y, Matsui T, Matta T, Higami A, Kohno K, Nakahata Y, Bessho Y. 3'-UTR-dependent regulation of mRNA turnover is critical for differential distribution patterns of cyclic gene mRNAs. FEBS J 2013; 281:146-56. [PMID: 24165510 DOI: 10.1111/febs.12582] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 08/30/2013] [Accepted: 10/22/2013] [Indexed: 12/18/2022]
Abstract
Somite segmentation, a prominent periodic event in the development of vertebrates, is instructed by cyclic expression of several genes, including Hes7 and Lunatic fringe (Lfng). Transcriptional regulation accounts for the cyclic expression. In addition, because the expression patterns vary in a cycle, rapid turnover of mRNAs should be involved in the cyclic expression, although its contribution remains unclear. Here, we demonstrate that 3'-UTR-dependent rapid turnover of Lfng and Hes7 plays a critical role in their dynamic expression patterns. The regions active in the transcription of Lfng and Hes7 are wholly overlapped in the posterior presomitic mesoderm (PSM) of the mouse embryo. However, their distribution patterns are slightly different; Hes7 mRNA shows a broader distribution pattern than Lfng mRNA in the posterior PSM. Lfng mRNA is less stable than Hes7 mRNA, where their 3'-UTRs are responsible for the different stability. Using transgenic mice expressing Venus under the control of the Hes7 promoter, which leads to cyclic transcription in the PSM, we reveal that the Lfng 3'-UTR provides the narrow distribution pattern of Lfng mRNA, whereas the Hes7 3'-UTR contributes the relatively broad distribution pattern of Hes7 mRNA. Thus, we conclude that 3'-UTR-dependent mRNA stability accounts for the differential distribution patterns of Lfng and Hes7 mRNA. Our findings suggest that 3'-UTR-dependent regulation of mRNA turnover plays a crucial role in the diverse patterns of mRNA distribution during development.
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Affiliation(s)
- Yasuhide Nitanda
- Laboratory of Gene Regulation Research, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Japan
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74
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Ferg M, Armant O, Yang L, Dickmeis T, Rastegar S, Strähle U. Gene transcription in the zebrafish embryo: regulators and networks. Brief Funct Genomics 2013; 13:131-43. [PMID: 24152666 DOI: 10.1093/bfgp/elt044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The precise spatial and temporal control of gene expression is a key process in the development, maintenance and regeneration of the vertebrate body. A substantial proportion of vertebrate genomes encode genes that control the transcription of the genetic information into mRNA. The zebrafish is particularly well suited to investigate gene regulatory networks underlying the control of gene expression during development due to the external development of its transparent embryos and the increasingly sophisticated tools for genetic manipulation available for this model system. We review here recent data on the analysis of cis-regulatory modules, transcriptional regulators and their integration into gene regulatory networks in the zebrafish, using the developing spinal cord as example.
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Affiliation(s)
- Marco Ferg
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Postfach 3640, 76021 Karlsruhe, Germany.
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75
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Parfett C, Williams A, Zheng J, Zhou G. Gene batteries and synexpression groups applied in a multivariate statistical approach to dose–response analysis of toxicogenomic data. Regul Toxicol Pharmacol 2013; 67:63-74. [DOI: 10.1016/j.yrtph.2013.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/26/2013] [Indexed: 12/28/2022]
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76
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Scaling of dorsal-ventral patterning by embryo size-dependent degradation of Spemann's organizer signals. Cell 2013; 153:1296-311. [PMID: 23746842 DOI: 10.1016/j.cell.2013.05.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 02/15/2013] [Accepted: 05/01/2013] [Indexed: 11/24/2022]
Abstract
Spemann's organizer plays a key role in dorsal-ventral (DV) patterning in the amphibian embryo by secreting diffusible proteins such as Chordin, an antagonist to ventralizing bone morphogenetic proteins (BMPs). The DV patterning is so robust that an amphibian embryo with its ventral half surgically removed can develop into a smaller but proportionally patterned larva. Here, we show that this robust patterning depends on facilitated Chordin degradation and requires the expression of the Chordin-proteinase inhibitor Sizzled on the opposite side. Sizzled, which is stable and diffuses widely along the DV axis, stabilizes Chordin and expands its distribution in the ventral direction. This expanded Chordin distribution, in turn, limits BMP-dependent Sizzled production, forming an axis-wide feedback loop for shaping Chordin's activity. Using bisection assays, we demonstrate that Chordin degradation is dynamically controlled by embryo-size-coupled Sizzled accumulation. We propose a scaling model that enables the DV pattern to adjust proportionally to embryonic axis size.
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77
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Blüthgen N, Legewie S. Robustness of signal transduction pathways. Cell Mol Life Sci 2013; 70:2259-69. [PMID: 23007845 PMCID: PMC11113274 DOI: 10.1007/s00018-012-1162-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 09/05/2012] [Accepted: 09/06/2012] [Indexed: 10/27/2022]
Abstract
Signal transduction pathways transduce information about the outside of the cell to the nucleus, regulating gene expression and cell fate. To reliably inform the cell about its surroundings, information transfer has to be robust against typical perturbation that a cell experiences. Robustness of several mammalian signaling pathways has been studied recently by quantitative experimentation and using mathematical modeling. Here, we review these studies, and describe the emerging concepts of robustness and the underlying mechanisms.
