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Raghavan S, Brishti MA, Bernardelli A, Mata-Daboin A, Jaggar JH, Leo MD. Extracellular glucose and dysfunctional insulin receptor signaling independently upregulate arterial smooth muscle TMEM16A expression. Am J Physiol Cell Physiol 2024; 326:C1237-C1247. [PMID: 38581667 DOI: 10.1152/ajpcell.00555.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 04/08/2024]
Abstract
Diabetes alters the function of ion channels responsible for regulating arterial smooth muscle membrane potential, resulting in vasoconstriction. Our prior research demonstrated an elevation of TMEM16A in diabetic arteries. Here, we explored the mechanisms involved in Transmembrane protein 16A (TMEM16A) gene expression. Our data indicate that a Snail-mediated repressor complex regulates arterial TMEM16A gene transcription. Snail expression was reduced in diabetic arteries while TMEM16A expression was upregulated. The TMEM16A promoter contained three canonical E-box sites. Electrophoretic mobility and super shift assays revealed that the -154 nt E-box was the binding site of the Snail repressor complex and binding of the repressor complex decreased in diabetic arteries. High glucose induced a biphasic contractile response in pressurized nondiabetic mouse hindlimb arteries incubated ex vivo. Hindlimb arteries incubated in high glucose also showed decreased phospho-protein kinase D1 and TMEM16A expression. In hindlimb arteries from nondiabetic mice, administration of a bolus dose of glucose activated protein kinase D1 signaling to induce Snail degradation. In both in vivo and ex vivo conditions, Snail expression exhibited an inverse relationship with the expression of protein kinase D1 and TMEM16A. In diabetic mouse arteries, phospho-protein kinase D1 increased while Akt2 and pGSK3β levels declined. These results indicate that in nondiabetic mice, high glucose triggers a transient deactivation of the Snail repressor complex to increase arterial TMEM16A expression independently of insulin signaling. Conversely, insulin resistance activates GSK3β signaling and enhances arterial TMEM16A channel expression. These data have uncovered the Snail-mediated regulation of arterial TMEM16A expression and its dysfunction during diabetes.NEW & NOTEWORTHY The calcium-activated chloride channel, TMEM16A, is upregulated in the diabetic vasculature to cause increased vasoconstriction. In this paper, we have uncovered that the TMEM16A gene expression is controlled by a Snail-mediated repressor complex that uncouples with both insulin-dependent and -independent pathways to allow for upregulated arterial protein expression thereby causing vasoconstriction. The paper highlights the effect of short- and long-term glucose-induced dysfunction of an ion channel expression as a causative factor in diabetic vascular disease.
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Affiliation(s)
- Somasundaram Raghavan
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - Masuma Akter Brishti
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - Angelica Bernardelli
- Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - Alejandro Mata-Daboin
- Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - Jonathan H Jaggar
- Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, United States
| | - M Dennis Leo
- Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee, United States
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, Tennessee, United States
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Cheng R, Zhou S, K C R, Lizarazo S, Mouli L, Jayanth A, Liu Q, Van Bortle K. A Combinatorial Regulatory Platform Determines Expression of RNA Polymerase III Subunit RPC7α ( POLR3G) in Cancer. Cancers (Basel) 2023; 15:4995. [PMID: 37894362 PMCID: PMC10605170 DOI: 10.3390/cancers15204995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
RNA polymerase III (Pol III) subunit RPC7α, which is encoded by POLR3G in humans, has been linked to both tumor growth and metastasis. Accordantly, high POLR3G expression is a negative prognostic factor in multiple cancer subtypes. To date, the mechanisms underlying POLR3G upregulation have remained poorly defined. We performed a large-scale genomic survey of mRNA and chromatin signatures to predict drivers of POLR3G expression in cancer. Our survey uncovers positive determinants of POLR3G expression, including a gene-internal super-enhancer bound with multiple transcription factors (TFs) that promote POLR3G expression, as well as negative determinants that include gene-internal DNA methylation, retinoic-acid induced differentiation, and MXD4-mediated disruption of POLR3G expression. We show that novel TFs identified in our survey, including ZNF131 and ZNF207, functionally enhance POLR3G expression, whereas MXD4 likely obstructs MYC-driven expression of POLR3G and other growth-related genes. Integration of chromatin architecture and gene regulatory signatures identifies additional factors, including histone demethylase KDM5B, as likely influencers of POLR3G gene activity. Taken together, our findings support a model in which POLR3G expression is determined with multiple factors and dynamic regulatory programs, expanding our understanding of the circuitry underlying POLR3G upregulation and downstream consequences in cancer.
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Affiliation(s)
- Ruiying Cheng
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; (R.C.); (S.Z.)
| | - Sihang Zhou
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; (R.C.); (S.Z.)
| | - Rajendra K C
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA;
| | - Simon Lizarazo
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA;
| | - Leela Mouli
- School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; (L.M.); (A.J.)
| | - Anshita Jayanth
- School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; (L.M.); (A.J.)
| | - Qing Liu
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA;
- Center for Human Genetics, Clemson University, Greenwood, SC 29646, USA
| | - Kevin Van Bortle
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; (R.C.); (S.Z.)
- School of Molecular and Cellular Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; (L.M.); (A.J.)
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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3
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Liu T, Liao J, Shi M, Li L, Liu Q, Cui X, Ning W, Kai G. A jasmonate-responsive bHLH transcription factor TaMYC2 positively regulates triterpenes biosynthesis in Taraxacum antungense Kitag. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111506. [PMID: 36283577 DOI: 10.1016/j.plantsci.2022.111506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/18/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Dandelion is a well-known traditional medical herb, also used as functional food. Dandelion possesses many medical properties, such as anti-bacterial and antioxidant activity and contains a variety of triterpenes, such as α-amyrin, β-amyrin, taraxerol and taraxasterol. In this study, we found that triterpenes biosynthesis was promoted by methyl jasmonate (MeJA), while the transcriptional mechanism underlying triterpenes biosynthesis was rarely investigated. Here, a MeJA-induced bHLH transcription factor TaMYC2 was identified. The content of taraxasterol and taraxerol in dandelion was obviously enhanced in overexpression TaMYC2 transgenic lines and expression level of the squalene synthase gene (TaSS) was elevated to about 3-5 folds compared with the control lines. Dual-LUC, Y1H and EMSA experiments revealed that TaMYC2 bound to the E-box motif in the promoter of TaSS and activated its transcription. Taken together, this study suggested that TaMYC2 acted as a positive regulator for bioengineering approaches to produce high content triterpenes-producing dandelions.
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Affiliation(s)
- Tingyao Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Jingjing Liao
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, PR China
| | - Min Shi
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, School of Pharmacy and Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 311402, PR China
| | - Li Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Qun Liu
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, School of Pharmacy and Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 311402, PR China; Institute o f Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem.SunYat-Sen), Nanjing 210014, PR China
| | - Xin Cui
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Wei Ning
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, PR China.
| | - Guoyin Kai
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, School of Pharmacy and Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou 311402, PR China.
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4
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Stabilization of hypoxia-inducible factor-1α alleviates osteoarthritis via interacting with Per2 and resetting the circadian clock. Tissue Cell 2022; 79:101942. [DOI: 10.1016/j.tice.2022.101942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 11/20/2022]
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5
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Mattam AJ, Chaudhari YB, Velankar HR. Factors regulating cellulolytic gene expression in filamentous fungi: an overview. Microb Cell Fact 2022; 21:44. [PMID: 35317826 PMCID: PMC8939176 DOI: 10.1186/s12934-022-01764-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/27/2022] [Indexed: 12/19/2022] Open
Abstract
The growing demand for biofuels such as bioethanol has led to the need for identifying alternative feedstock instead of conventional substrates like molasses, etc. Lignocellulosic biomass is a relatively inexpensive feedstock that is available in abundance, however, its conversion to bioethanol involves a multistep process with different unit operations such as size reduction, pretreatment, saccharification, fermentation, distillation, etc. The saccharification or enzymatic hydrolysis of cellulose to glucose involves a complex family of enzymes called cellulases that are usually fungal in origin. Cellulose hydrolysis requires the synergistic action of several classes of enzymes, and achieving the optimum secretion of these simultaneously remains a challenge. The expression of fungal cellulases is controlled by an intricate network of transcription factors and sugar transporters. Several genetic engineering efforts have been undertaken to modulate the expression of cellulolytic genes, as well as their regulators. This review, therefore, focuses on the molecular mechanism of action of these transcription factors and their effect on the expression of cellulases and hemicellulases.
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Affiliation(s)
- Anu Jose Mattam
- Hindustan Petroleum Green R and D Centre (HPGRDC), KIADB Industrial Area, Tarabanahalli, Devanagundi, Hoskote, Bangalore, 560067, India
| | - Yogesh Babasaheb Chaudhari
- Hindustan Petroleum Green R and D Centre (HPGRDC), KIADB Industrial Area, Tarabanahalli, Devanagundi, Hoskote, Bangalore, 560067, India
| | - Harshad Ravindra Velankar
- Hindustan Petroleum Green R and D Centre (HPGRDC), KIADB Industrial Area, Tarabanahalli, Devanagundi, Hoskote, Bangalore, 560067, India.
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6
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Zhang L, He G, Li Y, Yang Z, Liu T, Xie X, Kong X, Sun J. PIL transcription factors directly interact with SPLs and repress tillering/branching in plants. THE NEW PHYTOLOGIST 2022; 233:1414-1425. [PMID: 34800046 DOI: 10.1111/nph.17872] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/14/2021] [Indexed: 05/27/2023]
Abstract
Tillering is an important parameter of plant architecture in cereal crops. In this study, we identified the PHYTOCHROME-INTERACTING FACTOR-LIKE (PIL) family transcription factors as new repressors of tillering in cereal crops. Using biochemical and genetic approaches, we explore the roles of TaPIL1 in regulating wheat plant architecture. We found that the PIL protein TaPIL1 controls tiller number in wheat. Overexpression of TaPIL1 reduces wheat tiller number; additionally, overexpression of TaPIL1-SUPERMAN repression domain increases wheat tiller number. Furthermore, we show that TaPIL1 activates the transcriptional expression of wheat TEOSINTE BRANCHED1 (TaTB1); moreover, TaPIL1 physically interacts with wheat SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (TaSPL)3/17, which are activators of TaTB1 transcription. In rice, overexpression and loss-of-function mutations of OsPIL11 reduce or increase tiller number by regulating the expression of OsTB1. In Arabidopsis, we demonstrate that PHYTOCHROME-INTERACTING FACTOR 4 interacts with SPL9 to inhibit shoot branching. This study reveals that PIL family transcription factors directly interact with SPLs and play an important role in repressing tillering/branching in plants.
