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Morau MV, Seguin CS, Visacri MB, Pincinato EDC, Moriel P. Genetic Variants in the ABCB1 and ABCG2 Gene Drug Transporters Involved in Gefitinib-Associated Adverse Reaction: A Systematic Review and Meta-Analysis. Genes (Basel) 2024; 15:591. [PMID: 38790220 PMCID: PMC11120674 DOI: 10.3390/genes15050591] [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: 04/09/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
This systematic review and meta-analysis aimed to verify the association between the genetic variants of adenosine triphosphate (ATP)-binding cassette subfamily B member 1 (ABCB1) and ATP-binding cassette subfamily G member 2 (ABCG2) genes and the presence and severity of gefitinib-associated adverse reactions. We systematically searched PubMed, Virtual Health Library/Bireme, Scopus, Embase, and Web of Science databases for relevant studies published up to February 2024. In total, five studies were included in the review. Additionally, eight genetic variants related to ABCB1 (rs1045642, rs1128503, rs2032582, and rs1025836) and ABCG2 (rs2231142, rs2231137, rs2622604, and 15622C>T) genes were analyzed. Meta-analysis showed a significant association between the ABCB1 gene rs1045642 TT genotype and presence of diarrhea (OR = 5.41, 95% CI: 1.38-21.14, I2 = 0%), the ABCB1 gene rs1128503 TT genotype and CT + TT group and the presence of skin rash (OR = 4.37, 95% CI: 1.51-12.61, I2 = 0% and OR = 6.99, 95%CI: 1.61-30.30, I2= 0%, respectively), and the ABCG2 gene rs2231142 CC genotype and presence of diarrhea (OR = 3.87, 95% CI: 1.53-9.84, I2 = 39%). No ABCB1 or ABCG2 genes were positively associated with the severity of adverse reactions associated with gefitinib. In conclusion, this study showed that ABCB1 and ABCG2 variants are likely to exhibit clinical implications in predicting the presence of adverse reactions to gefitinib.
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Affiliation(s)
- Mariana Vieira Morau
- Department of Pharmacology, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas 13083-888, SP, Brazil; (M.V.M.); (C.S.S.)
| | - Cecília Souto Seguin
- Department of Pharmacology, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas 13083-888, SP, Brazil; (M.V.M.); (C.S.S.)
| | - Marília Berlofa Visacri
- Department of Pharmacy, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil;
| | - Eder de Carvalho Pincinato
- Department of Clinical Pathology, Faculdade de Ciências Médicas, Universidade Estadual de Campinas, Campinas 13083-888, SP, Brazil;
| | - Patricia Moriel
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas 13083-859, SP, Brazil
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Gautam B, Pandi A, Girija ASS, Arumugam P, Priyadharsini VJ. Genetic Association of Toll-Like Receptor 4 (TLR4) Gene Polymorphism (rs4986790) With Oral Squamous Cell Carcinoma (OSCC): A Pilot Case-Control Study. Cureus 2024; 16:e56021. [PMID: 38606218 PMCID: PMC11007480 DOI: 10.7759/cureus.56021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/13/2024] Open
Abstract
Introduction Oral squamous cell carcinoma (OSCC) is a highly prevalent and most common form of oral malignancy in the Indian population. Toll-like receptors belong to an important family of receptors that are involved in the process of pathogen recognition and mounting immune response. The expression of this receptor is dysregulated on the tumor cells as reported across several cancer types. The genetic variants in this gene could have a profound impact on the expression of the Toll-like receptor 4 (TLR4) gene. Objective This study aimed to understand the association of TLR4 gene polymorphism (rs4986790) with OSCC. The objective of this study was to compare the allele and genotype frequencies between the two groups, viz., OSCC and normal healthy subjects, recruited in the study. Materials and methods The blood samples were collected from normal healthy subjects (N = 25) and OSCC patients (N = 25). Genomic DNA was isolated from all samples, and genotyping was performed for the TLR4 gene polymorphism (rs4986790) employing the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) approach. The frequency distribution of genotypes and alleles across the study groups was determined by the Chi-square test. Results The allele frequency for TLR4 gene polymorphism (rs4986790) in the case group was found to be 60% (A allele) and 40% (G allele), respectively. The study population in both groups were found to agree with the Hardy-Weinberg equilibrium (HWE). The genotype frequency did not differ significantly among the two study groups which was evident from the p-value = 0.8285. Conclusion The present study did not report any significant association of the TLR4 polymorphic marker rs4986790 with OSCC. Further investigations into the association of other polymorphic markers in the TLR4 gene, among the larger population of OSCC patients, could provide evidence of their association with OSCC.