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Affiliation(s)
- Nils Blüthgen
- Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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78
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Song Y, Ahn J, Suh Y, Davis ME, Lee K. Identification of novel tissue-specific genes by analysis of microarray databases: a human and mouse model. PLoS One 2013; 8:e64483. [PMID: 23741331 PMCID: PMC3669334 DOI: 10.1371/journal.pone.0064483] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 04/15/2013] [Indexed: 12/15/2022] Open
Abstract
Understanding the tissue-specific pattern of gene expression is critical in elucidating the molecular mechanisms of tissue development, gene function, and transcriptional regulations of biological processes. Although tissue-specific gene expression information is available in several databases, follow-up strategies to integrate and use these data are limited. The objective of the current study was to identify and evaluate novel tissue-specific genes in human and mouse tissues by performing comparative microarray database analysis and semi-quantitative PCR analysis. We developed a powerful approach to predict tissue-specific genes by analyzing existing microarray data from the NCBI′s Gene Expression Omnibus (GEO) public repository. We investigated and confirmed tissue-specific gene expression in the human and mouse kidney, liver, lung, heart, muscle, and adipose tissue. Applying our novel comparative microarray approach, we confirmed 10 kidney, 11 liver, 11 lung, 11 heart, 8 muscle, and 8 adipose specific genes. The accuracy of this approach was further verified by employing semi-quantitative PCR reaction and by searching for gene function information in existing publications. Three novel tissue-specific genes were discovered by this approach including AMDHD1 (amidohydrolase domain containing 1) in the liver, PRUNE2 (prune homolog 2) in the heart, and ACVR1C (activin A receptor, type IC) in adipose tissue. We further confirmed the tissue-specific expression of these 3 novel genes by real-time PCR. Among them, ACVR1C is adipose tissue-specific and adipocyte-specific in adipose tissue, and can be used as an adipocyte developmental marker. From GEO profiles, we predicted the processes in which AMDHD1 and PRUNE2 may participate. Our approach provides a novel way to identify new sets of tissue-specific genes and to predict functions in which they may be involved.
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Affiliation(s)
- Yan Song
- Department of Animal Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Jinsoo Ahn
- Department of Animal Sciences, The Ohio State University, Columbus, Ohio, United States of America
- The Ohio State University Interdisciplinary PhD Program in Nutrition (OSUN), The Ohio State University, Columbus, Ohio, United States of America
| | - Yeunsu Suh
- Department of Animal Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Michael E. Davis
- Department of Animal Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, Ohio, United States of America
- The Ohio State University Interdisciplinary PhD Program in Nutrition (OSUN), The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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79
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Armant O, März M, Schmidt R, Ferg M, Diotel N, Ertzer R, Bryne JC, Yang L, Baader I, Reischl M, Legradi J, Mikut R, Stemple D, van IJcken W, van der Sloot A, Lenhard B, Strähle U, Rastegar S. Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos. Dev Biol 2013; 380:351-62. [PMID: 23684812 DOI: 10.1016/j.ydbio.2013.05.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 01/20/2023]
Abstract
Transcription is the primary step in the retrieval of genetic information. A substantial proportion of the protein repertoire of each organism consists of transcriptional regulators (TRs). It is believed that the differential expression and combinatorial action of these TRs is essential for vertebrate development and body homeostasis. We mined the zebrafish genome exhaustively for genes encoding TRs and determined their expression in the zebrafish embryo by sequencing to saturation and in situ hybridisation. At the evolutionary conserved phylotypic stage, 75% of the 3302 TR genes encoded in the genome are already expressed. The number of expressed TR genes increases only marginally in subsequent stages and is maintained during adulthood suggesting important roles of the TR genes in body homeostasis. Fewer than half of the TR genes (45%, n=1711 genes) are expressed in a tissue-restricted manner in the embryo. Transcripts of 207 genes were detected in a single tissue in the 24h embryo, potentially acting as regulators of specific processes. Other TR genes were expressed in multiple tissues. However, with the exception of certain territories in the nervous system, we did not find significant synexpression suggesting that most tissue-restricted TRs act in a freely combinatorial fashion. Our data indicate that elaboration of body pattern and function from the phylotypic stage onward relies mostly on redeployment of TRs and post-transcriptional processes.
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Affiliation(s)
- Olivier Armant
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Postfach 3640, 76021 Karlsruhe, Germany
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80
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Dhorne-Pollet S, Thélie A, Pollet N. Validation of novel reference genes for RT-qPCR studies of gene expression in Xenopus tropicalis during embryonic and post-embryonic development. Dev Dyn 2013; 242:709-17. [PMID: 23559567 DOI: 10.1002/dvdy.23972] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 02/04/2013] [Accepted: 03/26/2013] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Accurate interpretation of transcriptome profiling by quantitative PCR requires the establishment of species-specific standards. However, the selection of reference genes for assessing RNA expression profiles in Xenopus laevis and Xenopus tropicalis was mostly based on historical reasons and they often only reflect the traditions of a laboratory. RESULTS We investigated the expression stability of 10 genes (dicer1, drosha, eef1a1, elavl3, gsc, h4, odc1, rpl8, smn2, tbp), 8 of which are commonly used as internal controls in published RT-qPCR experiments. We defined specific primer pairs and evaluated their suitability as reference genes by performing RT-qPCR expression profiling in Xenopus tropicalis. Gene expression stability was assayed in a set of 15 developmental stages from the egg to the froglet, and in dissected embryos. CONCLUSIONS Overall, we determined a set of qualified reference genes for distinct developmental periods. We recommend the use of dicer1, drosha, eef1a1, and smn2 from early embryonic development up to the end of metamorphosis. During early embryogenesis drosha, eef1a1, smn2 are suitable. For the whole post-embryonic development and for metamorphic stages including pro-metamorphosis and metamorphic climax, we recommend the use of drosha and smn2. These reference genes should prove their usefulness for data comparison across studies.