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Affiliation(s)
- Lichao Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guanhua He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yaping Li
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Ziyi Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tianqi Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianzhi Xie
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Xiuying Kong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiaqiang Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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7
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Zhao L, Chen P, Liu P, Song Y, Zhang D. Genetic Effects and Expression Patterns of the Nitrate Transporter (NRT) Gene Family in Populus tomentosa. FRONTIERS IN PLANT SCIENCE 2021; 12:661635. [PMID: 34054902 PMCID: PMC8155728 DOI: 10.3389/fpls.2021.661635] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/06/2021] [Indexed: 05/22/2023]
Abstract
Nitrate is an important source of nitrogen for poplar trees. The nitrate transporter (NRT) gene family is generally responsible for nitrate absorption and distribution. However, few analyses of the genetic effects and expression patterns of NRT family members have been conducted in woody plants. Here, using poplar as a model, we identified and characterized 98 members of the PtoNRT gene family. We calculated the phylogenetic and evolutionary relationships of the PtoNRT family and identified poplar-specific NRT genes and their expression patterns. To construct a core triple genetic network (association - gene expression - phenotype) for leaf nitrogen content, a candidate gene family association study, weighted gene co-expression network analysis (WGCNA), and mapping of expression quantitative trait nucleotides (eQTNs) were combined, using data from 435 unrelated Populus. tomentosa individuals. PtoNRT genes exhibited distinct expression patterns between twelve tissues, circadian rhythm points, and stress responses. The association study showed that genotype combinations of allelic variations of three PtoNRT genes had a strong effect on leaf nitrogen content. WGCNA produced two co-expression modules containing PtoNRT genes. We also found that four PtoNRT genes defined thousands of eQTL signals. WGCNA and eQTL provided comprehensive analysis of poplar nitrogen-related regulatory factors, including MYB17 and WRKY21. NRT genes were found to be regulated by five plant hormones, among which abscisic acid was the main regulator. Our study provides new insights into the NRT gene family in poplar and enables the exploitation of novel genetic factors to improve the nitrate use efficiency of trees.
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Affiliation(s)
- Lei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Panfei Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Peng Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yuepeng Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Deqiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Deqiang Zhang,
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8
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Hassani D, Fu X, Shen Q, Khalid M, Rose JKC, Tang K. Parallel Transcriptional Regulation of Artemisinin and Flavonoid Biosynthesis. TRENDS IN PLANT SCIENCE 2020; 25:466-476. [PMID: 32304658 DOI: 10.1016/j.tplants.2020.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 11/27/2019] [Accepted: 01/13/2020] [Indexed: 06/11/2023]
Abstract
Plants regulate the synthesis of specialized compounds through the actions of individual transcription factors (TFs) or sets of TFs. One such compound, artemisinin from Artemisia annua, is widely used as a pharmacological product in the first-line treatment of malaria. However, the emergence of resistance to artemisinin in Plasmodium species, as well as its low production rates, have required innovative treatments such as exploiting the synergistic effects of flavonoids with artemisinin. We overview current knowledge about flavonoid and artemisinin transcriptional regulation in A. annua, and review the dual action of TFs and structural genes that can regulate both pathways simultaneously. Understanding the concerted action of these TFs and their associated structural genes can guide the development of strategies to further improve flavonoid and artemisinin production.
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Affiliation(s)
- Danial Hassani
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China
| | - Xueqing Fu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China
| | - Qian Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China
| | - Muhammad Khalid
- Key Laboratory of Urban Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Kexuan Tang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University (SJTU), Shanghai 200240, China.
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9
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Fan X, Jin S, Li Y, Khadaroo PA, Dai Y, He L, Zhou D, Lin H. Genetic And Epigenetic Regulation Of E-Cadherin Signaling In Human Hepatocellular Carcinoma. Cancer Manag Res 2019; 11:8947-8963. [PMID: 31802937 PMCID: PMC6801489 DOI: 10.2147/cmar.s225606] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/27/2019] [Indexed: 12/24/2022] Open
Abstract
E-cadherin is well known as a growth and invasion suppressor and belongs to the large cadherin family. Loss of E-cadherin is widely known as the hallmark of epithelial-to-mesenchymal transition (EMT) with the involvement of transcription factors such as Snail, Slug, Twist and Zeb1/2. Tumor cells undergoing EMT could migrate to distant sites and become metastases. Recently, numerous studies have revealed how the expression of E-cadherin is regulated by different kinds of genetic and epigenetic alteration, which are implicated in several crucial transcription factors and pathways. E-cadherin signaling plays an important role in hepatocellular carcinoma (HCC) initiation and progression considering the highly mutated frequency of CTNNB1 (27%). Combining the data from The Cancer Genome Atlas (TCGA) database and previous studies, we have summarized the roles of gene mutations, chromosome instability, DNA methylation, histone modifications and non-coding RNA in E-cadherin in HCC. In this review, we discuss the current understanding of the relationship between these modifications and HCC. Perspectives on E-cadherin-related research in HCC are provided.
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Affiliation(s)
- Xiaoxiao Fan
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Shengxi Jin
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China.,School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Yirun Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Parikshit Asutosh Khadaroo
- School of Medicine, Zhejiang University, Hangzhou, People's Republic of China.,School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Yili Dai
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China.,School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Lifeng He
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Daizhan Zhou
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Hui Lin
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
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10
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Choudhury S. Genomics of the OLIG family of a bHLH transcription factor associated with oligo dendrogenesis. Bioinformation 2019; 15:430-438. [PMID: 31312081 PMCID: PMC6614118 DOI: 10.6026/97320630015430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/07/2019] [Indexed: 01/28/2023] Open
Abstract
The glial cell neoplasms are not fully classified by using cellular morphology. However, this is possible using known molecular markers in
glial development. Oligo-dendrocyte lineage gene induces differentiation of neural progenitors and putative immature progenitor cells of
the adult central nervous system. These oligo-dendrocyte lineage genes OLIG1 and OLIG2 encode basic helix-loop-helix transcription
factors. The murine bHLH transcription factors found in chromosome 21 are essential for oligo-dendrocyte development. Moreover, OLIG3
of the OLIG family is known to be linked with the brain and spinal cord development. Therefore, it is of interest to analyse oligodendrocyte
lineage genes in the OLIG family of bHLH domain for the understanding of oligo-dendrogenesis in eukaryotes. Several bHLH
domain linked basic-helix-loop-helix transcription factors in Homo sapiens and Mus musculus from this analysis are reported. Thus,
genomics data analysis of OLIG family of bHLH transcription factors help explain observed similarity and differences within the molecular
evolutionary context and hence assess the functional significance of the distinct genetic blueprints
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11
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Detection of nucleotide sequences capable of forming non-canonical DNA structures: Application of automata theory. Comput Biol Chem 2019; 80:278-283. [PMID: 31054540 DOI: 10.1016/j.compbiolchem.2019.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 11/24/2022]
Abstract
In this study, we develop a program that allows us to reveal DNA receptors, i.e. nucleotide sequences that may form more than one non-canonical structure. The data obtained may be analysed either experimentally or using DNA banks, and refers to the coding, non-coding or promotor region of the gene. These results provide a better understanding of the role that non-canonical structures play in pathological modifications of the genetic apparatus, resulting in tumour formation or inherited disease. They also reveal the effect of single nucleotide polymorphisms on gene expression, indicate so-called "risk regions" in which the substitution of a single nucleotide may lead to increased formation of non-canonical structures, and elucidate the epigenetic mechanisms of microorganism adaptation.
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Onoue T, Nishi G, Hikima JI, Sakai M, Kono T. Circadian oscillation of TNF-α gene expression regulated by clock gene, BMAL1 and CLOCK1, in the Japanese medaka (Oryzias latipes). Int Immunopharmacol 2019; 70:362-371. [DOI: 10.1016/j.intimp.2019.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/02/2019] [Accepted: 02/04/2019] [Indexed: 01/08/2023]
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Lu Y, Liao S, Tu W, Yang B, Liu S, Pei X, Tao D, Lu Y, Ma Y, Yang Y, Liu Y. DNA demethylation facilitates the specific transcription of the mouse X-linked Tsga8 gene in round spermatids†. Biol Reprod 2019; 100:994-1007. [PMID: 30541061 DOI: 10.1093/biolre/ioy255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 10/08/2018] [Accepted: 12/11/2018] [Indexed: 02/05/2023] Open
Abstract
Some X-linked genes necessary for spermiogenesis are specifically activated in the postmeiotic germ cells. However, the regulatory mechanism about this activation is not clearly understood. Here, we examined the potential mechanism controlling the transcriptional activation of the mouse testis specific gene A8 (Tsga8) gene in round spermatids. We observed that the Tsga8 expression was negatively correlated with the methylation level of the CpG sites in its core promoter. During spermatogenesis, the Tsga8 promoter was methylated in spermatogonia, and then demethylated in spermatocytes. The demethylation status of Tsga8 promoter was maintained through the postmeiotic germ cells, providing a potentially active chromatin for Tsga8 transcription. In vitro investigation showed that the E12 and Spz1 transcription factors can enhance the Tsga8 promoter activity by binding to the unmethylated E-box motif within the Tsga8 promoter. Additionally, the core Tsga8 promoter drove green fluorescent protein (GFP) expression in the germ cells of Tsga8-GFP transgenic mice, and the GFP expression pattern was similar to that of endogenous Tsga8. Moreover, the DNA methylation profile of the Tsga8-promoter-driven transgene was consistent with that of the endogenous Tsga8 promoter, indicating the existence of a similar epigenetic modification for the Tsga8 promoter to ensure its spatiotemporal expression in vivo. Taken together, this study reports the details of a regulatory mechanism that includes DNA methylation and transcription factors to mediate the postmeiotic expression of an X-linked gene.
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Affiliation(s)
- Yongjie Lu
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan Province, China
| | - Shunyao Liao
- Diabetic Center and Institute of Transplantation, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
| | - Wenling Tu
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan Province, China
| | - Bo Yang
- Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shasha Liu
- Diabetic Center and Institute of Transplantation, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
| | - Xue Pei
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan Province, China
| | - Dachang Tao
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan Province, China
| | - Yilu Lu
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan Province, China
| | - Yongxin Ma
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan Province, China
| | - Yuan Yang
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan Province, China
| | - Yunqiang Liu
- Department of Medical Genetics and Division of Human Morbid Genomics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan Province, China
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Jin K, Xiang M. Transcription factor Ptf1a in development, diseases and reprogramming. Cell Mol Life Sci 2019; 76:921-940. [PMID: 30470852 PMCID: PMC11105224 DOI: 10.1007/s00018-018-2972-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022]
Abstract
The transcription factor Ptf1a is a crucial helix-loop-helix (bHLH) protein selectively expressed in the pancreas, retina, spinal cord, brain, and enteric nervous system. Ptf1a is preferably assembled into a transcription trimeric complex PTF1 with an E protein and Rbpj (or Rbpjl). In pancreatic development, Ptf1a is indispensable in controlling the expansion of multipotent progenitor cells as well as the specification and maintenance of the acinar cells. In neural tissues, Ptf1a is transiently expressed in the post-mitotic cells and specifies the inhibitory neuronal cell fates, mostly mediated by downstream genes such as Tfap2a/b and Prdm13. Mutations in the coding and non-coding regulatory sequences resulting in Ptf1a gain- or loss-of-function are associated with genetic diseases such as pancreatic and cerebellar agenesis in the rodent and human. Surprisingly, Ptf1a alone is sufficient to reprogram mouse or human fibroblasts into tripotential neural stem cells. Its pleiotropic functions in many biological processes remain to be deciphered in the future.