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Affiliation(s)
- Britina Gautam
- Department of Dentistry, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Anitha Pandi
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - A S Smiline Girija
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Paramasivam Arumugam
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Vijayashree J Priyadharsini
- Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
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Zhang C, Dai Z, Ferrier T, Orduña L, Santiago A, Peris A, Wong DCJ, Kappel C, Savoi S, Loyola R, Amato A, Kozak B, Li M, Liang A, Carrasco D, Meyer-Regueiro C, Espinoza C, Hilbert G, Figueroa-Balderas R, Cantu D, Arroyo-Garcia R, Arce-Johnson P, Claudel P, Errandonea D, Rodríguez-Concepción M, Duchêne E, Huang SSC, Castellarin SD, Tornielli GB, Barrieu F, Matus JT. MYB24 orchestrates terpene and flavonol metabolism as light responses to anthocyanin depletion in variegated grape berries. THE PLANT CELL 2023; 35:4238-4265. [PMID: 37648264 PMCID: PMC10689149 DOI: 10.1093/plcell/koad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/13/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Variegation is a rare type of mosaicism not fully studied in plants, especially fruits. We examined red and white sections of grape (Vitis vinifera cv. 'Béquignol') variegated berries and found that accumulation of products from branches of the phenylpropanoid and isoprenoid pathways showed an opposite tendency. Light-responsive flavonol and monoterpene levels increased in anthocyanin-depleted areas in correlation with increasing MYB24 expression. Cistrome analysis suggested that MYB24 binds to the promoters of 22 terpene synthase (TPS) genes, as well as 32 photosynthesis/light-related genes, including carotenoid pathway members, the flavonol regulator HY5 HOMOLOGUE (HYH), and other radiation response genes. Indeed, TPS35, TPS09, the carotenoid isomerase gene CRTISO2, and HYH were activated in the presence of MYB24 and MYC2. We suggest that MYB24 modulates ultraviolet and high-intensity visible light stress responses that include terpene and flavonol synthesis and potentially affects carotenoids. The MYB24 regulatory network is developmentally triggered after the onset of berry ripening, while the absence of anthocyanin sunscreens accelerates its activation, likely in a dose-dependent manner due to increased radiation exposure. Anthocyanins and flavonols in variegated berry skins act as effective sunscreens but for different wavelength ranges. The expression patterns of stress marker genes in red and white sections of 'Béquignol' berries strongly suggest that MYB24 promotes light stress amelioration but only partly succeeds during late ripening.
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Affiliation(s)
- Chen Zhang
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Thilia Ferrier
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Arnau Peris
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm 14476, Germany
| | - Stefania Savoi
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin 10124, Italy
| | - Rodrigo Loyola
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alessandra Amato
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Bartosz Kozak
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia V1V 1V7, Canada
| | - Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Akun Liang
- Departamento de Física Aplicada-ICMUV-MALTA Consolider Team, Universitat de València, Burjassot 46100, Valencia, Spain
| | - David Carrasco
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid-INIA, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Carlos Meyer-Regueiro
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Carmen Espinoza
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8380453, Chile
| | - Ghislaine Hilbert
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Rosa Arroyo-Garcia
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid-INIA, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Patricio Arce-Johnson
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería Universidad Autónoma deChile
| | | | - Daniel Errandonea
- Departamento de Física Aplicada-ICMUV-MALTA Consolider Team, Universitat de València, Burjassot 46100, Valencia, Spain
| | - Manuel Rodríguez-Concepción
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de València, Valencia 46022, Spain
| | - Eric Duchêne
- SVQV, University of Strasbourg, INRAE, Colmar 68000, France
| | - Shao-shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Simone Diego Castellarin
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia V1V 1V7, Canada
| | | | - Francois Barrieu
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
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Roy BC, Shukla N, Gachhui R, Mukherjee A. Genome-wide analysis of glutamate receptor gene family in allopolyploid Brassica napus and its diploid progenitors. Genetica 2023; 151:293-310. [PMID: 37624443 DOI: 10.1007/s10709-023-00192-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
Ionotropic glutamate receptors are ligand-gated nonselective cation channels that mediate neurotransmission in the central nervous system of animals. Plants possess homologous proteins called glutamate receptor-like channels (GLRs) which are involved in vital physiological processes including seed germination, long-distance signaling, chemotaxis, Ca2+ signaling etc. Till now, a comprehensive genome-wide analysis of the GLR gene family members in different economically important species of Brassica is missing. Considering the origin of allotetraploid Brassica napus from the hybridization between the diploid Brassica oleracea and Brassica rapa, we have identified 11, 27 and 65 GLR genes in B. oleracea, B. rapa and B. napus, respectively showing an expansion of this gene family in B. napus. Chromosomal locations revealed several tandemly duplicated GLR genes in all the three species. Moreover, the gene family expanded in B. napus after allopolyploidization. The phylogenetic analysis showed that the 103 GLRs are classified into three main groups. The exon-intron structures of these genes are not very conserved and showed wide variation in intron numbers. However, protein sequences are much conserved as shown by the presence of ten short amino acid sequence motifs. Predicted cis-acting elements in 1 kb promoters of GLR genes are mainly involved in light, stress and hormone responses. RNA-seq analysis showed that in B. oleracea and B. rapa, some GLRs are more tissue specific than others. In B. napus, some GLRs are downregulated under cold stress, while others are upregulated. In summary, this bioinformatic study of the GLR gene family of the three Brassica species provides evidence for the expansion of this gene family in B. napus and also provided useful information for in-depth studies of their biological functions in Brassica.
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Affiliation(s)
- Bidhan Chandra Roy
- Department of Botany, Dinabandhu Mahavidyalaya, North 24 Parganas, Bongaon, West Bengal, 743235, India
- Department of Life Science & Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata, West Bengal, 700032, India
| | - Nikita Shukla
- Department of Life Science & Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata, West Bengal, 700032, India
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Hyderabad, 500007, India
| | - Ratan Gachhui
- Department of Life Science & Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata, West Bengal, 700032, India
| | - Ashutosh Mukherjee
- Department of Botany, Vivekananda College, 269, Diamond Harbour Road, Thakurpukur, Kolkata, West Bengal, 700063, India.