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81
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Natarajan M. Unsupervised Methods to Identify Cellular Signaling Networks from Perturbation Data. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The inference of cellular architectures from detailed time-series measurements of intracellular variables is an active area of research. High throughput measurements of responses to cellular perturbations are usually analyzed using a variety of machine learning methods that typically only work within one type of measurement. Here, summaries of some recent research attempts are presented–these studies have expanded the scope of the problem by systematically integrating measurements across multiple layers of regulation including second messengers, protein phosphorylation markers, transcript levels, and functional phenotypes into signaling vectors or signatures of signal transduction. Data analyses through simple unsupervised methods provide rich insight into the biology of the underlying network, and in some cases reconstruction of key architectures of the underlying network from perturbation data. The methodological advantages provided by these efforts are examined using data from a publicly available database of responses to systematic perturbations of cellular signaling networks generated by the Alliance for Cellular Signaling (AfCS).
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82
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Röttinger E, Dahlin P, Martindale MQ. A framework for the establishment of a cnidarian gene regulatory network for "endomesoderm" specification: the inputs of ß-catenin/TCF signaling. PLoS Genet 2012; 8:e1003164. [PMID: 23300467 PMCID: PMC3531958 DOI: 10.1371/journal.pgen.1003164] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 10/27/2012] [Indexed: 12/03/2022] Open
Abstract
Understanding the functional relationship between intracellular factors and
extracellular signals is required for reconstructing gene regulatory networks
(GRN) involved in complex biological processes. One of the best-studied
bilaterian GRNs describes endomesoderm specification and predicts that both
mesoderm and endoderm arose from a common GRN early in animal evolution.
Compelling molecular, genomic, developmental, and evolutionary evidence supports
the hypothesis that the bifunctional gastrodermis of the cnidarian-bilaterian
ancestor is derived from the same evolutionary precursor of both endodermal and
mesodermal germ layers in all other triploblastic bilaterian animals. We have
begun to establish the framework of a provisional cnidarian
“endomesodermal” gene regulatory network in the sea anemone,
Nematostella vectensis, by using a genome-wide microarray
analysis on embryos in which the canonical Wnt/ß-catenin pathway was
ectopically targeted for activation by two distinct pharmaceutical agents
(lithium chloride and 1-azakenpaullone) to identify potential targets of
endomesoderm specification. We characterized 51 endomesodermally expressed
transcription factors and signaling molecule genes (including 18 newly
identified) with fine-scale temporal (qPCR) and spatial (in
situ) analysis to define distinct co-expression domains within the
animal plate of the embryo and clustered genes based on their earliest zygotic
expression. Finally, we determined the input of the canonical
Wnt/ß-catenin pathway into the cnidarian endomesodermal GRN using
morpholino and mRNA overexpression experiments to show that NvTcf/canonical Wnt
signaling is required to pattern both the future endomesodermal and ectodermal
domains prior to gastrulation, and that both BMP and FGF (but not Notch)
pathways play important roles in germ layer specification in this animal. We
show both evolutionary conserved as well as profound differences in
endomesodermal GRN structure compared to bilaterians that may provide
fundamental insight into how GRN subcircuits have been adopted, rewired, or
co-opted in various animal lineages that give rise to specialized endomesodermal
cell types. Cnidarians (anemones, corals, and “jellyfish”) are an animal group
whose adults possess derivatives of only two germ layers: ectoderm and a
bifunctional (absorptive and contractile) gastrodermal (gut) layer. Cnidarians
are the closest living relatives to bilaterally symmetrical animals that possess
all three germ layers (ecto, meso, and endoderm); and compelling molecular,
genomic, developmental, and evolutionary evidence exists to demonstrate that the
cnidarian gastrodermis is evolutionarily related to both endodermal and
mesodermal germ layers in all other triploblastic bilaterian animals. Little is
known about endomesoderm specification in cnidarians. In this study, we
constructed the framework of a cnidarian endomesodermal gene regulatory network
in the sea anemone, Nematostella vectensis, using a combination
of experimental approaches. We identified and characterized by both qPCR and
in situ hybridization 51 genes expressed in defined domains
within the presumptive endomesoderm. In addition, we functionally demonstrate
that Wnt/Tcf signaling is crucial for regionalized expression of a defined
subset of these genes prior to gut formation and endomesoderm maintenance. Our
results support the idea of an ancient gene regulatory network underlying
endomesoderm specification that involves inputs from multiple signaling pathways
(Wnt, FGF, BMP, but not Notch) early in development, that are temporarily
uncoupled in bilaterian animals.