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Affiliation(s)
- Kangxin Jin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
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15
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Kurafeiski JD, Pinto P, Bornberg-Bauer E. Evolutionary Potential of Cis-Regulatory Mutations to Cause Rapid Changes in Transcription Factor Binding. Genome Biol Evol 2019; 11:406-414. [PMID: 30597011 PMCID: PMC6370388 DOI: 10.1093/gbe/evy269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2018] [Indexed: 01/25/2023] Open
Abstract
Transcriptional regulation is crucial for all biological processes and well investigated at the molecular level for a wide range of organisms. However, it is quite unclear how innovations, such as the activity of a novel regulatory element, evolve. In the case of transcription factor (TF) binding, both a novel TF and a novel-binding site would need to evolve concertedly. Since promiscuous functions have recently been identified as important intermediate steps in creating novel specific functions in many areas such as enzyme evolution and protein-protein interactions, we ask here how promiscuous binding of TFs to TF-binding sites (TFBSs) affects the robustness and evolvability of this tightly regulated system. Specifically, we investigate the binding behavior of several hundred TFs from different species at unprecedented breadth. Our results illustrate multiple aspects of TF-binding interactions, ranging from correlations between the strength of the interaction bond and specificity, to preferences regarding TFBS nucleotide composition in relation to both domains and binding specificity. We identified a subset of high A/T binding motifs. Motifs in this subset had many functionally neutral one-error mutants, and were bound by multiple different binding domains. Our results indicate that, especially for some TF-TFBS associations, low binding specificity confers high degrees of evolvability, that is that few mutations facilitate rapid changes in transcriptional regulation, in particular for large and old TF families. In this study we identify binding motifs exhibiting behavior indicating high evolutionary potential for innovations in transcriptional regulation.
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Affiliation(s)
| | - Paulo Pinto
- Molecular Evolution and Bioinformatics, University of Muenster, Germany
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Shishay G, Liu G, Jiang X, Yu Y, Teketay W, Du D, Jing H, Liu C. Variation in the Promoter Region of the MC4R Gene Elucidates the Association of Body Measurement Traits in Hu Sheep. Int J Mol Sci 2019; 20:E240. [PMID: 30634446 PMCID: PMC6358852 DOI: 10.3390/ijms20020240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/24/2018] [Accepted: 12/30/2018] [Indexed: 12/15/2022] Open
Abstract
The melanocortin 4 receptor (MC4R) gene is expressed in the appetite-regulating areas of the brain and is engaged in the leptin signaling pathway. Although previous studies have identified variants in the coding region of the sheep MC4R gene showing significant associations with birth weight, weaning weight, and backfat thickness, no such associations have been reported for the promoter region. Besides, the essential promoter region of the sheep MC4R has not been delineated. In this study, to better understand the transcriptional regulation of MC4R and to elucidate the association between regulatory variants and haplotypes with body measurement traits in sheep, we cloned and characterized the MC4R promoter. We found that the minimal promoter of the gene is located within the region -1207/-880 bp upstream of the first exon. Real-time quantitative PCR (RT-qPCR) data revealed the mRNA expression of the MC4R gene had a significant difference between sex and age. In the association analysis, eight single nucleotide polymorphisms (SNPs) had a significant association with one or more traits (p < 0.05); of these, two SNPs were novel. Notably, individuals with haplotype H1H2 (CT-GA-GT-GA-GT-GA-GA-CG) were heavier in body weight than other haplotypes. Altogether, variations in the MC4R gene promoter, most notably haplotype H1H2, may greatly benefit marker-assisted selection in sheep.
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Affiliation(s)
- Girmay Shishay
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Guiqiong Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yun Yu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wassie Teketay
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dandan Du
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Huang Jing
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chenghui Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.
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Gotoh H, Wood WM, Patel KD, Factor DC, Boshans LL, Nomura T, Tesar PJ, Ono K, Nishiyama A. NG2 expression in NG2 glia is regulated by binding of SoxE and bHLH transcription factors to a Cspg4 intronic enhancer. Glia 2018; 66:2684-2699. [PMID: 30306660 PMCID: PMC6309483 DOI: 10.1002/glia.23521] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 07/27/2018] [Accepted: 08/03/2018] [Indexed: 11/08/2022]
Abstract
NG2 is a type 1 integral membrane glycoprotein encoded by the Cspg4 gene. It is expressed on glial progenitor cells known as NG2 glial cells or oligodendrocyte precursor cells that exist widely throughout the developing and mature central nervous system and vascular mural cells but not on mature oligodendrocytes, astrocytes, microglia, neurons, or neural stem cells. Hence NG2 is widely used as a marker for NG2 glia in the rodent and human. The regulatory elements of the mouse Cspg4 gene and its flanking sequences have been used successfully to target reporter and Cre recombinase to NG2 glia in transgenic mice when used in a large 200 kb bacterial artificial chromosome cassette containing the 38 kb Cspg4 gene in the center. Despite the tightly regulated cell type- and stage-specific expression of NG2 in the brain and spinal cord, the mechanisms that regulate its transcription have remained unknown. Here, we describe a 1.45 kb intronic enhancer of the mouse Cspg4 gene that directed transcription of EGFP reporter to NG2 glia but not to pericytes in vitro and in transgenic mice. The 1.45 kb enhancer contained binding sites for SoxE and basic helix-loop-helix transcription factors, and its enhancer activity was augmented cooperatively by these factors, whose respective binding elements were found in close proximity to each other. Mutations in these binding elements abrogated the enhancer activity when tested in the postnatal mouse brain.
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Affiliation(s)
- Hitoshi Gotoh
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, 06269-3156, USA
- Department of Biology, Kyoto Prefectural University of Medicine, Kyoto, 606-0823, Japan
| | - William M. Wood
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, 06269-3156, USA
| | - Kiran D. Patel
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, 06269-3156, USA
| | - Daniel C. Factor
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland OH, 44106, USA
| | - Linda L. Boshans
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, 06269-3156, USA
| | - Tadashi Nomura
- Department of Biology, Kyoto Prefectural University of Medicine, Kyoto, 606-0823, Japan
| | - Paul J. Tesar
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland OH, 44106, USA
- Department of Neurosciences, Case Western Reserve University School of Medicine
| | - Katsuhiko Ono
- Department of Biology, Kyoto Prefectural University of Medicine, Kyoto, 606-0823, Japan
| | - Akiko Nishiyama
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, 06269-3156, USA
- Institute of Systems Genomics, University of Connecticut
- Institute of Brain and Cognitive Science, University of Connecticut
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Yang X, Vingron M. Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions. BMC Biol 2018; 16:138. [PMID: 30442124 PMCID: PMC6238301 DOI: 10.1186/s12915-018-0585-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 10/04/2018] [Indexed: 12/14/2022] Open
Abstract
Background Characterizing recurring sequence patterns in human promoters has been a challenging undertaking even nowadays where a near-complete overview of promoters exists. However, with the more recent availability of genomic location (ChIP-seq) data, one can approach that question through the identification of characteristic patterns of transcription factor occupancy and histone modifications. Results Based on the ENCODE annotation and integration of sequence motifs as well as three-dimensional chromatin data, we have undertaken a re-analysis of occupancy and sequence patterns in human promoters. We identify clear groups of CAAT-box and E-box sequence motif containing promoters, as well as a group of promoters whose interaction with an enhancer appears to be mediated by CCCTC-binding factor (CTCF) binding on the promoter. We also extend our analysis to inactive promoters, showing that only a surprisingly small number of inactive promoters is repressed by the polycomb complex. We also identify combinatorial patterns of transcription factor interactions indicated by the ChIP-seq signals. Conclusion Our analysis defines subgroups of promoters characterized by stereotypic patterns of transcription factor occupancy, and combinations of specific sequence patterns which are required for their binding. This grouping provides new hypotheses concerning the assembly and dynamics of transcription factor complexes at their respective promoter groups, as well as questions on the evolutionary origin of these groups. Electronic supplementary material The online version of this article (10.1186/s12915-018-0585-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xinyi Yang
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Ihnestraße 63-73, Berlin, 14195, Germany
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany, Ihnestraße 63-73, Berlin, 14195, Germany.
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19
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Oxygen-dependent distinct expression of hif-1α gene in aerobic and anaerobic tissues of the Amazon Oscar, Astronotus crassipinnis. Comp Biochem Physiol B Biochem Mol Biol 2018; 227:31-38. [PMID: 30201405 DOI: 10.1016/j.cbpb.2018.08.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 11/24/2022]
Abstract
The aquatic habitats of the Amazon basin present dramatic variation of oxygen level, and, to survive such changes, many aquatic animals developed biochemical and physiological adaptations. The advanced teleost Astronotus crassipinnis (Perciformes) is a fish tolerant to hypoxia and known to endure such naturally variable environments. Hypoxia-Inducible factor-1α (hif-1α) is among the most important and studied genes related to hypoxia-tolerance, maintaining regular cellular function and controlling anaerobic metabolism. In the present work, we studied hif-1α expression and related it to changes in metabolic pathways of Astronotus crassipinnis exposed to 1, 3 and 5 h of hypoxia, followed by 3 h of recovery. The results show that A. crassipinnis depresses aerobic metabolic under hypoxia, with a decrease in glycolysis and oxidative enzyme activities, and increases its anaerobic metabolism with an increase in LDH activity coupled with a decrease in oxygen consumption, which indicates an increase in anaerobic capacity. In addition, the animal differentially regulates hif-1α gene in each tissue studied, with a positive relationship to its metabolic profile, suggesting that hif-1α might be one of the most important induction factors that regulate hypoxia tolerance in this species.
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20
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Zhao Y, Meng J, Cao G, Gao P, Dong C. Screening the optimal activity region of the dopachrome tautomerase gene promoter in sheep skin melanocytes. JOURNAL OF APPLIED ANIMAL RESEARCH 2018. [DOI: 10.1080/09712119.2018.1512497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Yuanyuan Zhao
- Wujiang college, Tongren University, Tongren, People's Republic of China
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu, People’s Republic of China
| | - Jinzhu Meng
- Wujiang college, Tongren University, Tongren, People's Republic of China
| | - Guoqing Cao
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu, People’s Republic of China
| | - Pengfei Gao
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu, People’s Republic of China
| | - Changsheng Dong
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu, People’s Republic of China
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21
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Xu YH, Liao YC, Lv FF, Zhang Z, Sun PW, Gao ZH, Hu KP, Sui C, Jin Y, Wei JH. Transcription Factor AsMYC2 Controls the Jasmonate-Responsive Expression of ASS1 Regulating Sesquiterpene Biosynthesis in Aquilaria sinensis (Lour.) Gilg. PLANT & CELL PHYSIOLOGY 2017; 58:1924-1933. [PMID: 29016977 DOI: 10.1093/pcp/pcx122] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/17/2017] [Indexed: 05/25/2023]
Abstract
Sesquiterpenes are one of the most important defensive secondary metabolite components of agarwood. Agarwood, which is a product of the Aquilaria sinensis response to external damage, is a fragrant and resinous wood that is widely used in traditional medicines, incense and perfume. We previously reported that jasmonic acid (JA) plays an important role in promoting agarwood sesquiterpene biosynthesis and induces expression of the sesquiterpene synthase ASS1, which is a key enzyme that is responsible for the biosynthesis of agarwood sesquiterpenes in A. sinensis. However, little is known about this molecular regulation mechanism. Here, we characterized a basic helix-loop-helix transcription factor, AsMYC2, from A. sinensis as an activator of ASS1 expression. AsMYC2 is an immediate-early jasmonate-responsive gene and is co-induced with ASS1. Using a combination of yeast one-hybrid assays and chromatin immunoprecipitation analyses, we showed that AsMYC2 bound the promoter of ASS1 containing a G-box motif. AsMYC2 activated expression of ASS1 in tobacco epidermis cells and up-regulated expression of sesquiterpene synthase genes (TPS21 and TPS11) in Arabidopsis, which was also promoted by methyl jasmonate. Our results suggest that AsMYC2 participates in the regulation of agarwood sesquiterpene biosynthesis in A. sinensis by controlling the expression of ASS1 through the JA signaling pathway.