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5
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Ma S, Guo Y, Liu D, Zhang X, Guo J, Zhang T, Lai L, Li Y, Chen Q, Yu L. Genome-Wide Analysis of the Membrane Attack Complex and Perforin Genes and Their Expression Pattern under Stress in the Solanaceae. Int J Mol Sci 2023; 24:13193. [PMID: 37686000 PMCID: PMC10487776 DOI: 10.3390/ijms241713193] [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: 07/27/2023] [Revised: 08/17/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
The Membrane Attack Complex and Perforin (MACPF) proteins play a crucial role in plant development and adaptation to environmental stresses. Heretofore, few MACPF genes have been functionally identified, leaving gaps in our understanding of MACPF genes in other plants, particularly in the Solanaceae family, which includes economically and culturally significant species, such as tomato, potato, and pepper. In this study, we have identified 26 MACPF genes in three Solanaceae species and in the water lily, which serves as the base group for angiosperms. Phylogenetic analysis indicates that angiosperm MACPF genes could be categorized into three distinct groups, with another moss and spikemoss lineage-specific group, which is further supported by the examination of gene structures and domain or motif organizations. Through inter-genome collinearity analysis, it is determined that there are 12 orthologous SolMACPF gene pairs. The expansion of SolMACPF genes is primarily attributed to dispersed duplications, with purifying selection identified as the principal driving force in their evolutionary process, as indicated by the ω values. Furthermore, the analysis of expression patterns revealed that Solanaceae genes are preferentially expressed in reproductive tissues and regulated by various environmental stimuli, particularly induced by submergence. Taken together, these findings offer valuable insights into and a fresh perspective on the evolution and function of SolMACPF genes, thereby establishing a foundation for further investigations into their phenotypic and functional characteristics.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Lujun Yu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (S.M.); (Y.G.); (D.L.); (X.Z.); (J.G.); (T.Z.); (L.L.); (Y.L.); (Q.C.)
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6
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Dai Y, Ma S, Guo Y, Zhang X, Liu D, Gao Y, Zhai C, Chen Q, Xiao S, Zhang Z, Yu L. Evolution and Expression of the Meprin and TRAF Homology Domain-Containing Gene Family in Solanaceae. Int J Mol Sci 2023; 24:ijms24108782. [PMID: 37240124 DOI: 10.3390/ijms24108782] [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: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Meprin and TRAF homology (MATH)-domain-containing proteins are pivotal in modulating plant development and environmental stress responses. To date, members of the MATH gene family have been identified only in a few plant species, including Arabidopsis thaliana, Brassica rapa, maize, and rice, and the functions of this gene family in other economically important crops, especially the Solanaceae family, remain unclear. The present study identified and analyzed 58 MATH genes from three Solanaceae species, including tomato (Solanum lycopersicum), potato (Solanum tuberosum), and pepper (Capsicum annuum). Phylogenetic analysis and domain organization classified these MATH genes into four groups, consistent with those based on motif organization and gene structure. Synteny analysis found that segmental and tandem duplication might have contributed to MATH gene expansion in the tomato and the potato, respectively. Collinearity analysis revealed high conservation among Solanaceae MATH genes. Further cis-regulatory element prediction and gene expression analysis showed that Solanaceae MATH genes play essential roles during development and stress response. These findings provide a theoretical basis for other functional studies on Solanaceae MATH genes.
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Affiliation(s)
- Yangshuo Dai
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Sirui Ma
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yixian Guo
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xue Zhang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Di Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yan Gao
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chendong Zhai
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Qinfang Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shi Xiao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhenfei Zhang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Lujun Yu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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Zhang Y, Guo S, Zhang F, Gan P, Li M, Wang C, Li H, Gao G, Wang X, Kang Z, Zhang X. CaREM1.4 interacts with CaRIN4 to regulate Ralstonia solanacearum tolerance by triggering cell death in pepper. HORTICULTURE RESEARCH 2023; 10:uhad053. [PMID: 37213684 PMCID: PMC10199716 DOI: 10.1093/hr/uhad053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 03/17/2023] [Indexed: 05/23/2023]
Abstract
Remorins, plant-specific proteins, have a significant role in conferring on plants the ability to adapt to adverse environments. However, the precise function of remorins in resistance to biological stress remains largely unknown. Eighteen CaREM genes were identified in pepper genome sequences based on the C-terminal conserved domain that is specific to remorin proteins in this research. Phylogenetic relations, chromosomal localization, motif, gene structures, and promoter regions of these remorins were analyzed and a remorin gene, CaREM1.4, was cloned for further study. The transcription of CaREM1.4 in pepper was induced by infection with Ralstonia solanacearum. Knocking down CaREM1.4 in pepper using virus-induced gene silencing (VIGS) technologies reduced the resistance of pepper plants to R. solanacearum and downregulated the expression of immunity-associated genes. Conversely, transient overexpression of CaREM1.4 in pepper and Nicotiana benthamiana plants triggered hypersensitive response-mediated cell death and upregulated expression of defense-related genes. In addition, CaRIN4-12, which interacted with CaREM1.4 at the plasma membrane and cell nucleus, was knocked down with VIGS, decreasing the susceptibility of Capsicum annuum to R. solanacearum. Furthermore, CaREM1.4 reduced ROS production by interacting with CaRIN4-12 upon co-injection in pepper. Taken together, our findings suggest that CaREM1.4 may function as a positive regulator of the hypersensitive response, and it interacts with CaRIN4-12, which negatively regulates plant immune responses of pepper to R. solanacearum. Our study provides new evidence for comprehending the molecular regulatory network of plant cell death.