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Affiliation(s)
- Eric Röttinger
- Kewalo Marine Laboratory, Pacific Biosciences Research Center,
University of Hawai'i, Honolulu, Hawai'i, United States of
America
| | - Paul Dahlin
- Kewalo Marine Laboratory, Pacific Biosciences Research Center,
University of Hawai'i, Honolulu, Hawai'i, United States of
America
| | - Mark Q. Martindale
- Kewalo Marine Laboratory, Pacific Biosciences Research Center,
University of Hawai'i, Honolulu, Hawai'i, United States of
America
- * E-mail:
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83
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Chen CH, Chuang HC, Huang CC, Fang FM, Huang HY, Tsai HT, Su LJ, Shiu LY, Leu S, Chien CY. Overexpression of Rap-1A indicates a poor prognosis for oral cavity squamous cell carcinoma and promotes tumor cell invasion via Aurora-A modulation. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 182:516-28. [PMID: 23219753 DOI: 10.1016/j.ajpath.2012.10.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 08/10/2012] [Accepted: 10/12/2012] [Indexed: 12/25/2022]
Abstract
The functions of Rap-1A in oral carcinogenesis are largely unexplored. In this study, we examined the expression of Rap-1A at different malignant stages of oral cavity squamous cell carcinoma (OCSCC). Semiquantitative RT-PCR, quantitative RT-PCR, and Western blotting were used to evaluate Rap-1A mRNA and protein expressions, respectively, in paired OCSCC patient specimens. To determine the possible correlation between Rap-1A expression and various clinical characteristics, 256 samples from patients with OCSCC were evaluated by immunohistochemical staining. Strong Rap-1A expression was a significant prognostic marker and predictor of aggressive OCSCC. The overall and disease-specific 5-year survival rates were significantly correlated with strong expression of Rap-1A (P < 0.001). Functionally, overexpressed Rap-1A could promote oral cancer cell migration and invasion by Transwell chambers and wound healing assay. Conversely, the suppression of Rap-1A expression using Rap-1A-mediated siRNA was sufficient to decrease cell motility. Furthermore, our data also illustrated that Aurora-A could not only induce mRNA and protein expressions of Rap-1A for enhancing cancer cell motility but also co-localize and form a complex with Rap-1A in the oral cancer cell line. Finally, immunohistochemical staining, indirect immunofluorescence, and Western blotting analysis of human aggressive OCSCC specimens revealed a significantly positive correlation between Rap-1A and Aurora-A expression. Taken together, our results suggest that the Aurora-A/Rap-1A pathway is associated with survival, tumor progression, and metastasis of OCSCC patients.
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Affiliation(s)
- Chang-Han Chen
- Center for Translational Research in Biomedical Sciences, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan
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84
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Robertson RD, Mukherjee A. Synexpression group analyses identify new functions of FSTL3, a TGFβ ligand inhibitor. Biochem Biophys Res Commun 2012; 427:568-73. [DOI: 10.1016/j.bbrc.2012.09.098] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 09/18/2012] [Indexed: 12/20/2022]
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85
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Schmiedel JM, Axmann IM, Legewie S. Multi-target regulation by small RNAs synchronizes gene expression thresholds and may enhance ultrasensitive behavior. PLoS One 2012; 7:e42296. [PMID: 22927924 PMCID: PMC3424230 DOI: 10.1371/journal.pone.0042296] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 07/02/2012] [Indexed: 01/05/2023] Open
Abstract
Cells respond to external cues by precisely coordinating multiple molecular events. Co-regulation may be established by the so-called single-input module (SIM), where a common regulator controls multiple targets. Using mathematical modeling, we compared the ability of SIM architectures to precisely coordinate protein levels despite environmental fluctuations and uncertainties in parameter values. We find that post-transcriptional co-regulation as exemplified by bacterial small RNAs (sRNAs) is particularly robust: sRNA-mediated regulation establishes highly synchronous gene expression thresholds for all mRNA targets without a need for fine-tuning of kinetic parameters. Our analyses reveal that the non-catalytic nature of sRNA action is essential for robust gene expression synchronization, and that sRNA sequestration effects underlie coupling of multiple mRNA pools. This principle also operates in the temporal regime, implying that sRNAs could robustly coordinate the kinetics of mRNA induction as well. Moreover, we observe that multi-target regulation by a small RNA can strongly enhance ultrasensitivity in mRNA expression when compared to the single-target case. Our findings may explain why bacterial small RNAs frequently coordinate all-or-none responses to cellular stress.
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Affiliation(s)
| | - Ilka Maria Axmann
- Institute for Theoretical Biology, Charité-Universitätsmedizin, Berlin, Berlin, Germany
| | - Stefan Legewie
- Institute of Molecular Biology, Mainz, Rheinland-Pfalz, Germany
- * E-mail:
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86
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From networks of protein interactions to networks of functional dependencies. BMC SYSTEMS BIOLOGY 2012; 6:44. [PMID: 22607727 PMCID: PMC3434018 DOI: 10.1186/1752-0509-6-44] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 05/20/2012] [Indexed: 11/23/2022]
Abstract
Background As protein-protein interactions connect proteins that participate in either the same or different functions, networks of interacting and functionally annotated proteins can be converted into process graphs of inter-dependent function nodes (each node corresponding to interacting proteins with the same functional annotation). However, as proteins have multiple annotations, the process graph is non-redundant, if only proteins participating directly in a given function are included in the related function node. Results Reasoning that topological features (e.g., clusters of highly inter-connected proteins) might help approaching structured and non-redundant understanding of molecular function, an algorithm was developed that prioritizes inclusion of proteins into the function nodes that best overlap protein clusters. Specifically, the algorithm identifies function nodes (and their mutual relations), based on the topological analysis of a protein interaction network, which can be related to various biological domains, such as cellular components (e.g., peroxisome and cellular bud) or biological processes (e.g., cell budding) of the model organism S. cerevisiae. Conclusions The method we have described allows converting a protein interaction network into a non-redundant process graph of inter-dependent function nodes. The examples we have described show that the resulting graph allows researchers to formulate testable hypotheses about dependencies among functions and the underlying mechanisms.