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Affiliation(s)
- Yan-Hong Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Yong-Cui Liao
- Basic Medical School, Jiangxi University of Traditional Chinese Medicine, Xingwan Road 818, Nanchang, Jiangx, 330004, China
| | - Fei-Fei Lv
- Hainan Branch Institute of Medicinal Plant (Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine), Chinese Academy of Medical Sciences & Peking Union Medical College, Wanning 571533, China
| | - Zheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
- Hainan Branch Institute of Medicinal Plant (Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine), Chinese Academy of Medical Sciences & Peking Union Medical College, Wanning 571533, China
| | - Pei-Wen Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Zhi-Hui Gao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Ke-Ping Hu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Chun Sui
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Yue Jin
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
| | - Jian-He Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151, Malianwa North Road, Haidian District, Beijing 100193, China
- Hainan Branch Institute of Medicinal Plant (Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine), Chinese Academy of Medical Sciences & Peking Union Medical College, Wanning 571533, China
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Mammoto T, Jiang A, Jiang E, Mammoto A. Role of Twist1 Phosphorylation in Angiogenesis and Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2017; 55:633-644. [PMID: 27281171 DOI: 10.1165/rcmb.2016-0012oc] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Idiopathic pulmonary fibrosis is a chronic and progressive lung disease in which microvessel remodeling is deregulated. However, the mechanism by which deregulated angiogenesis contributes to the pathogenesis of pulmonary fibrosis remains unclear. Here we show that a transcription factor, Twist1, controls angiogenesis through the angiopoietin-Tie2 pathway, and that deregulation of this mechanism mediates pathological angiogenesis and collagen deposition in a bleomycin-induced mouse pulmonary fibrosis model. Twist1 knockdown decreases Tie2 expression and attenuates endothelial cell sprouting in vitro. Angiogenesis is also inhibited in fibrin gel implanted on Tie2-specific Twist1 conditional knockout (Twist1fl/fl/Tie2-cre) mouse lung in vivo. Inhibition of Twist1 phosphorylation at the serine 42 (Ser42) residue by treating endothelial cells with a mutant construct (Twist1S42A) decreases Tie2 expression and attenuates angiogenesis compared with full-length Twist1 in vitro and in vivo. Bleomycin challenge up-regulates Twist1 Ser42 phosphorylation and Tie2 expression, increases blood vessel density, and induces collagen deposition in the mouse lung, whereas these effects are attenuated in Twist1fl/fl/Tie2-cre mice or in mice treated with Twist1S42A mutant construct. These results indicate that Twist1 Ser42 phosphorylation contributes to the pathogenesis of bleomycin-induced pulmonary fibrosis through angiopoietin-Tie2 signaling.
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Affiliation(s)
- Tadanori Mammoto
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Amanda Jiang
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Elisabeth Jiang
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Akiko Mammoto
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
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23
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Benocci T, Aguilar-Pontes MV, Zhou M, Seiboth B, de Vries RP. Regulators of plant biomass degradation in ascomycetous fungi. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:152. [PMID: 28616076 PMCID: PMC5468973 DOI: 10.1186/s13068-017-0841-x] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/06/2017] [Indexed: 05/05/2023]
Abstract
Fungi play a major role in the global carbon cycle because of their ability to utilize plant biomass (polysaccharides, proteins, and lignin) as carbon source. Due to the complexity and heterogenic composition of plant biomass, fungi need to produce a broad range of degrading enzymes, matching the composition of (part of) the prevalent substrate. This process is dependent on a network of regulators that not only control the extracellular enzymes that degrade the biomass, but also the metabolic pathways needed to metabolize the resulting monomers. This review will summarize the current knowledge on regulation of plant biomass utilization in fungi and compare the differences between fungal species, focusing in particular on the presence or absence of the regulators involved in this process.
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Affiliation(s)
- Tiziano Benocci
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Maria Victoria Aguilar-Pontes
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Bernhard Seiboth
- Research Area Biochemical Technology, Institute of Chemical and Biological Engineering, TU Wien, 1060 Vienna, Austria
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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24
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Rabissi A, Vilela B, Lumbreras V, Ludevid D, Culiáñez-Macià FA, Pagés M. Molecular characterization of maize bHLH transcription factor (ZmKS), a new ZmOST1 kinase substrate. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 253:1-12. [PMID: 27968978 DOI: 10.1016/j.plantsci.2016.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/07/2016] [Accepted: 09/08/2016] [Indexed: 05/08/2023]
Abstract
In order to identify potential substrates of the maize kinase in the ABA signalling network, ZmOST1 was used as bait against a library of cDNAs from dehydrated young leaves. A ZmOST1-interactive polypeptide ZmKS (gene locus tag: GRMZM2G114873), showing homology with the Arabidopsis thaliana basic helix-loop-helix (bHLH) DNA-binding transcription factor was identified. Using a comparative genomic approach, the ZmKS corresponding protein was identified as conceptual translated bHLH transcription factor ABA-responsive kinase substrate. ZmKS is localized in the nucleus, shows a potential binding specificity preferentially detectable on cis-acting E-box like heptameric motifs CCACTTG and CAAGTTG, and is phosphorylated by maize protein kinase ZmOST1. ZmKS is expressed in embryo, leaf and root, expression being affected by ABA and osmotic stress. Transgenic Arabidopsis plants, with gain of ZmKS function, show a delay in germination and a transcriptional stomatal opening-facilitator activity, switchover upon ZmKS phosphorylation, suggesting that ZmKS is an ABA-repressed trans-acting activator.
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Affiliation(s)
- Agnese Rabissi
- Centre de Recerca en Agrigenòmica 20 (CRAG), Consortium CSIC-IRTA-UAB-UB. Campus UAB - Edifici CRAG, 21 Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Belmiro Vilela
- Centre de Recerca en Agrigenòmica 20 (CRAG), Consortium CSIC-IRTA-UAB-UB. Campus UAB - Edifici CRAG, 21 Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Victoria Lumbreras
- Centre de Recerca en Agrigenòmica 20 (CRAG), Consortium CSIC-IRTA-UAB-UB. Campus UAB - Edifici CRAG, 21 Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Dolors Ludevid
- Centre de Recerca en Agrigenòmica 20 (CRAG), Consortium CSIC-IRTA-UAB-UB. Campus UAB - Edifici CRAG, 21 Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Francisco A Culiáñez-Macià
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-C.S.I.C, Camino de Vera, s/n. 46022, Valencia, Spain.
| | - Montserrat Pagés
- Centre de Recerca en Agrigenòmica 20 (CRAG), Consortium CSIC-IRTA-UAB-UB. Campus UAB - Edifici CRAG, 21 Cerdanyola del Vallès, 08193 Barcelona, Spain
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Yang D, Zhang W, Padhiar A, Yue Y, Shi Y, Zheng T, Davis K, Zhang Y, Huang M, Li Y, Sha L. NPAS3 Regulates Transcription and Expression of VGF: Implications for Neurogenesis and Psychiatric Disorders. Front Mol Neurosci 2016; 9:109. [PMID: 27877109 PMCID: PMC5099284 DOI: 10.3389/fnmol.2016.00109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/12/2016] [Indexed: 01/01/2023] Open
Abstract
Neuronal PAS domain protein 3 (NPAS3) and VGF (VGF Nerve Growth Factor (NGF) Inducible) are important for neurogenesis and psychiatric disorders. Previously, we have demonstrated that NPAS3 regulates VGF at the transcriptional level. In this study, VGF (non-acronymic) was found regulated by NPAS3 in neuronal stem cells. However, the underlying mechanism of this regulation remains unclear. The aim of this study was to explore the correlation of NPAS3 and VGF, and their roles in neural cell proliferation, in the context of psychiatric illnesses. First, we focused on the structure of NPAS3, to identify the functional domain of NPAS3. Truncated NPAS3 lacking transactivation domain was also found to activate VGF, which suggested that not only transactivation domain but other structural motifs were also involved in the regulation. Second, Mutated enhancer box (E-box) of VGF promoter showed a significant response to this basic helix-loop-helix (bHLH) transcription factor, which suggested an indirect regulatory mechanism for controlling VGF expression by NPAS3. κB site within VGF promoter was identified for VGF activation induced by NPAS3, apart from direct binding to E-box. Furthermore, ectopically expressed NPAS3 in PC12 cells produced parallel responses for nuclear factor kappa-light-chain-enhancer of activated B cells [NF-κB (P65)] expression, which specifies that NPAS3 regulates VGF through the NF-κB signaling pathway. Over-expression of NPAS3 also enhances the cell proliferation, which can be blocked by knockdown of VGF. Finally, NPAS3 was found to influence proliferation of neural cells through VGF. Therefore, downstream signaling pathways that are responsible for NPAS3-VGF induced proliferation via glutamate receptors were explored. Combining this work and published literature, a potential network composed by NPAS3, NF-κB, Brain-Derived Neurotrophic Factor (BDNF), NGF and VGF, was proposed. This network collectively detailed how NPAS3 connects with VGF and intersected neural cell proliferation, synaptic activity and psychiatric disorders.
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Affiliation(s)
- Dongxue Yang
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Wenbo Zhang
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Arshad Padhiar
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Yao Yue
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Yonghui Shi
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Tiezheng Zheng
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Kaspar Davis
- Department of Physical Education, Dalian University of Technology Dalian, China
| | - Yu Zhang
- Department of Physical Education, Dalian University of Technology Dalian, China
| | - Min Huang
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Yuyuan Li
- College of Basic Medicine, Dalian Medical University Dalian, China
| | - Li Sha
- College of Basic Medicine, Dalian Medical University Dalian, China
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Dhokane D, Karre S, Kushalappa AC, McCartney C. Integrated Metabolo-Transcriptomics Reveals Fusarium Head Blight Candidate Resistance Genes in Wheat QTL-Fhb2. PLoS One 2016; 11:e0155851. [PMID: 27232496 PMCID: PMC4883744 DOI: 10.1371/journal.pone.0155851] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/05/2016] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Fusarium head blight (FHB) caused by Fusarium graminearum not only causes severe losses in yield, but also reduces quality of wheat grain by accumulating mycotoxins. Breeding for host plant resistance is considered as the best strategy to manage FHB. Resistance in wheat to FHB is quantitative in nature, involving cumulative effects of many genes governing resistance. The poor understanding of genetics and lack of precise phenotyping has hindered the development of FHB resistant cultivars. Though more than 100 QTLs imparting FHB resistance have been reported, none discovered the specific genes localized within the QTL region, nor the underlying mechanisms of resistance. FINDINGS In our study recombinant inbred lines (RILs) carrying resistant (R-RIL) and susceptible (S-RIL) alleles of QTL-Fhb2 were subjected to metabolome and transcriptome profiling to discover the candidate genes. Metabolome profiling detected a higher abundance of metabolites belonging to phenylpropanoid, lignin, glycerophospholipid, flavonoid, fatty acid, and terpenoid biosynthetic pathways in R-RIL than in S-RIL. Transcriptome analysis revealed up-regulation of several receptor kinases, transcription factors, signaling, mycotoxin detoxification and resistance related genes. The dissection of QTL-Fhb2 using flanking marker sequences, integrating metabolomic and transcriptomic datasets, identified 4-Coumarate: CoA ligase (4CL), callose synthase (CS), basic Helix Loop Helix (bHLH041) transcription factor, glutathione S-transferase (GST), ABC transporter-4 (ABC4) and cinnamyl alcohol dehydrogenase (CAD) as putative resistance genes localized within the QTL-Fhb2 region. CONCLUSION Some of the identified genes within the QTL region are associated with structural resistance through cell wall reinforcement, reducing the spread of pathogen through rachis within a spike and few other genes that detoxify DON, the virulence factor, thus eventually reducing disease severity. In conclusion, we report that the wheat resistance QTL-Fhb2 is associated with high rachis resistance through additive resistance effects of genes, based on cell wall enforcement and detoxification of DON. Following further functional characterization and validation, these resistance genes can be used to replace the genes in susceptible commercial cultivars, if nonfunctional, based on genome editing to improve FHB resistance.