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Affiliation(s)
- Yanqin Zhang
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Shuangyuan Guo
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Feng Zhang
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Pengfei Gan
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Min Li
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Cong Wang
- College of Life Sciences, Shanxi Normal University, Taiyuan 030000, Shanxi, China
| | - Huankun Li
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Gang Gao
- College of Life Sciences, Shanxi Normal University, Taiyuan 030000, Shanxi, China
| | - Xiaojie Wang
- College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100 Shaanxi, China
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8
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Ding K, Sun S, Luo Y, Long C, Zhai J, Zhai Y, Wang G. PlantCADB: A Comprehensive Plant Chromatin Accessibility Database. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:311-323. [PMID: 36328151 PMCID: PMC10626055 DOI: 10.1016/j.gpb.2022.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 09/25/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022]
Abstract
Chromatin accessibility landscapes are essential for detecting regulatory elements, illustrating the corresponding regulatory networks, and, ultimately, understanding the molecular basis underlying key biological processes. With the advancement of sequencing technologies, a large volume of chromatin accessibility data has been accumulated and integrated for humans and other mammals. These data have greatly advanced the study of disease pathogenesis, cancer survival prognosis, and tissue development. To advance the understanding of molecular mechanisms regulating plant key traits and biological processes, we developed a comprehensive plant chromatin accessibility database (PlantCADB) from 649 samples of 37 species. These samples are abiotic stress-related (such as heat, cold, drought, and salt; 159 samples), development-related (232 samples), and/or tissue-specific (376 samples). Overall, 18,339,426 accessible chromatin regions (ACRs) were compiled. These ACRs were annotated with genomic information, associated genes, transcription factor footprint, motif, and single-nucleotide polymorphisms (SNPs). Additionally, PlantCADB provides various tools to visualize ACRs and corresponding annotations. It thus forms an integrated, annotated, and analyzed plant-related chromatin accessibility resource, which can aid in better understanding genetic regulatory networks underlying development, important traits, stress adaptations, and evolution.PlantCADB is freely available at https://bioinfor.nefu.edu.cn/PlantCADB/.
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Affiliation(s)
- Ke Ding
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; College of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China
| | - Shanwen Sun
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yang Luo
- College of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China
| | - Chaoyue Long
- College of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China
| | - Jingwen Zhai
- College of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China
| | - Yixiao Zhai
- College of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China
| | - Guohua Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; College of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China.
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9
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Swida-Barteczka A, Pacak A, Kruszka K, Nuc P, Karlowski WM, Jarmolowski A, Szweykowska-Kulinska Z. MicroRNA172b-5p/trehalose-6-phosphate synthase module stimulates trehalose synthesis and microRNA172b-3p/AP2-like module accelerates flowering in barley upon drought stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1124785. [PMID: 36950348 PMCID: PMC10025483 DOI: 10.3389/fpls.2023.1124785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
MicroRNAs (miRNAs) are major regulators of gene expression during plant development under normal and stress conditions. In this study, we analyzed the expression of 150 conserved miRNAs during drought stress applied to barley ready to flower. The dynamics of miRNAs expression was also observed after rewatering. Target messenger RNA (mRNAs) were experimentally identified for all but two analyzed miRNAs, and 41 of the targets were not reported before. Drought stress applied to barley induced accelerated flowering coordinated by a pair of two differently expressed miRNAs originating from a single precursor: hvu-miR172b-3p and hvu-miR172b-5p. Increased expression of miRNA172b-3p during drought leads to the downregulation of four APETALA2(AP2)-like genes by their mRNA cleavage. In parallel, the downregulation of the miRNA172b-5p level results in an increased level of a newly identified target, trehalose-6-phosphate synthase, a key enzyme in the trehalose biosynthesis pathway. Therefore, drought-treated plants have higher trehalose content, a known osmoprotectant, whose level is rapidly dropping after watering. In addition, trehalose-6-phosphate, an intermediate of the trehalose synthesis pathway, is known to induce flowering. The hvu-miRNA172b-5p/trehalose-6-phosphate synthase and hvu-miRNA172b-3p/AP2-like create a module leading to osmoprotection and accelerated flowering induction during drought.
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Affiliation(s)
- Aleksandra Swida-Barteczka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Przemyslaw Nuc
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Wojciech M. Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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10
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Was the Last Bacterial Common Ancestor a Monoderm after All? Genes (Basel) 2022; 13:genes13020376. [PMID: 35205421 PMCID: PMC8871954 DOI: 10.3390/genes13020376] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022] Open
Abstract
The very nature of the last bacterial common ancestor (LBCA), in particular the characteristics of its cell wall, is a critical issue to understand the evolution of life on earth. Although knowledge of the relationships between bacterial phyla has made progress with the advent of phylogenomics, many questions remain, including on the appearance or disappearance of the outer membrane of diderm bacteria (also called Gram-negative bacteria). The phylogenetic transition between monoderm (Gram-positive bacteria) and diderm bacteria, and the associated peptidoglycan expansion or reduction, requires clarification. Herein, using a phylogenomic tree of cultivated and characterized bacteria as an evolutionary framework and a literature review of their cell-wall characteristics, we used Bayesian ancestral state reconstruction to infer the cell-wall architecture of the LBCA. With the same phylogenomic tree, we further revisited the evolution of the division and cell-wall synthesis (dcw) gene cluster using homology- and model-based methods. Finally, extensive similarity searches were carried out to determine the phylogenetic distribution of the genes involved with the biosynthesis of the outer membrane in diderm bacteria. Quite unexpectedly, our analyses suggest that all cultivated and characterized bacteria might have evolved from a common ancestor with a monoderm cell-wall architecture. If true, this would indicate that the appearance of the outer membrane was not a unique event and that selective forces have led to the repeated adoption of such an architecture. Due to the lack of phenotypic information, our methodology cannot be applied to all extant bacteria. Consequently, our conclusion might change once enough information is made available to allow the use of an even more diverse organism selection.