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87
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Chen CH, Shiu LY, Su LJ, Huang CYF, Huang SC, Huang CC, Yin YF, Wang WS, Tsai HT, Fang FM, Chuang WC, Kang HC, Hwang CF. FLJ10540 is associated with tumor progression in nasopharyngeal carcinomas and contributes to nasopharyngeal cell proliferation, and metastasis via osteopontin/CD44 pathway. J Transl Med 2012; 10:93. [PMID: 22591637 PMCID: PMC3419101 DOI: 10.1186/1479-5876-10-93] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 05/02/2012] [Indexed: 01/01/2023] Open
Abstract
Background Nasopharyngeal carcinoma (NPC) is well-known for its highly metastatic characteristics, but little is known of its molecular mechanisms. New biomarkers that predict clinical outcome, in particular the ability of the primary tumor to develop metastatic tumors are urgently needed. The aim of this study is to investigate the role of FLJ10540 in human NPC development. Methods A bioinformatics approach was used to explore the potentially important regulatory genes involved in the growth/metastasis control of NPC. FLJ10540 was chosen for this study. Two co-expression strategies from NPC microarray were employed to identify the relationship between FLJ10540 and osteopontin. Quantitative-RT-PCR, immunoblotting, and immunohistochemistry analysis were used to investigate the mRNA and protein expression profiles of FLJ10540 and osteopontin in the normal and NPC tissues to confirm microarray results. TW01 and Hone1 NPC cells with overexpression FLJ10540 or siRNA to repress endogenous FLJ10540 were generated by stable transfection to further elucidate the molecular mechanisms of FLJ10540-elicited cell growth and metastasis under osteopontin stimulation. Results We found that osteopontin expression exhibited a positive correlation with FLJ10540 in NPC microarray. We also demonstrated comprehensively that FLJ10540 and osteopontin were not only overexpressed in NPC specimens, but also significantly correlated with advanced tumor and lymph node-metastasis stages, and had a poor 5-year survival rate, respectively. Stimulation of NPC parental cells with osteopontin results in an increase in FLJ10540 mRNA and protein expressions. Functionally, FLJ10540 transfectant alone, or stimulated with osteopontin, exhibited fast growth and increased metastasis as compared to vehicle control with or without osteopontin stimulation. Conversely, knockdown of FLJ10540 by siRNA results in the suppression of NPC cell growth and motility. Treatment with anti-CD44 antibodies in NPC parental cells not only resulted in a decrease of FLJ10540 protein, but also affected the abilities of FLJ10540-elicited cell growth and motility in osteopontin stimulated-NPC cells. Conclusions These findings suggest that FLJ10540 may be critical regulator of disease progression in NPC, and the underlying mechanism may involve in the osteopontin/CD44 pathway.
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Affiliation(s)
- Chang-Han Chen
- Center for Translational Research in Biomedical Sciences, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
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88
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Ramialison M, Reinhardt R, Henrich T, Wittbrodt B, Kellner T, Lowy CM, Wittbrodt J. Cis-regulatory properties of medaka synexpression groups. Development 2012; 139:917-28. [PMID: 22318626 DOI: 10.1242/dev.071803] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
During embryogenesis, tissue specification is triggered by the expression of a unique combination of developmental genes and their expression in time and space is crucial for successful development. Synexpression groups are batteries of spatiotemporally co-expressed genes that act in shared biological processes through their coordinated expression. Although several synexpression groups have been described in numerous vertebrate species, the regulatory mechanisms that orchestrate their common complex expression pattern remain to be elucidated. Here we performed a pilot screen on 560 genes of the vertebrate model system medaka (Oryzias latipes) to systematically identify synexpression groups and investigate their regulatory properties by searching for common regulatory cues. We find that synexpression groups share DNA motifs that are arranged in various combinations into cis-regulatory modules that drive co-expression. In contrast to previous assumptions that these genes are located randomly in the genome, we discovered that genes belonging to the same synexpression group frequently occur in synexpression clusters in the genome. This work presents a first repertoire of synexpression group common signatures, a resource that will contribute to deciphering developmental gene regulatory networks.
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Affiliation(s)
- Mirana Ramialison
- University of Heidelberg, Centre for Organismal Studies, Heidelberg, Germany.