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Affiliation(s)
- Dhananjay Dhokane
- Department of Plant Science, Macdonald Campus, McGill University, 21,111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Shailesh Karre
- Department of Plant Science, Macdonald Campus, McGill University, 21,111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Ajjamada C. Kushalappa
- Department of Plant Science, Macdonald Campus, McGill University, 21,111 Lakeshore Road, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Curt McCartney
- Agriculture and Agri-Food Canada, 195 Dafoe Road, Winnipeg, Manitoba, R3T 2M9, Canada
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Xue T, Song C, Wang Q, Wang Y, Chen G. Investigations of the CLOCK and BMAL1 Proteins Binding to DNA: A Molecular Dynamics Simulation Study. PLoS One 2016; 11:e0155105. [PMID: 27153104 PMCID: PMC4859532 DOI: 10.1371/journal.pone.0155105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/25/2016] [Indexed: 11/18/2022] Open
Abstract
The circadian locomotor output cycles kaput (CLOCK), and brain and muscle ARNT-like 1 (BMAL1) proteins are important transcriptional factors of the endogenous circadian clock. The CLOCK and BMAL1 proteins can regulate the transcription-translation activities of the clock-related genes through the DNA binding. The hetero-/homo-dimerization and DNA combination of the CLOCK and BMAL1 proteins play a key role in the positive and negative transcriptional feedback processes. In the present work, we constructed a series of binary and ternary models for the bHLH/bHLH-PAS domains of the CLOCK and BMAL1 proteins, and the DNA molecule, and carried out molecular dynamics simulations, free energy calculations and conformational analysis to explore the interaction properties of the CLOCK and BMAL1 proteins with DNA. The results show that the bHLH domains of CLOCK and BMAL1 can favorably form the heterodimer of the bHLH domains of CLOCK and BMAL1 and the homodimer of the bHLH domains of BMAL1. And both dimers could respectively bind to DNA at its H1-H1 interface. The DNA bindings of the H1 helices in the hetero- and homo-bHLH dimers present the rectangular and diagonal binding modes, respectively. Due to the function of the α-helical forceps in these dimers, the tight gripping of the H1 helices to the major groove of DNA would cause the decrease of interactions at the H1-H2 interfaces in the CLOCK and BMAL1 proteins. The additional PAS domains in the CLOCK and BMAL1 proteins affect insignificantly the interactions of the CLOCK and BMAL1 proteins with the DNA molecule due to the flexible and long loop linkers located at the middle of the PAS and bHLH domains. The present work theoretically explains the interaction mechanisms of the bHLH domains of the CLOCK and BMAL1 proteins with DNA.
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Affiliation(s)
- Tuo Xue
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Chunnian Song
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Qing Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Yan Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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Overexpression of SlUPA-like induces cell enlargement, aberrant development and low stress tolerance through phytohormonal pathway in tomato. Sci Rep 2016; 6:23818. [PMID: 27025226 PMCID: PMC4812305 DOI: 10.1038/srep23818] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 03/15/2016] [Indexed: 11/24/2022] Open
Abstract
upa20 induces cell enlargement and hypertrophy development. In our research, overexpression of SlUPA-like, orthologous to upa20, severely affected the growth of vegetative and reproductive tissues. Wilted leaves curled upwardly and sterile flowers were found in transgenic lines. Through anatomical analysis, palisade and spongy tissues showed fluffy and hypertrophic development in transgenic plants. Gene expression analysis showed that GA responsive, biosynthetic and signal transduction genes (e.g. GAST1, SlGA20OXs, SlGA3OXs, SlGID1s, and SlPREs) were significantly upregulated, indicating that GA response is stimulated by overproduction of SlUPA-like. Furthermore, SlUPA-like was strongly induced by exogenous JA and wounding. Decreased expression of PI-I and induced expression of SlJAZs (including SlJAZ2, SlJAZ10 and SlJAZ11) were observed in transgenic plants, suggesting that JA response is repressed. In addition, SlUPA-like overexpressed plant exhibited more opened stoma and higher water loss than the control when treated with dehydration stress, which was related to decreased ABA biosynthesis, signal transduction and response. Particularly, abnormal developments of transgenic plants promote the plant susceptibility to Xanthomonas campestris pv. campestris. Therefore, it is deduced from these results that SlUPA-like plays vital role in regulation of plant development and stress tolerance through GA, JA and ABA pathways.
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W-box and G-box elements play important roles in early senescence of rice flag leaf. Sci Rep 2016; 6:20881. [PMID: 26864250 PMCID: PMC4749992 DOI: 10.1038/srep20881] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/12/2016] [Indexed: 01/01/2023] Open
Abstract
Plant cis-elements play important roles in global regulation of gene expression. Based on microarray data from rice flag leaves during early senescence, we identified W-box and G-box cis-elements as positive regulators of senescence in the important rice variety Minghui 63. Both cis-elements were bound by leaf senescence-specific proteins in vitro and influenced senescence in vivo. Furthermore, combination of the two elements drove enhanced expression during leaf senescence, and copy numbers of the cis-elements significantly affected the levels of expression. The W-box is the cognate cis-element for WRKY proteins, while the G-box is the cognate cis-element for bZIP, bHLH and NAC proteins. Consistent with this, WRKY, bZIP, bHLH and NAC family members were overrepresented among transcription factor genes up-regulated according during senescence. Crosstalk between ABA, CTK, BR, auxin, GA and JA during senescence was uncovered by comparing expression patterns of senescence up-regulated transcription factors. Together, our results indicate that hormone-mediated signaling could converge on leaf senescence at the transcriptional level through W-box and G-box elements. Considering that there are very few documented early senescence-related cis-elements, our results significantly contribute to understanding the regulation of flag leaf senescence and provide prioritized targets for stay-green trait improvement.
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Isolation, expression analysis and characterization of NEFA-interacting nuclear protein 30 and RING finger and SPRY domain containing 1 in skeletal muscle. Gene 2016; 576:319-32. [DOI: 10.1016/j.gene.2015.10.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 10/07/2015] [Accepted: 10/16/2015] [Indexed: 11/18/2022]
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Song Y, Pan G, Chen L, Ma S, Zeng T, Man Chan TH, Li L, Lian Q, Chow R, Cai X, Li Y, Li Y, Liu M, Li Y, Zhu Y, Wong N, Yuan YF, Pei D, Guan XY. Loss of ATOH8 Increases Stem Cell Features of Hepatocellular Carcinoma Cells. Gastroenterology 2015; 149:1068-81.e5. [PMID: 26099525 DOI: 10.1053/j.gastro.2015.06.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 06/10/2015] [Accepted: 06/13/2015] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS Levels of atonal homolog 8 (ATOH8) are reduced in 48% of hepatitis B virus-associated hepatocellular carcinoma cells (HCCs). ATOH8 downregulation is associated with loss of tumor differentiation, indicating an effect mediated by cancer stem cells. We investigated the effects of loss of ATOH8 in human hepatocellular carcinoma (HCC) cells and cell lines. METHODS HCC and adjacent nontumor tissues were collected, from 2001 through 2012, from 242 patients undergoing hepatectomy at Sun Yat-Sen University Cancer Center in China; 83% of HCCs were associated with hepatitis B virus (HBV) infection. CD133(+) cells were isolated from tumor tissues by flow cytometry. Experiments were performed in HBV-positive and HBV-negative HCC cell lines, the immortalized liver cell line LO2, and 8 other HCC cell lines. ATOH8 was expressed from lentiviral vectors in PLC8024 and Huh7 cells; levels were knocked down with small interfering RNAs in QSG7701 cells. Cells carrying empty vectors were used as controls. Gene regulation by ATOH8 was assessed in mobility shift and luciferase reporter assays. Cells were analyzed in proliferation, foci formation, and colony formation assays. The tumorigenic and chemo-resistant potential of cells were investigated by assessing growth of xenograft tumors in immunocompromised mice. Metastatic features of cells were assessed in Matrigel invasion assays and wound healing analyses. RESULTS Levels of ATOH8 mRNA were reduced by more than 4-fold, compared to nontumor tissues, in 118 of 242 HCC samples (48.8%). Patients with tumor reductions in ATOH8 had significantly shorter times of disease-free survival (mean, 41.4 months) than patients with normal tissue levels (mean, 52.6 months). ATOH8 expression was reduced in HepG2, Huh7, PLC8024 and CRL8064 HCC cells, as well as CD133(+) cells isolated from human HCC samples. Transgenic expression of ATOH8 in HCC cell lines significantly reduced proliferation and foci colony formation, as well as their invasive and migratory abilities. Transgenic expression of ATOH8 reduced the ability of HBV-positive PLC8024 cells to form tumors in mice, compared to control cells. Cells with ATOH8 knockdown formed xenograft tumors more rapidly, in more mice, than control cells. ATOH8 repressed transcription of stem-cell associated genes including OCT4, NANOG, and CD133. Knockdown of ATOH8 in CD133-negative QSG7701 cells caused them to express CD133; acquire self-renewal, differentiation, chemo-resistance properties; form more xenograft tumors in mice; and generate induced pluripotent stem cells (based on staining for alkaline phosphatase and their ability to form embryoid bodies and teratomas). Alternatively, expression of ATOH8 in PLC8024 and Huh7 cells significantly reduced the numbers of cells expressing CD133, and increased the chemo-sensitivity of Huh7 cells to 5-fluorouracil (5-FU) and cisplatin, in vitro and in mice. CONCLUSIONS ATOH8 appears to be a tumor suppressor that induces stem-cell features and chemoresistance in HCC cells. Strategies to restore its levels and activities might be developed to treat patients with liver cancer.
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Affiliation(s)
- Yangyang Song
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Guangjin Pan
- Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Anatomy, National University of Singapore, Singapore
| | - Stephanie Ma
- Department of Anatomy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Centre for Cancer Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Tingting Zeng
- State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Tim Hon Man Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Lei Li
- State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qizhou Lian
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Raymond Chow
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Centre for Cancer Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xiujuan Cai
- Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yan Li
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Centre for Cancer Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yan Li
- State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ming Liu
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Centre for Cancer Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yun Li
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Centre for Cancer Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yinghui Zhu
- State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Nathalie Wong
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yun-Fei Yuan
- State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Duanqing Pei
- Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xin-Yuan Guan
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Centre for Cancer Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Liver Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Oncology in Southern China, Sun Yat-sen University Cancer Center, Guangzhou, China.