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11
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Production of combined-cross-linked hemicellulosic enzyme aggregates from paperboard residues. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00890-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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12
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Erdene‐Ochir E, Shin B, Huda MN, Lee EH, Song D, Jung C, Pan C. Characterization of endogenous promoters of GapC1 and GS for recombinant protein expression in Phaeodactylum tricornutum. Microbiologyopen 2021; 10:e1239. [PMID: 34713604 PMCID: PMC8545674 DOI: 10.1002/mbo3.1239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/14/2021] [Indexed: 11/11/2022] Open
Abstract
Although diatoms have been utilized as a cellular factory to produce biopharmaceuticals, recombinant proteins, and biofuels, only a few numbers of gene promoters are available. Therefore, the development of novel endogenous promoters is essential for the production of a range of bioactive substances. Here, we characterized the activities of endogenous promoters glyceraldehyde-3-phosphate dehydrogenase (GapC1) and glutamine synthetase (GS) of Phaeodactylum tricornutum using green fluorescent protein (GFP) under different culture conditions. Compared with the widely used fucoxanthin chlorophyll-binding protein A (fcpA) promoter, the GS promoter constitutively drove the expression of GFP throughout all growth phases of P. tricornutum, regardless of culture conditions. Additionally, the GFP level driven by the GapC1 promoter was the highest at the log phase, similar to the fcpA promoter, and increased light and nitrogen-starvation conditions reduced GFP levels by inhibiting promoter activity. These results suggested that the GS promoter could be utilized as a strong endogenous promoter for the genetic engineering of P. tricornutum.
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Affiliation(s)
- Erdenedolgor Erdene‐Ochir
- Natural Product Informatics Research CenterKIST Gangneung Institute of Natural ProductsGangneungRepublic of Korea
- Division of Bio‐Medical Science and Technology, KIST SchoolKorea University of Science and TechnologySeoulRepublic of Korea
| | | | - Md Nazmul Huda
- Natural Product Informatics Research CenterKIST Gangneung Institute of Natural ProductsGangneungRepublic of Korea
- Division of Bio‐Medical Science and Technology, KIST SchoolKorea University of Science and TechnologySeoulRepublic of Korea
| | - Eun Ha Lee
- Natural Product Informatics Research CenterKIST Gangneung Institute of Natural ProductsGangneungRepublic of Korea
| | - Dae‐Geun Song
- Natural Product Informatics Research CenterKIST Gangneung Institute of Natural ProductsGangneungRepublic of Korea
| | - Choonkyun Jung
- Department of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangRepublic of Korea
- Department of Agriculture, Forestry, and Bioresources and Integrated Major in Global Smart Farm, College of Agriculture and Life SciencesSeoul National UniversitySeoulRepublic of Korea
| | - Cheol‐Ho Pan
- Natural Product Informatics Research CenterKIST Gangneung Institute of Natural ProductsGangneungRepublic of Korea
- Division of Bio‐Medical Science and Technology, KIST SchoolKorea University of Science and TechnologySeoulRepublic of Korea
- Microalgae Ask Us Co., Ltd.GangneungRepublic of Korea
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13
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Gao W, Li Z, Chen W, Zhang S. Performance Evaluation of Warfarin Dose Prediction Algorithms and Effects of Clinical Factors on Warfarin Dose in Chinese Patients. Ther Drug Monit 2021; 43:527-535. [PMID: 34250965 DOI: 10.1097/ftd.0000000000000880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/06/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND The clinical utility of warfarin dose prediction algorithms remains controversial, our purpose is to evaluate the performance of warfarin dose prediction algorithms and the effects of clinical factors on warfarin dose in Chinese patients. METHODS Clinical data of 217 patients who received warfarin treatment were used to assess 6 warfarin dose prediction algorithms (OHNO, IWPC [International Warfarin Pharmacogenetics Consortium], HUANG, KIM, BRESS, and MIAO). The predicted dose (PD) was compared with the warfarin optimal dose (WOD, defined as the dose that maintains the international normalized ratio within the target range of 2.0-3.0). A multiple regression analysis with WOD as the dependent variable was performed to evaluate the effects of clinical factors on warfarin dose. RESULTS The mean absolute error analysis ranked the predictive accuracies of the algorithms as OHNO > IWPC > HUANG > KIM > BRESS > MIAO. Stratified analysis indicated that HUANG most accurately predicted that patients required lower WODs (≤3 mg/d), whereas OHNO was the most effective in predicting medium WODs (3-5 mg/d). KIM was effective in predicting high WODs (>5 mg/d). Multiple linear regression analysis showed that VKORC1 (rs9923231) and body mass index were significantly positively correlated with WOD, whereas concurrent atrial fibrillation status, CYP2C9*3 (rs1057910), and sex were significantly negatively correlated with WOD. CONCLUSIONS In Chinese patients, OHNO should be given priority during the prediction and selection of warfarin dose. When using OHNO to predict warfarin dose (≤3 mg/d or >5 mg/d), HUANG or KIM algorithms can provide precise predictions. At the same time, physicians should pay close attention to clinical factors, such as VKORC1 (rs9923231), concurrent atrial fibrillation status, CYP2C9*3 (rs1057910), body mass index, and sex, to improve warfarin dose adjustment strategies in Chinese patients.