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89
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Christ A, Maegele I, Ha N, Nguyen HH, Crespi MD, Maizel A. In silico identification and in vivo validation of a set of evolutionary conserved plant root-specific cis-regulatory elements. Mech Dev 2012; 130:70-81. [PMID: 22504372 DOI: 10.1016/j.mod.2012.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 03/07/2012] [Accepted: 03/27/2012] [Indexed: 10/28/2022]
Abstract
Marker genes are specifically expressed in a tissue, organ or time of development. Here we used a computational screen to identify marker genes of the root in Arabidopsis thaliana. We mined the existing transcriptome datasets for genes having high expression in roots while being low in all other organs under a wide range of growth conditions. We show that the root-specificity of these genes is conserved in the sister species Arabidopsis lyrata, indicating that their expression pattern is under selective pressure. We delineated the cis-regulatory elements responsible for root-specific expression and validated two third of those in planta as bona fide root-specific regulatory sequences. We identified three motifs over-represented in these sequences, which mutation resulted in alteration of root-specific expression, demonstrating that these motifs are functionally relevant. In addition, the three motifs are also over-represented in the cis-regulatory regions of the A. lyrata orthologs of our root-specific genes, and this despite an overall low degree of sequence conservation of these regions. Our results provide a resource to assess root-identity in the model genus Arabidopsis and shed light on the evolutionary history of gene regulation in plants.
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Affiliation(s)
- Aurélie Christ
- Institut des Sciences du Végétal CNRS UPR2355, F-91190 Gif-sur-Yvette, France
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90
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Mar JC, Matigian NA, Quackenbush J, Wells CA. attract: A method for identifying core pathways that define cellular phenotypes. PLoS One 2011; 6:e25445. [PMID: 22022396 PMCID: PMC3194807 DOI: 10.1371/journal.pone.0025445] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 09/05/2011] [Indexed: 11/23/2022] Open
Abstract
attract is a knowledge-driven analytical approach for identifying and annotating the gene-sets that best discriminate between cell phenotypes. attract finds distinguishing patterns within pathways, decomposes pathways into meta-genes representative of these patterns, and then generates synexpression groups of highly correlated genes from the entire transcriptome dataset. attract can be applied to a wide range of biological systems and is freely available as a Bioconductor package and has been incorporated into the MeV software system.
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Affiliation(s)
- Jessica C. Mar
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- * E-mail: (CAW); (JQ); (JCM)
| | - Nicholas A. Matigian
- National Centre for Adult Stem Cell Research, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, Queensland, Australia
| | - John Quackenbush
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- National Centre for Adult Stem Cell Research, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, Queensland, Australia
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- * E-mail: (CAW); (JQ); (JCM)
| | - Christine A. Wells
- National Centre for Adult Stem Cell Research, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Brisbane, Queensland, Australia
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- * E-mail: (CAW); (JQ); (JCM)
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91
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Ormestad M, Martindale MQ, Röttinger E. A comparative gene expression database for invertebrates. EvoDevo 2011; 2:17. [PMID: 21861937 PMCID: PMC3180427 DOI: 10.1186/2041-9139-2-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 08/24/2011] [Indexed: 12/02/2022] Open
Abstract
Background As whole genome and transcriptome sequencing gets cheaper and faster, a great number of 'exotic' animal models are emerging, rapidly adding valuable data to the ever-expanding Evo-Devo field. All these new organisms serve as a fantastic resource for the research community, but the sheer amount of data, some published, some not, makes detailed comparison of gene expression patterns very difficult to summarize - a problem sometimes even noticeable within a single lab. The need to merge existing data with new information in an organized manner that is publicly available to the research community is now more necessary than ever. Description In order to offer a homogenous way of storing and handling gene expression patterns from a variety of organisms, we have developed the first web-based comparative gene expression database for invertebrates that allows species-specific as well as cross-species gene expression comparisons. The database can be queried by gene name, developmental stage and/or expression domains. Conclusions This database provides a unique tool for the Evo-Devo research community that allows the retrieval, analysis and comparison of gene expression patterns within or among species. In addition, this database enables a quick identification of putative syn-expression groups that can be used to initiate, among other things, gene regulatory network (GRN) projects.
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Affiliation(s)
- Mattias Ormestad
- Kewalo Marine Laboratory, PBRC, University of Hawaii at Manoa, 41, Ahui Street, Honolulu, 96734, HI, USA.
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Negative feedback in the bone morphogenetic protein 4 (BMP4) synexpression group governs its dynamic signaling range and canalizes development. Proc Natl Acad Sci U S A 2011; 108:10202-7. [PMID: 21633009 DOI: 10.1073/pnas.1100179108] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
What makes embryogenesis a robust and canalized process is an important question in developmental biology. A bone morphogenetic protein (BMP) morphogen gradient plays a key role in embryonic development, and we are beginning to understand how the self-regulating properties of its signaling circuitry ensure robust embryonic patterning. An unexplored question is why the BMP signaling circuit is organized as a modular synexpression group, with a prevalence of feedback inhibitors. Here, we provide evidence from direct experimentation and mathematical modeling that the synexpressed feedback inhibitors BAMBI, SMAD6, and SMAD7 (i) expand the dynamic BMP signaling range essential for proper embryonic patterning and (ii) reduce interindividual phenotypic and molecular variability in Xenopus embryos. Thereby, negative feedback linearizes signaling responses and confers robust patterning, thus promoting canalized development. The presence of negative feedback inhibitors in other growth factor synexpression groups suggests that these properties may constitute a general principle.