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Li Y, Huang X, Guan Y, Shi Y, Zhang H, He M. DNA methylation is associated with expression level changes of galectin gene in mantle wound healing process of pearl oyster, Pinctada fucata. FISH & SHELLFISH IMMUNOLOGY 2015; 45:912-918. [PMID: 26093206 DOI: 10.1016/j.fsi.2015.06.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/07/2015] [Accepted: 06/13/2015] [Indexed: 06/04/2023]
Abstract
Galectin is one important member of pattern recognition proteins that plays a pivotal role in regulating innate immune response of invertebrates. In this study, we cloned the promoter sequence of a tandem-repeat galectin from the pearl oyster Pinctada fucata (P. fucata). The quantitative real-time PCR analysis revealed that galectin mRNA expression in mantle tissues were firstly up-regulated from time points of 2 h-24 h, and then down-regulated from time points of 24 h-168 h after mantle injury. The genome methylation level of mantle tissue was inversely related to galectin mRNA expression (Pearson correlation: -0.554, P: 0.154). The "CpG4-6" methylation level in promoter region of galectin was significant positive correlated with the mRNA expression (Pearson correlation: 0.313, P: 0.049). The results indicated that galectin gene may be involved in immune response in mantle wound healing process of P. fucata, and DNA methylation may be a regulation factor of gene expression.
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Affiliation(s)
- Yaoguo Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiande Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yunyan Guan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yu Shi
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Hua Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing, China
| | - Maoxian He
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
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Chistiakov DA, Sobenin IA, Orekhov AN, Bobryshev YV. Myeloid dendritic cells: Development, functions, and role in atherosclerotic inflammation. Immunobiology 2015; 220:833-44. [DOI: 10.1016/j.imbio.2014.12.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/07/2014] [Accepted: 12/22/2014] [Indexed: 12/21/2022]
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Samanta S, Sun H, Goel HL, Pursell B, Chang C, Khan A, Greiner DL, Cao S, Lim E, Shultz LD, Mercurio AM. IMP3 promotes stem-like properties in triple-negative breast cancer by regulating SLUG. Oncogene 2015; 35:1111-21. [PMID: 25982283 DOI: 10.1038/onc.2015.164] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/19/2015] [Accepted: 03/23/2015] [Indexed: 12/20/2022]
Abstract
IMP3 (insulin-like growth factor-2 mRNA binding protein 3) is an oncofetal protein whose expression is prognostic for poor outcome in several cancers. Although IMP3 is expressed preferentially in triple-negative breast cancer (TNBC), its function is poorly understood. We observed that IMP3 expression is significantly higher in tumor initiating than in non-tumor initiating breast cancer cells and we demonstrate that IMP3 contributes to self-renewal and tumor initiation, properties associated with cancer stem cells (CSCs). The mechanism by which IMP3 contributes to this phenotype involves its ability to induce the stem cell factor SOX2. IMP3 does not interact with SOX2 mRNA significantly or regulate SOX2 expression directly. We discovered that IMP3 binds avidly to SNAI2 (SLUG) mRNA and regulates its expression by binding to the 5' UTR. This finding is significant because SLUG has been implicated in breast CSCs and TNBC. Moreover, we show that SOX2 is a transcriptional target of SLUG. These data establish a novel mechanism of breast tumor initiation involving IMP3 and they provide a rationale for its association with aggressive disease and poor outcome.
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Affiliation(s)
- S Samanta
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - H Sun
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - H L Goel
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - B Pursell
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - C Chang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - A Khan
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - D L Greiner
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - S Cao
- Dana Farber Cancer Institute, Boston, MA, USA
| | - E Lim
- Dana Farber Cancer Institute, Boston, MA, USA
| | - L D Shultz
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - A M Mercurio
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
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Liu B, Zhu Y, Zhang T. The R3-MYB gene GhCPC negatively regulates cotton fiber elongation. PLoS One 2015; 10:e0116272. [PMID: 25646816 PMCID: PMC4315419 DOI: 10.1371/journal.pone.0116272] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/03/2014] [Indexed: 11/18/2022] Open
Abstract
Cotton (Gossypium spp.) fibers are single-cell trichomes that arise from the outer epidermal layer of seed coat. Here, we isolated a R3-MYB gene GhCPC, identified by cDNA microarray analysis. The only conserved R3 motif and different expression between TM-1 and fuzzless-lintless mutants suggested that it might be a negative regulator in fiber development. Transgenic evidence showed that GhCPC overexpression not only delayed fiber initiation but also led to significant decreases in fiber length. Interestingly, Yeast two-hybrid analysis revealed an interaction complex, in which GhCPC and GhTTG1/4 separately interacted with GhMYC1. In transgenic plants, Q-PCR analysis showed that GhHOX3 (GL2) and GhRDL1 were significantly down regulated in -1-5 DPA ovules and fibers. In addition, Yeast one-hybrid analysis demonstrated that GhMYC1 could bind to the E-box cis-elements and the promoter of GhHOX3. These results suggested that GhHOX3 (GL2) might be downstream gene of the regulatory complex. Also, overexpression of GhCPC in tobacco led to differential loss of pigmentation. Taken together, the results suggested that GhCPC might negatively regulate cotton fiber initiation and early elongation by a potential CPC-MYC1-TTG1/4 complex. Although the fibers were shorter in transgenic cotton lines than in the wild type, no significant difference was detected in stem or leaf trichomes, even in cotton mutants (five naked seed or fuzzless), suggesting that fiber and trichome development might be regulated by two sets of genes sharing a similar model.
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Affiliation(s)
- Bingliang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Yichao Zhu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, China
| | - Tianzhen Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing, China
- * E-mail:
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Derntl C, Rassinger A, Srebotnik E, Mach RL, Mach-Aigner AR. Xpp1 regulates the expression of xylanases, but not of cellulases in Trichoderma reesei. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:112. [PMID: 26246855 PMCID: PMC4526299 DOI: 10.1186/s13068-015-0298-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/24/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND The ascomycete Trichoderma reesei is industrially used for the production of cellulases. During the production process xylanases are co-secreted, which uses energy and nutrients. Cellulases and xylanases share the same main regulators, which makes a knowledge-based strain design difficult. However, previously a cis-element in the promoter of the main xylanase-encoding gene was identified as binding site for a putative repressor. Subsequently, three candidate repressors were identified in a pull-down approach. The expression of the most promising candidate, Xpp1 (Xylanase promoter-binding protein 1), was reported to be up-regulated on the repressing carbon source d-glucose and to bind the cis-element in vitro. RESULTS In this study, Xpp1 was deleted and over-expressed in T. reesei. An in vivo DNA-footprint assay indicated that Xpp1 binds a palindromic sequence in the xyn2 promoter. Comparison of the deletion, the over-expression, and the parent strain demonstrated that Xpp1 regulates gene expression of xylanolytic enzymes at later cultivation stages. Xpp1 expression was found to be up-regulated, additionally to d-glucose, by high d-xylose availability. These findings together with the observed xyn2 transcript levels during growth on xylan suggest that Xpp1 is the mediator of a feedback mechanism. Notably, Xpp1 has neither influence on the d-xylose metabolism nor on the expression of cellulases. CONCLUSIONS Xpp1 as regulator acting on the expression of xylanases, but not cellulases, is a highly promising candidate for knowledge-based strain design to improve the cellulases-to-xylanases ratio during industrial cellulase production.
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Affiliation(s)
- Christian Derntl
- />Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
| | - Alice Rassinger
- />Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
| | - Ewald Srebotnik
- />Department of Biochemical Engineering, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
| | - Robert L Mach
- />Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
| | - Astrid R Mach-Aigner
- />Department for Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria
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Ravel C, Fiquet S, Boudet J, Dardevet M, Vincent J, Merlino M, Michard R, Martre P. Conserved cis-regulatory modules in promoters of genes encoding wheat high-molecular-weight glutenin subunits. FRONTIERS IN PLANT SCIENCE 2014; 5:621. [PMID: 25429295 PMCID: PMC4228979 DOI: 10.3389/fpls.2014.00621] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/21/2014] [Indexed: 05/19/2023]
Abstract
The concentration and composition of the gliadin and glutenin seed storage proteins (SSPs) in wheat flour are the most important determinants of its end-use value. In cereals, the synthesis of SSPs is predominantly regulated at the transcriptional level by a complex network involving at least five cis-elements in gene promoters. The high-molecular-weight glutenin subunits (HMW-GS) are encoded by two tightly linked genes located on the long arms of group 1 chromosomes. Here, we sequenced and annotated the HMW-GS gene promoters of 22 electrophoretic wheat alleles to identify putative cis-regulatory motifs. We focused on 24 motifs known to be involved in SSP gene regulation. Most of them were identified in at least one HMW-GS gene promoter sequence. A common regulatory framework was observed in all the HMW-GS gene promoters, as they shared conserved cis-regulatory modules (CCRMs) including all the five motifs known to regulate the transcription of SSP genes. This common regulatory framework comprises a composite box made of the GATA motifs and GCN4-like Motifs (GLMs) and was shown to be functional as the GLMs are able to bind a bZIP transcriptional factor SPA (Storage Protein Activator). In addition to this regulatory framework, each HMW-GS gene promoter had additional motifs organized differently. The promoters of most highly expressed x-type HMW-GS genes contain an additional box predicted to bind R2R3-MYB transcriptional factors. However, the differences in annotation between promoter alleles could not be related to their level of expression. In summary, we identified a common modular organization of HMW-GS gene promoters but the lack of correlation between the cis-motifs of each HMW-GS gene promoter and their level of expression suggests that other cis-elements or other mechanisms regulate HMW-GS gene expression.
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Affiliation(s)
- Catherine Ravel
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Samuel Fiquet
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Julie Boudet
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Mireille Dardevet
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Jonathan Vincent
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Marielle Merlino
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Robin Michard
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
| | - Pierre Martre
- Institut National de la Recherche Agronomique, UMR1095, Genetics, Diversity and Ecophysiology of Cereals Clermont-Ferrand, France ; UMR1095, Genetics, Diversity and Ecophysiology of Cereals, Department of Biology, Blaise Pascal University Aubière, France
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Gesell A, Yoshida K, Tran LT, Constabel CP. Characterization of an apple TT2-type R2R3 MYB transcription factor functionally similar to the poplar proanthocyanidin regulator PtMYB134. PLANTA 2014; 240:497-511. [PMID: 24923676 DOI: 10.1007/s00425-014-2098-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 05/19/2014] [Indexed: 05/06/2023]
Abstract
The apple MdMYB9 gene encodes a positive regulator of proanthocyanidin synthesis that activates anthocyanidin reductase promoters from apple and poplar via interaction with basic helix-loop-helix proteins. The regulation of proanthocyanidins (PAs, condensed tannins) is of great importance in food plants due to the many benefits of PAs in the human diet. Two candidate flavonoid MYB regulators, MdMYB9 and MdMYB11, were cloned from apple (Malus × domestica) based on their similarity to known MYB PA regulators. Transcript accumulation of both MdMYB9 and MdMYB11 was induced by high light and wounding, similar to the poplar (Populus spp) PA regulator PtMYB134. In transient activation assays with various basic helix-loop-helix (bHLH) co-regulators, MdMYB9 activated apple and poplar anthocyanidin reductase (ANR) promoters, while MdMYB11 showed no activity. Potential transcription factor binding elements were found within several ANR promoters, and the importance of the bHLH binding site (E-box) on ANR promoter activation was demonstrated via mutational analysis. The ability of MdMYB9 and PtMYB134 to reciprocally activate ANR promoters from both apple and poplar and to partner with heterologous bHLH co-factors from these plants confirms the high degree of conservation of PA regulatory complexes across species. The similarity in apple and poplar PA regulation suggests that regulatory genes from poplar could be effectively employed for metabolic engineering of the PA pathway in apple.