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Affiliation(s)
- Weiqi Gao
- School of Pharmacy, Shanxi Medical University, Taiyuan, China; and
- Department of Pharmacy, Shanxi Bethune Hospital, Third Hospital of Shanxi Medical University, Shanxi Academy of Medical Sciences, Taiyuan, China
| | - Zhihong Li
- Department of Pharmacy, Shanxi Bethune Hospital, Third Hospital of Shanxi Medical University, Shanxi Academy of Medical Sciences, Taiyuan, China
| | - Weihong Chen
- Department of Pharmacy, Shanxi Bethune Hospital, Third Hospital of Shanxi Medical University, Shanxi Academy of Medical Sciences, Taiyuan, China
| | - Shuqiu Zhang
- School of Pharmacy, Shanxi Medical University, Taiyuan, China; and
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14
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Singh P, Mukhopadhyay K. Comprehensive molecular dissection of TIFY Transcription factors reveal their dynamic responses to biotic and abiotic stress in wheat (Triticum aestivum L.). Sci Rep 2021; 11:9739. [PMID: 33958607 PMCID: PMC8102568 DOI: 10.1038/s41598-021-87722-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/31/2021] [Indexed: 02/03/2023] Open
Abstract
The plant specific TIFY (previously known as ZIM) transcription factor (TF) family plays crucial roles in cross talk between Jasmonic Acid and other phytohormones like gibberellins, salicylic acid, abscisic acid, auxin, and ethylene signaling pathways. Wheat yield is severely affected by rust diseases and many abiotic stresses, where different phytohormone signaling pathways are involved. TIFYs have been studied in many plants yet reports describing their molecular structure and function in wheat are lacking. In the present study, we have identified 23 novel TIFY genes in wheat genome using in silico approaches. The identified proteins were characterized based on their conserved domains and phylogenetically classified into nine subfamilies. Chromosomal localization of the identified TIFY genes showed arbitrary distribution. Forty cis-acting elements including phytohormone, stress and light receptive elements were detected in the upstream regions of TIFY genes. Seventeen wheat microRNAs targeted the identified wheat TIFY genes. Gene ontological studies revealed their major contribution in defense response and phytohormone signaling. Secondary structure of TIFY proteins displayed the characteristic alpha-alpha-beta fold. Synteny analyses indicated all wheat TIFY genes had orthologous sequences in sorghum, rice, maize, barley and Brachypodium indicating presence of similar TIFY domains in monocot plants. Six TIFY genes had been cloned from wheat genomic and cDNA. Sequence characterization revealed similar characteristics as the in silico identified novel TIFY genes. Tertiary structures predicted the active sites in these proteins to play critical roles in DNA binding. Expression profiling of TIFY genes showed their contribution during incompatible and compatible leaf rust infestation. TIFY genes were also highly expressed during the initial hours of phytohormone induced stress. This study furnishes fundamental information on characterization and putative functions of TIFY genes in wheat.
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Affiliation(s)
- Poonam Singh
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India.
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15
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Andersen EJ, Nepal MP, Ali S. Necrotrophic Fungus Pyrenophora tritici-repentis Triggers Expression of Multiple Resistance Components in Resistant and Susceptible Wheat Cultivars. THE PLANT PATHOLOGY JOURNAL 2021; 37:99-114. [PMID: 33866753 PMCID: PMC8053848 DOI: 10.5423/ppj.oa.06.2020.0109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/16/2021] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Tan spot of wheat, caused by Pyrenophora tritici-repentis (Ptr), results in a yield loss through chlorosis and necrosis of healthy leaf tissue. The major objective of this study was to compare gene expression in resistant and susceptible wheat cultivars after infection with Ptr ToxA-producing race 2 and direct infiltration with Ptr ToxA proteins. Greenhouse experiments included exposure of the wheat cultivars to pathogen inoculum or direct infiltration of leaf tissue with Ptr-ToxA protein isolate. Samples from the experiments were subjected to RNA sequencing. Results showed that ToxA RNA sequences were first detected in samples collected eight hours after treatments indicating that upon Ptr contact with wheat tissue, Ptr started expressing ToxA. The resistant wheat cultivar, in response to Ptr inoculum, expressed genes associated with plant resistance responses that were not expressed in the susceptible cultivar; genes of interest included five chitinases, eight transporters, five pathogen-detecting receptors, and multiple classes of signaling factors. Resistant and susceptible wheat cultivars therefore differed in their response in the expression of genes that encode chitinases, transporters, wall-associated kinases, permeases, and wound-induced proteins, among others. Plants exposed to Ptr inoculum expressed transcription factors, kinases, receptors, and peroxidases, which are not expressed as highly in the control samples or samples infiltrated with ToxA. Several of the differentially expressed genes between cultivars were found in the Ptr resistance QTLs on chromosomes 1A, 2D, 3B, and 5A. Future studies should elucidate the specific roles these genes play in the wheat response to Ptr.
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Affiliation(s)
- Ethan J. Andersen
- Department of Biology, Francis Marion University, Florence, SC 29506,
USA
| | - Madhav P. Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007,
USA
| | - Shaukat Ali
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007,
USA
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16
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Yan Z, Shen Z, Li Z, Chao Q, Kong L, Gao ZF, Li QW, Zheng HY, Zhao CF, Lu CM, Wang YW, Wang BC. Genome-wide transcriptome and proteome profiles indicate an active role of alternative splicing during de-etiolation of maize seedlings. PLANTA 2020; 252:60. [PMID: 32964359 DOI: 10.1007/s00425-020-03464-5] [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: 05/22/2020] [Accepted: 09/12/2020] [Indexed: 06/11/2023]
Abstract
AS events affect genes encoding protein domain composition and make the single gene produce more proteins with a certain number of genes to satisfy the establishment of photosynthesis during de-etiolation. The drastic switch from skotomorphogenic to photomorphogenic development is an excellent system to elucidate rapid developmental responses to environmental stimuli in plants. To decipher the effects of different light wavelengths on de-etiolation, we illuminated etiolated maize seedlings with blue, red, blue-red mixed and white light, respectively. We found that blue light alone has the strongest effect on photomorphogenesis and that this effect can be attributed to the higher number and expression levels of photosynthesis and chlorosynthesis proteins. Deep sequencing-based transcriptome analysis revealed gene expression changes under different light treatments and a genome-wide alteration in alternative splicing (AS) profiles. We discovered 41,188 novel transcript isoforms for annotated genes, which increases the percentage of multi-exon genes with AS to 63% in maize. We provide peptide support for all defined types of AS, especially retained introns. Further in silico prediction revealed that 58.2% of retained introns have changes in domains compared with their most similar annotated protein isoform. This suggests that AS acts as a protein function switch allowing rapid light response through the addition or removal of functional domains. The richness of novel transcripts and protein isoforms also demonstrates the potential and importance of integrating proteomics into genome annotation in maize.