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93
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High-throughput analysis of gene expression on tissue sections by in situ hybridization. Methods 2011; 53:417-23. [DOI: 10.1016/j.ymeth.2010.12.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 12/07/2010] [Accepted: 12/17/2010] [Indexed: 11/18/2022] Open
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94
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Morris AR, Mukherjee N, Keene JD. Systematic analysis of posttranscriptional gene expression. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 2:162-180. [PMID: 20836020 DOI: 10.1002/wsbm.54] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent systems studies of gene expression have begun to dissect the layers of regulation that underlie the eukaryotic transcriptome, the combined consequence of transcriptional and posttranscriptional events. Among the regulatory layers of the transcriptome are those of the ribonome, a highly dynamic environment of ribonucleoproteins in which RNA-binding proteins (RBPs), noncoding regulatory RNAs (ncRNAs) and messenger RNAs (mRNAs) interact. While multiple mRNAs are coordinated together in groups within the ribonome of a eukaryotic cell, each individual type of mRNA consists of multiple copies, each of which has an opportunity to be a member of more than one modular group termed a posttranscriptional RNA operon or regulon (PTRO). The mRNAs associated with each PTRO encode functionally related proteins and are coordinated at the levels of RNA stability and translation by the actions of the specific RBPs and noncoding regulatory RNAs. This article examines the methods that led to the elucidation of PTROs and the coordinating mechanisms that appear to regulate the RNA components of PTROs. Moreover, the article considers the characteristics of the dynamic systems that drive PTROs and how mRNA components are bound collectively in physical 'states' to respond to cellular perturbations and diseases. In conclusion, these studies have challenged the extent to which cellular mRNA abundance can inform investigators of the functional status of a biological system. We argue that understanding the ribonome has greater potential for illuminating the underlying coordination principles of growth, differentiation, and disease.
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Affiliation(s)
- Adam R Morris
- University Program in Genetics and Genomics, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Neelanjan Mukherjee
- University Program in Genetics and Genomics, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Jack D Keene
- University Program in Genetics and Genomics, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
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95
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Transcription factors expressed in olfactory bulb local progenitor cells revealed by genome-wide transcriptome profiling. Mol Cell Neurosci 2010; 46:548-61. [PMID: 21194568 DOI: 10.1016/j.mcn.2010.12.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/30/2010] [Accepted: 12/22/2010] [Indexed: 12/26/2022] Open
Abstract
The local progenitor population in the olfactory bulb (OB) gives rise to mitral and tufted projection neurons during embryonic development. In contrast, OB interneurons are derived from sources outside the bulb where neurogenesis continues throughout life. While many of the genes involved in OB interneuron development have been characterized, the genetic pathways driving local progenitor cell differentiation in this tissue are largely unknown. To better understand this process, we used transcriptional profiling to monitor gene expression of whole OB at daily intervals from embryonic day 11 through birth, generating a compendium of gene expression encompassing the major developmental events of this tissue. Through hierarchical clustering, bioinformatics analysis, and validation by RNA in situ hybridizations, we identified a large number of transcription factors, DNA binding proteins, and cell cycle-related genes expressed by the local neural progenitor cells (NPCs) of the embryonic OB. Further in silico analysis of transcription factor binding sites identified an enrichment of genes regulated by the E2F-Rb pathway among those expressed in the local NPC population. Together these results provide initial insights into the molecular identity of the OB local NPC population and the transcription factor networks that may regulate their function.
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96
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Fraser GJ, Cerny R, Soukup V, Bronner-Fraser M, Streelman JT. The odontode explosion: the origin of tooth-like structures in vertebrates. Bioessays 2010; 32:808-17. [PMID: 20730948 DOI: 10.1002/bies.200900151] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Essentially we show recent data to shed new light on the thorny controversy of how teeth arose in evolution. Essentially we show (a) how teeth can form equally from any epithelium, be it endoderm, ectoderm or a combination of the two and (b) that the gene expression programs of oral versus pharyngeal teeth are remarkably similar. Classic theories suggest that (i) skin denticles evolved first and odontode-inductive surface ectoderm merged inside the oral cavity to form teeth (the 'outside-in' hypothesis) or that (ii) patterned odontodes evolved first from endoderm deep inside the pharyngeal cavity (the 'inside-out' hypothesis). We propose a new perspective that views odontodes as structures sharing a deep molecular homology, united by sets of co-expressed genes defining a competent thickened epithelium and a collaborative neural crest-derived ectomesenchyme. Simply put, odontodes develop 'inside and out', wherever and whenever these co-expressed gene sets signal to one another. Our perspective complements the classic theories and highlights an agenda for specific experimental manipulations in model and non-model organisms.
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Affiliation(s)
- Gareth J Fraser
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
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97
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Systematic analysis of gene expression level with tissue-specificity, function and protein subcellular localization in human transcriptome. Mol Biol Rep 2010; 38:2597-602. [PMID: 21088908 DOI: 10.1007/s11033-010-0400-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
Abstract
Recent studies have shown that, in mammals, the highly expressed genes have shorter gene length and their protein products have relatively lower evolutionary rates. However, the global relationship between genes' expression level and their features such as tissue-specificity, function and protein subcellular localization has not been investigated extensively, especially in mammalian. In order to solve it, we analysed 8,570 genes across 46 human tissues. Our results suggest that widely expressed genes have higher mean expression levels than tissue-specific ones and genes encoding zinc-finger proteins have low expression levels similar to that of DNA-binding proteins. In the analysis of protein subcellular localization, it is shown that nuclear and Golgi apparatus proteins have lower mean expression levels than those of mitochondria, endoplasmic reticulum and membrane proteins, while genes encoding cytoplasm and extracellular components display the highest expression levels. When comparing the gene expression levels and the number of expressed genes in different tissues, we found that some tissues have less active genes while single gene encodes relatively more transcripts. Taken together, gene expression levels are clearly correlated with their tissue-specificity, function and protein subcellular localization, and are highly conserved during evolution.