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Affiliation(s)
- Andreas Gesell
- Department of Biology & Centre for Forest Biology, University of Victoria, Station CSC, Box 3020, Victoria, BC, V8W 3N5, Canada
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Shao C, Li Q, Chen S, Zhang P, Lian J, Hu Q, Sun B, Jin L, Liu S, Wang Z, Zhao H, Jin Z, Liang Z, Li Y, Zheng Q, Zhang Y, Wang J, Zhang G. Epigenetic modification and inheritance in sexual reversal of fish. Genome Res 2014; 24:604-15. [PMID: 24487721 PMCID: PMC3975060 DOI: 10.1101/gr.162172.113] [Citation(s) in RCA: 224] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Environmental sex determination (ESD) occurs in divergent, phylogenetically unrelated taxa, and in some species, co-occurs with genetic sex determination (GSD) mechanisms. Although epigenetic regulation in response to environmental effects has long been proposed to be associated with ESD, a systemic analysis on epigenetic regulation of ESD is still lacking. Using half-smooth tongue sole (Cynoglossus semilaevis) as a model—a marine fish that has both ZW chromosomal GSD and temperature-dependent ESD—we investigated the role of DNA methylation in transition from GSD to ESD. Comparative analysis of the gonadal DNA methylomes of pseudomale, female, and normal male fish revealed that genes in the sex determination pathways are the major targets of substantial methylation modification during sexual reversal. Methylation modification in pseudomales is globally inherited in their ZW offspring, which can naturally develop into pseudomales without temperature incubation. Transcriptome analysis revealed that dosage compensation occurs in a restricted, methylated cytosine enriched Z chromosomal region in pseudomale testes, achieving equal expression level in normal male testes. In contrast, female-specific W chromosomal genes are suppressed in pseudomales by methylation regulation. We conclude that epigenetic regulation plays multiple crucial roles in sexual reversal of tongue sole fish. We also offer the first clues on the mechanisms behind gene dosage balancing in an organism that undergoes sexual reversal. Finally, we suggest a causal link between the bias sex chromosome assortment in the offspring of a pseudomale family and the transgenerational epigenetic inheritance of sexual reversal in tongue sole fish.
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Affiliation(s)
- Changwei Shao
- Yellow Sea Fisheries Research Institute, CAFS, Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao 266071, China
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Toward Translating Molecular Ear Development to Generate Hair Cells from Stem Cells. ADULT STEM CELLS 2014. [DOI: 10.1007/978-1-4614-9569-7_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Mammoto T, Jiang E, Jiang A, Lu Y, Juan AM, Chen J, Mammoto A. Twist1 controls lung vascular permeability and endotoxin-induced pulmonary edema by altering Tie2 expression. PLoS One 2013; 8:e73407. [PMID: 24023872 PMCID: PMC3759405 DOI: 10.1371/journal.pone.0073407] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 07/20/2013] [Indexed: 11/19/2022] Open
Abstract
Tight regulation of vascular permeability is necessary for normal development and deregulated vascular barrier function contributes to the pathogenesis of various diseases, including acute respiratory distress syndrome, cancer and inflammation. The angiopoietin (Ang)-Tie2 pathway is known to control vascular permeability. However, the mechanism by which the expression of Tie2 is regulated to control vascular permeability has not been fully elucidated. Here we show that transcription factor Twist1 modulates pulmonary vascular leakage by altering the expression of Tie2 in a context-dependent way. Twist1 knockdown in cultured human lung microvascular endothelial cells decreases Tie2 expression and phosphorylation and increases RhoA activity, which disrupts cell-cell junctional integrity and increases vascular permeability in vitro. In physiological conditions, where Ang1 is dominant, pulmonary vascular permeability is elevated in the Tie2-specific Twist1 knockout mice. However, depletion of Twist1 and resultant suppression of Tie2 expression prevent increase in vascular permeability in an endotoxin-induced lung injury model, where the balance of Angs shifts toward Ang2. These results suggest that Twist1-Tie2-Angs signaling is important for controlling vascular permeability and modulation of this mechanism may lead to the development of new therapeutic approaches for pulmonary edema and other diseases caused by abnormal vascular permeability.
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Affiliation(s)
- Tadanori Mammoto
- 1 Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Elisabeth Jiang
- 1 Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Amanda Jiang
- 1 Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yongbo Lu
- 2 Department of Biomedical Sciences, Baylor College of Dentistry, Texas A&M Health Science Center, Dallas, Texas, United States of America
| | - Aimee M. Juan
- 3 Department of Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jing Chen
- 3 Department of Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Akiko Mammoto
- 1 Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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Premachandra HKA, Wan Q, Elvitigala DAS, De Zoysa M, Choi CY, Whang I, Lee J. Genomic characterization and expression profiles upon bacterial infection of a novel cystatin B homologue from disk abalone (Haliotis discus discus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2012; 38:495-504. [PMID: 22878425 DOI: 10.1016/j.dci.2012.06.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/13/2012] [Accepted: 06/28/2012] [Indexed: 06/01/2023]
Abstract
Cystatins are a large family of cysteine proteinase inhibitors which are involved in diverse biological and pathological processes. In the present study, we identified a gene related to cystatin superfamily, AbCyt B, from disk abalone Haliotis discus discus by expressed sequence tag (EST) analysis and BAC library screening. The complete cDNA sequence of AbCyt B is comprised of 1967 nucleotides with a 306 bp open reading frame (ORF) encoding for 101 amino acids. The amino acid sequence consists of a single cystatin-like domain, which has a cysteine proteinase inhibitor signature, a conserved Gly in N-terminal region, QVVAG motif and a variant of PW motif. No signal peptide, disulfide bonds or carbohydrate side chains were identified. Analysis of deduced amino acid sequence revealed that AbCyt B shares up to 44.7% identity and 65.7% similarity with the cystatin B genes from other organisms. The genomic sequence of AbCyt B is approximately 8.4 Kb, consisting of three exons and two introns. Phylogenetic tree analysis showed that AbCyt B was closely related to the cystatin B from pacific oyster (Crassostrea gigas) under the family 1.Functional analysis of recombinant AbCyt B protein exhibited inhibitory activity against the papain, with almost 84% inhibition at a concentration of 3.5 μmol/L. In tissue expression analysis, AbCyt B transcripts were expressed abundantly in the hemocyte, gill, mantle, and digestive tract, while weakly in muscle, testis, and hepatopancreas. After the immune challenge with Vibrio parahemolyticus, the AbCyt B showed significant (P<0.05) up-regulation of relative mRNA expression in gill and hemocytes at 24 and 6 h of post infection, respectively. These results collectively suggest that AbCyst B is a potent inhibitor of cysteine proteinases and is also potentially involved in immune responses against invading bacterial pathogens in abalone.
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Affiliation(s)
- H K A Premachandra
- Department of Marine Life Sciences, School of Marine Biomedical Science, Jeju National University, Jeju Special Self-Governing Province, Republic of Korea
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Park YM, Lee YH, Kim SH, Lee EY, Kim KS, Williams DR, Lee HC. Snail, a transcriptional regulator, represses adiponectin expression by directly binding to an E-box motif in the promoter. Metabolism 2012; 61:1622-32. [PMID: 22595290 DOI: 10.1016/j.metabol.2012.04.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 03/21/2012] [Accepted: 04/13/2012] [Indexed: 10/28/2022]
Abstract
OBJECTIVE Adiponectin is a hormone that modulates many metabolic processes and is exclusively expressed in adipose tissue. However, complete understanding of the factors that regulate adiponectin expression is lacking. The following were investigated: (1) functional analysis of the human adiponectin promoter, (2) putative adiponectin repressor sequence activity in 3T3-L1 adipocytes using promoter mutagenesis, (3) whether Snail, an E-box binding transcription factor, binds this repressor sequence, (4) if Snail regulates adiponectin expression in 3T3-L1 pre-adipocytes. MATERIALS/METHODS To further understand how adiponectin expression is regulated, we isolated the human adiponectin promoter and analyzed its activity after serial deletions. RESULTS We found a negative cis-regulatory element located in the adiponectin proximal promoter sequence (-174 to -152 bp), which contained an E-box site (CAACTG). The DNA binding activity of this putative negative regulatory factor was found to be sequence-specific and the binding activity is decreased during adipocyte differentiation time-dependently. Affinity chromatography identified the zinc-finger transcription factor Snail (SNAI1) as the putative negative regulatory factor. Chromatin immunoprecipitation assay and electrophoretic mobility shift assay confirmed that Snail binds to this negative cis-regulatory element in pre-adipocytes, exclusively. Inhibition of Snail expression using small interfering RNA techniques increased adiponectin expression in 3T3-L1 adipocytes, while overexpression of Snail reduced adiponectin expression. Furthermore, we observed an inverse relation between the expression of Snail and the expression of CCAAT-enhancer-binding protein alpha and peroxisome proliferator-activated receptor gamma, which are transcription factors that regulate adipogenesis. CONCLUSIONS Snail is a novel regulator of adiponectin expression and probably has a role in regulating adipogenesis.
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Affiliation(s)
- Young Mi Park
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
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Wong MV, Jiang S, Palasingam P, Kolatkar PR. A divalent ion is crucial in the structure and dominant-negative function of ID proteins, a class of helix-loop-helix transcription regulators. PLoS One 2012; 7:e48591. [PMID: 23119064 PMCID: PMC3484135 DOI: 10.1371/journal.pone.0048591] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 09/28/2012] [Indexed: 01/28/2023] Open
Abstract
Inhibitors of DNA binding and differentiation (ID) proteins, a dominant-negative group of helix-loop-helix (HLH) transcription regulators, are well-characterized key players in cellular fate determination during development in mammals as well as Drosophila. Although not oncogenes themselves, their upregulation by various oncogenic proteins (such as Ras, Myc) and their inhibitory effects on cell cycle proteins (such as pRb) hint at their possible roles in tumorigenesis. Furthermore, their potency as inhibitors of cellular differentiation, through their heterodimerization with subsequent inactivation of the ubiquitous E proteins, suggest possible novel roles in engineering induced pluripotent stem cells (iPSCs). We present the high-resolution 2.1Å crystal structure of ID2 (HLH domain), coupled with novel biochemical insights in the presence of a divalent ion, possibly calcium (Ca2+), in the loop of ID proteins, which appear to be crucial for the structure and activity of ID proteins. These new insights will pave the way for new rational drug designs, in addition to current synthetic peptide options, against this potent player in tumorigenesis as well as more efficient ways for stem cells reprogramming.