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Affiliation(s)
- Zhen Yan
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhuo Shen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China
| | - Zhe Li
- Precision Scientific (Beijing) Co., Ltd., Beijing, 100085, China
| | - Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100039, China
| | - Lei Kong
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhi-Fang Gao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Qing-Wei Li
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hai-Yan Zheng
- Center for Advanced Biotechnology and Medicine, Biological Mass Spectrometry Facility, Rutgers University, Piscataway, NJ, 08855, USA
| | - Cai-Feng Zhao
- Center for Advanced Biotechnology and Medicine, Biological Mass Spectrometry Facility, Rutgers University, Piscataway, NJ, 08855, USA
| | - Cong-Ming Lu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Ying-Wei Wang
- Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100039, China.
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17
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Evolution and Expression of the Membrane Attack Complex and Perforin Gene Family in the Poaceae. Int J Mol Sci 2020; 21:ijms21165736. [PMID: 32785137 PMCID: PMC7460961 DOI: 10.3390/ijms21165736] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 01/02/2023] Open
Abstract
Membrane Attack Complex and Perforin (MACPF) proteins play crucial roles in plant development and plant responses to environmental stresses. To date, only four MACPF genes have been identified in Arabidopsis thaliana, and the functions of the MACPF gene family members in other plants, especially in important crop plants, such as the Poaceae family, remain largely unknown. In this study, we identified and analyzed 42 MACPF genes from six completely sequenced and well annotated species representing the major Poaceae clades. A phylogenetic analysis of MACPF genes resolved four groups, characterized by shared motif organizations and gene structures within each group. MACPF genes were unevenly distributed along the Poaceae chromosomes. Moreover, segmental duplications and dispersed duplication events may have played significant roles during MACPF gene family expansion and functional diversification in the Poaceae. In addition, phylogenomic synteny analysis revealed a high degree of conservation among the Poaceae MACPF genes. In particular, Group I, II, and III MACPF genes were exposed to strong purifying selection with different evolutionary rates. Temporal and spatial expression analyses suggested that Group III MACPF genes were highly expressed relative to the other groups. In addition, most MACPF genes were highly expressed in vegetative tissues and up-regulated by several biotic and abiotic stresses. Taken together, these findings provide valuable information for further functional characterization and phenotypic validation of the Poaceae MACPF gene family.
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18
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Transcriptome Analysis Reveals Long Intergenic Non-Coding RNAs Contributed to Intramuscular Fat Content Differences between Yorkshire and Wei Pigs. Int J Mol Sci 2020; 21:ijms21051732. [PMID: 32138348 PMCID: PMC7084294 DOI: 10.3390/ijms21051732] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/23/2020] [Accepted: 03/01/2020] [Indexed: 12/12/2022] Open
Abstract
Intramuscular fat (IMF) content is closely related to various meat traits, such as tenderness, juiciness, and flavor. The IMF content varies considerably among pig breeds with different genetic backgrounds. Long intergenic non-coding RNAs (lincRNAs) have been widely identified in many species and found to be an important class of regulators that can participate in multiple biological processes. However, the mechanism behind lincRNAs regulation of pig IMF content remains unknown and requires further study. In our study, we identified a total of 156 lincRNAs in the longissimus dorsi muscle of Wei (fat-type) and Yorkshire (lean-type) pigs using previously published data. These identified lincRNAs have shorter transcript length, longer exon length, lower exon number, and lower expression level as compared with protein-coding transcripts. We predicted potential target genes (PTGs) that are potentially regulated by lincRNAs in cis or trans regulation. Gene ontology and pathway analyses indicated that many potential lincRNAs target genes are involved in IMF-related processes or pathways, such as fatty acid catabolic process and adipocytokine signaling pathway. In addition, we analyzed quantitative trait locus (QTL) sites that differentially expressed lincRNAs (DE lincRNAs) between Wei and Yorkshire pigs co-localized. The QTL sites where DE lincRNAs co-localize are mostly related to IMF content. Furthermore, we constructed a co-expressed network between DE lincRNAs and their differentially expressed PTGs (DEPTGs). On the basis of their expression levels, we suggest that many DE lincRNAs can affect IMF development by positively or negatively regulating their PTGs. This study identified and analyzed some lincRNAs- and PTGs-related IMF development of the two pig breeds and provided new insight into research on the roles of lincRNAs in the two types of breeds.