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98
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Tirosh-Finkel L, Zeisel A, Brodt-Ivenshitz M, Shamai A, Yao Z, Seger R, Domany E, Tzahor E. BMP-mediated inhibition of FGF signaling promotes cardiomyocyte differentiation of anterior heart field progenitors. Development 2010; 137:2989-3000. [PMID: 20702560 DOI: 10.1242/dev.051649] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The anterior heart field (AHF) encompasses a niche in which mesoderm-derived cardiac progenitors maintain their multipotent and undifferentiated nature in response to signals from surrounding tissues. Here, we investigate the signaling mechanism that promotes the shift from proliferating cardiac progenitors to differentiating cardiomyocytes in chick embryos. Genomic and systems biology approaches, as well as perturbations of signaling molecules, in vitro and in vivo, reveal tight crosstalk between the bone morphogenetic protein (BMP) and fibroblast growth factor (FGF) signaling pathways within the AHF niche: BMP4 promotes myofibrillar gene expression and cardiomyocyte contraction by blocking FGF signaling. Furthermore, inhibition of the FGF-ERK pathway is both sufficient and necessary for these processes, suggesting that FGF signaling blocks premature differentiation of cardiac progenitors in the AHF. We further revealed that BMP4 induced a set of neural crest-related genes, including MSX1. Overexpression of Msx1 was sufficient to repress FGF gene expression and cell proliferation, thereby promoting cardiomyocyte differentiation. Finally, we show that BMP-induced cardiomyocyte differentiation is diminished following cranial neural crest ablation, underscoring the key roles of these cells in the regulation of AHF cell differentiation. Hence, BMP and FGF signaling pathways act via inter- and intra-regulatory loops in multiple tissues, to coordinate the balance between proliferation and differentiation of cardiac progenitors.
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Affiliation(s)
- Libbat Tirosh-Finkel
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
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99
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Xu Y, Zhang M, Wang Y, Kadambi P, Dave V, Lu LJ, Whitsett JA. A systems approach to mapping transcriptional networks controlling surfactant homeostasis. BMC Genomics 2010; 11:451. [PMID: 20659319 PMCID: PMC3091648 DOI: 10.1186/1471-2164-11-451] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Accepted: 07/26/2010] [Indexed: 12/15/2022] Open
Abstract
Background Pulmonary surfactant is required for lung function at birth and throughout life. Lung lipid and surfactant homeostasis requires regulation among multi-tiered processes, coordinating the synthesis of surfactant proteins and lipids, their assembly, trafficking, and storage in type II cells of the lung. The mechanisms regulating these interrelated processes are largely unknown. Results We integrated mRNA microarray data with array independent knowledge using Gene Ontology (GO) similarity analysis, promoter motif searching, protein interaction and literature mining to elucidate genetic networks regulating lipid related biological processes in lung. A Transcription factor (TF) - target gene (TG) similarity matrix was generated by integrating data from different analytic methods. A scoring function was built to rank the likely TF-TG pairs. Using this strategy, we identified and verified critical components of a transcriptional network directing lipogenesis, lipid trafficking and surfactant homeostasis in the mouse lung. Conclusions Within the transcriptional network, SREBP, CEBPA, FOXA2, ETSF, GATA6 and IRF1 were identified as regulatory hubs displaying high connectivity. SREBP, FOXA2 and CEBPA together form a common core regulatory module that controls surfactant lipid homeostasis. The core module cooperates with other factors to regulate lipid metabolism and transport, cell growth and development, cell death and cell mediated immune response. Coordinated interactions of the TFs influence surfactant homeostasis and regulate lung function at birth.
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Affiliation(s)
- Yan Xu
- Division of Pulmonary Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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100
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Hu J, Wan J, Hackler L, Zack DJ, Qian J. Computational analysis of tissue-specific gene networks: application to murine retinal functional studies. ACTA ACUST UNITED AC 2010; 26:2289-97. [PMID: 20616386 DOI: 10.1093/bioinformatics/btq408] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
MOTIVATION The vertebrate retina is a complex neuronal tissue, and its development, normal functioning and response to injury and disease is subject to a variety of genetic factors. To understand better the regulatory and functional relationships between the genes expressed within the retina, we constructed an interactive gene network of the mouse retina by applying a Bayesian statistics approach to information derived from a variety of gene expression, protein-protein interaction and gene ontology annotation databases. RESULTS The network contains 673 retina-related genes. Most of them are obtained through manual literature-based curation, while the others are the genes preferentially expressed in the retina. These retina-related genes are linked by 3403 potential functional associations in the network. The prediction on the gene functional association using the Bayesian approach outperforms predictions using only one source of information. The network includes five major gene clusters, each enriched in different biological activities. There are several applications to this network. First, we identified approximately 50 hub genes that are predicted to play particularly important roles in the function of the retina. Some of them are not yet well studied. Second, we can predict novel gene functions using 'guilt by association' method. Third, we also predicted novel retinal disease-associated genes based on the network analysis. AVAILABILITY To provide easy access to the retinal network, we constructed an interactive web tool, named MoReNet, which is available at http://bioinfo.wilmer.jhu.edu/morenet/.
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Affiliation(s)
- Jianfei Hu
- Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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