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Affiliation(s)
- Marie Vivian Wong
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Sizun Jiang
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore, Singapore
| | - Paaventhan Palasingam
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore, Singapore
| | - Prasanna R. Kolatkar
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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Waldhaus J, Cimerman J, Gohlke H, Ehrich M, Müller M, Löwenheim H. Stemness of the organ of Corti relates to the epigenetic status of Sox2 enhancers. PLoS One 2012; 7:e36066. [PMID: 22570694 PMCID: PMC3343037 DOI: 10.1371/journal.pone.0036066] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/30/2012] [Indexed: 12/11/2022] Open
Abstract
In the adult mammalian auditory epithelium, the organ of Corti, loss of sensory hair cells results in permanent hearing loss. The underlying cause for the lack of regenerative response is the depletion of otic progenitors in the cell pool of the sensory epithelium. Here, we show that an increase in the sequence-specific methylation of the otic Sox2 enhancers NOP1 and NOP2 is correlated with a reduced self-renewal potential in vivo and in vitro; additionally, the degree of methylation of NOP1 and NOP2 is correlated with the dedifferentiation potential of postmitotic supporting cells into otic stem cells. Thus, the stemness the organ of Corti is related to the epigenetic status of the otic Sox2 enhancers. These observations validate the continued exploration of treatment strategies for dedifferentiating or reprogramming of differentiated supporting cells into progenitors to regenerate the damaged organ of Corti.
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Affiliation(s)
- Jörg Waldhaus
- Department of Otorhinolaryngology, Head and Neck Surgery, Hearing Research Center Tübingen, University of Tübingen Medical Center, Tübingen, Germany
| | - Jelka Cimerman
- Department of Otorhinolaryngology, Head and Neck Surgery, Hearing Research Center Tübingen, University of Tübingen Medical Center, Tübingen, Germany
| | | | - Mathias Ehrich
- SEQUENOM Inc., San Diego, California, United States of America
| | - Marcus Müller
- Department of Otorhinolaryngology, Head and Neck Surgery, Hearing Research Center Tübingen, University of Tübingen Medical Center, Tübingen, Germany
| | - Hubert Löwenheim
- Department of Otorhinolaryngology, Head and Neck Surgery, Hearing Research Center Tübingen, University of Tübingen Medical Center, Tübingen, Germany
- * E-mail:
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Yang S, Yalamanchili HK, Li X, Yao KM, Sham PC, Zhang MQ, Wang J. Correlated evolution of transcription factors and their binding sites. ACTA ACUST UNITED AC 2011; 27:2972-8. [PMID: 21896508 DOI: 10.1093/bioinformatics/btr503] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION The interaction between transcription factor (TF) and transcription factor binding site (TFBS) is essential for gene regulation. Mutation in either the TF or the TFBS may weaken their interaction and thus result in abnormalities. To maintain such vital interaction, a mutation in one of the interacting partners might be compensated by a corresponding mutation in its binding partner during the course of evolution. Confirming this co-evolutionary relationship will guide us in designing protein sequences to target a specific DNA sequence or in predicting TFBS for poorly studied proteins, or even correcting and rescuing disease mutations in clinical applications. RESULTS Based on six, publicly available, experimentally validated TF-TFBS binding datasets for the basic Helix-Loop-Helix (bHLH) family, Homeo family, High-Mobility Group (HMG) family and Transient Receptor Potential channels (TRP) family, we showed that the evolutions of the TFs and their TFBSs are significantly correlated across eukaryotes. We further developed a mutual information-based method to identify co-evolved protein residues and DNA bases. This research sheds light on the dynamic relationship between TF and TFBS during their evolution. The same principle and strategy can be applied to co-evolutionary studies on protein-DNA interactions in other protein families. AVAILABILITY All the datasets, scripts and other related files have been made freely available at: http://jjwanglab.org/co-evo. CONTACT junwen@uw.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Shu Yang
- Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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Xue B, Oldfield CJ, Van YY, Dunker AK, Uversky VN. Protein intrinsic disorder and induced pluripotent stem cells. MOLECULAR BIOSYSTEMS 2011; 8:134-50. [PMID: 21761058 DOI: 10.1039/c1mb05163f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Induced pluripotent stem (iPS) cells can be obtained from terminally differentiated somatic cells by overexpression of defined sets of reprogramming transcription factors. These protein sets have been called the Yamanaka factors, namely Sox2, Oct3/4 (Pou5f1), Klf4, and c-Myc, and the Thomson factors, namely Sox2, Oct3, Lin28, and Nanog. Other sets of proteins, while not essential for the formation of iPS cells, are important for improving the efficiency of the induction and still other sets of proteins are important as markers for embryonic stem cells. Structural information about most of these important proteins is very sparse. Our bioinformatics analysis herein reveals that these reprogramming factors and most of the efficiency-improving and embryonic stem cell markers are highly enriched in intrinsic disorder. As is typical for transcription factors, these proteins are modular. Specific sites for interaction with other proteins and DNA are dispersed in the long regions of intrinsic disorder. These highly dynamic interaction sites are evidently responsible for the delicate interplay among various molecules. The bioinformatics analysis given herein should facilitate the investigation of the roles and organization of these modular interaction sites, thereby helping to shed further light on the pathways that underlie the mechanism(s) by which terminally differentiated cells are converted to iPS cells.
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Affiliation(s)
- Bin Xue
- Department of Molecular Medicine, College of Medicine, University of South Florida, Tampa, Florida 33612, USA.
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Li X, Panea C, Wiggins CH, Reinke V, Leslie C. Learning "graph-mer" motifs that predict gene expression trajectories in development. PLoS Comput Biol 2010; 6:e1000761. [PMID: 20454681 PMCID: PMC2861633 DOI: 10.1371/journal.pcbi.1000761] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Accepted: 03/24/2010] [Indexed: 12/19/2022] Open
Abstract
A key problem in understanding transcriptional regulatory networks is deciphering what cis regulatory logic is encoded in gene promoter sequences and how this sequence information maps to expression. A typical computational approach to this problem involves clustering genes by their expression profiles and then searching for overrepresented motifs in the promoter sequences of genes in a cluster. However, genes with similar expression profiles may be controlled by distinct regulatory programs. Moreover, if many gene expression profiles in a data set are highly correlated, as in the case of whole organism developmental time series, it may be difficult to resolve fine-grained clusters in the first place. We present a predictive framework for modeling the natural flow of information, from promoter sequence to expression, to learn cis regulatory motifs and characterize gene expression patterns in developmental time courses. We introduce a cluster-free algorithm based on a graph-regularized version of partial least squares (PLS) regression to learn sequence patterns--represented by graphs of k-mers, or "graph-mers"--that predict gene expression trajectories. Applying the approach to wildtype germline development in Caenorhabditis elegans, we found that the first and second latent PLS factors mapped to expression profiles for oocyte and sperm genes, respectively. We extracted both known and novel motifs from the graph-mers associated to these germline-specific patterns, including novel CG-rich motifs specific to oocyte genes. We found evidence supporting the functional relevance of these putative regulatory elements through analysis of positional bias, motif conservation and in situ gene expression. This study demonstrates that our regression model can learn biologically meaningful latent structure and identify potentially functional motifs from subtle developmental time course expression data.
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Affiliation(s)
- Xuejing Li
- Department of Physics, Columbia University, New York, New York, United States of America
| | - Casandra Panea
- Department of Genetics, Yale University, New Haven, Connecticut, United States of America
| | - Chris H. Wiggins
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York, United States of America
| | - Valerie Reinke
- Department of Genetics, Yale University, New Haven, Connecticut, United States of America
| | - Christina Leslie
- Computational Biology Program, Sloan-Kettering Institute, New York, New York, United States of America
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Martinez Barrio A, Eriksson O, Badhai J, Fröjmark AS, Bongcam-Rudloff E, Dahl N, Schuster J. Targeted resequencing and analysis of the Diamond-Blackfan anemia disease locus RPS19. PLoS One 2009; 4:e6172. [PMID: 19587786 PMCID: PMC2703794 DOI: 10.1371/journal.pone.0006172] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 05/27/2009] [Indexed: 11/19/2022] Open
Abstract
Background The Ribosomal protein S19 gene locus (RPS19) has been linked to two kinds of red cell aplasia, Diamond-Blackfan Anemia (DBA) and Transient Erythroblastopenia in Childhood (TEC). Mutations in RPS19 coding sequences have been found in 25% of DBA patients, but not in TEC patients. It has been suggested that non-coding RPS19 sequence variants contribute to the considerable clinical variability in red cell aplasia. We therefore aimed at identifying non-coding variations associated with DBA or TEC phenotypes. Methodology/Principal Findings We targeted a region of 19'980 bp encompassing the RPS19 gene in a cohort of 89 DBA and TEC patients for resequencing. We provide here a catalog of the considerable, previously unrecognized degree of variation in this region. We identified 73 variations (65 SNPs, 8 indels) that all are located outside of the RPS19 open reading frame, and of which 67.1% are classified as novel. We hypothesize that specific alleles in non-coding regions of RPS19 could alter the binding of regulatory proteins or transcription factors. Therefore, we carried out an extensive analysis to identify transcription factor binding sites (TFBS). A series of putative interaction sites coincide with detected variants. Sixteen of the corresponding transcription factors are of particular interest, as they are housekeeping genes or show a direct link to hematopoiesis, tumorigenesis or leukemia (e.g. GATA-1/2, PU.1, MZF-1). Conclusions Specific alleles at predicted TFBSs may alter the expression of RPS19, modify an important interaction between transcription factors with overlapping TFBS or remove an important stimulus for hematopoiesis. We suggest that the detected interactions are of importance for hematopoiesis and could provide new insights into individual response to treatment.
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Affiliation(s)
- Alvaro Martinez Barrio
- The Linnaeus Centre for Bioinformatics Uppsala University/Swedish University of Agricultural Sciences, Uppsala University, Uppsala, Sweden
| | - Oskar Eriksson
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Jitendra Badhai
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Anne-Sophie Fröjmark
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Erik Bongcam-Rudloff
- The Linnaeus Centre for Bioinformatics Uppsala University/Swedish University of Agricultural Sciences, Uppsala University, Uppsala, Sweden
- Department of Animal Breeding and Genetics, Uppsala University, Uppsala, Sweden
| | - Niklas Dahl
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Jens Schuster
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- * E-mail:
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Wood MA, Walker WH. USF1/2 transcription factor DNA-binding activity is induced during rat Sertoli cell differentiation. Biol Reprod 2008; 80:24-33. [PMID: 18768914 DOI: 10.1095/biolreprod.108.070037] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Each Sertoli cell can support a finite number of developing germ cells. During development of the testis, the cessation of Sertoli cell proliferation and the onset of differentiation determine the final number of Sertoli cells and, hence, the number of sperm that can be produced. We hypothesize that the transition from proliferation to differentiation is facilitated by E-box transcription factors that induce the expression of differentiation-promoting genes. The relative activities of E-box proteins were studied in primary Sertoli cells isolated from 5-, 11-, and 20-day-old rats, representing proliferating, differentiating, and differentiated cells, respectively. E-box DNA-binding activity is almost undetectable 5 days after birth but peaks with initiation of differentiation 11 days after birth and remains elevated. Upstream stimulatory factors 1 and 2 (USF1 and USF2) were found to be the predominant E-box proteins present within DNA-protein complexes formed after incubating E-box-containing probes with nuclear extracts from developing Sertoli cells. The known potentiator of Sertoli cell differentiation, thyroxine, increases USF DNA-binding activity in Sertoli cells before differentiation (5-day-old Sertoli cells) but not after differentiation is initiated (11- and 20-day-old Sertoli cells). The developmental-specific increase in USF1 and USF2 DNA-binding activity may facilitate the switch from proliferation to differentiation and, thus, determine the ultimate number of Sertoli cells present within the testes and the upper limit of fertility.
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Affiliation(s)
- Michelle A Wood
- Center for Research in Reproductive Physiology, Department of Cell Biology and Molecular Physiology, Magee Women's Research Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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