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19
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Hua W, Tan C, Xie J, Zhu J, Shang Y, Yang J, Zhang XQ, Wu X, Wang J, Li C. Alternative splicing of a barley gene results in an excess-tillering and semi-dwarf mutant. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:163-177. [PMID: 31690990 DOI: 10.1007/s00122-019-03448-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
An excess-tillering semi-dwarf gene Hvhtd was identified from an EMS-induced mutant in barley and alternative splicing results in excess-tillering semi-dwarf traits. Tillering and plant height are important traits determining plant architecture and grain production in cereal crops. This study identified an excess-tillering semi-dwarf mutant (htd) from an EMS-treated barley population. Genetic analysis of the F1, F2, and F2:3 populations showed that a single recessive gene controlled the excess-tillering semi-dwarf in htd. Using BSR-Seq and gene mapping, the Hvhtd gene was delimited within a 1.8 Mb interval on chromosome 2HL. Alignment of the RNA-Seq data with the functional genes in the interval identified a gene HORVU2Hr1G098820 with alternative splicing between exon2 and exon3 in the mutant, due to a G to A single-nucleotide substitution at the exon and intron junction. An independent mutant with a similar phenotype confirmed the result, with alternative splicing between exon3 and exon4. In both cases, the alternative splicing resulted in a non-functional protein. And the gene HORVU2Hr1G098820 encodes a trypsin family protein and may be involved in the IAA signaling pathway and differs from the mechanism of Green Revolution genes in the gibberellic acid metabolic pathway.
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Affiliation(s)
- Wei Hua
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Cong Tan
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Jingzhong Xie
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinghuan Zhu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yi Shang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jianming Yang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Xiaojian Wu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Junmei Wang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Chengdao Li
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia.
- Department of Primary Industry and Regional Development, 3 Baron-Hay Court, South Perth, WA, 6151, Australia.
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, 434025, Hubei, China.
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20
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Mattila TM, Laenen B, Horvath R, Hämälä T, Savolainen O, Slotte T. Impact of demography on linked selection in two outcrossing Brassicaceae species. Ecol Evol 2019; 9:9532-9545. [PMID: 31534673 PMCID: PMC6745670 DOI: 10.1002/ece3.5463] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 12/13/2022] Open
Abstract
Genetic diversity is shaped by mutation, genetic drift, gene flow, recombination, and selection. The dynamics and interactions of these forces shape genetic diversity across different parts of the genome, between populations and species. Here, we have studied the effects of linked selection on nucleotide diversity in outcrossing populations of two Brassicaceae species, Arabidopsis lyrata and Capsella grandiflora, with contrasting demographic history. In agreement with previous estimates, we found evidence for a modest population size expansion thousands of generations ago, as well as efficient purifying selection in C. grandiflora. In contrast, the A. lyrata population exhibited evidence for very recent strong population size decline and weaker efficacy of purifying selection. Using multiple regression analyses with recombination rate and other genomic covariates as explanatory variables, we can explain 47% of the variance in neutral diversity in the C. grandiflora population, while in the A. lyrata population, only 11% of the variance was explained by the model. Recombination rate had a significant positive effect on neutral diversity in both species, suggesting that selection at linked sites has an effect on patterns of neutral variation. In line with this finding, we also found reduced neutral diversity in the vicinity of genes in the C. grandiflora population. However, in A. lyrata no such reduction in diversity was evident, a finding that is consistent with expectations of the impact of a recent bottleneck on patterns of neutral diversity near genes. This study thus empirically demonstrates how differences in demographic history modulate the impact of selection at linked sites in natural populations.
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Affiliation(s)
- Tiina M. Mattila
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Present address:
Department of Organismal BiologyUppsala UniversityUppsalaSweden
| | - Benjamin Laenen
- Science for Life Laboratory, Department of Ecology, Environment, and Plant SciencesStockholm UniversityStockholmSweden
| | - Robert Horvath
- Science for Life Laboratory, Department of Ecology, Environment, and Plant SciencesStockholm UniversityStockholmSweden
| | - Tuomas Hämälä
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
- Present address:
Department of Plant and Microbial BiologyUniversity of Minnesota Twin CitiesSt. PaulMNUSA
| | - Outi Savolainen
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
- Biocenter OuluUniversity of OuluOuluFinland
| | - Tanja Slotte
- Science for Life Laboratory, Department of Ecology, Environment, and Plant SciencesStockholm UniversityStockholmSweden
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Milutinovic M, Lindsey BE, Wijeratne A, Hernandez JM, Grotewold N, Fernández V, Grotewold E, Brkljacic J. Arabidopsis EMSY-like (EML) histone readers are necessary for post-fertilization seed development, but prevent fertilization-independent seed formation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 285:99-109. [PMID: 31203898 DOI: 10.1016/j.plantsci.2019.04.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/07/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Seed development is a complex regulatory process that includes a transition from gametophytic to sporophytic program. The synchronized development of different seed compartments (seed coat, endosperm and embryo) depends on a balance in parental genome contributions. In the most severe cases, the disruption of the balance leads to seed abortion. This represents one of the main obstacles for the engineering of asexual reproduction through seeds (apomixis), and for generating new interspecies hybrids. The repression of auxin synthesis by the Polycomb Repressive Complex 2 (PRC2) is a major mechanism contributing to sensing genome balance. However, current efforts focusing on decreasing PRC2 or elevating auxin levels have not yet resulted in the production of apomictic seed. Here, we show that EMSY-Like Tudor/Agenet H3K36me3 histone readers EML1 and EML3 are necessary for early stages of seed development to proceed at a normal rate in Arabidopsis. We further demonstrate that both EML1 and EML3 are required to prevent the initiation of seed development in the absence of fertilization. Based on the whole genome expression analysis, we identify auxin transport and signaling genes as the most enriched downstream targets of EML1 and EML3. We hypothesize that EML1 and EML3 function to repress and soften paternal gene expression by fine-tuning auxin responses. Discovery of this pathway may contribute to the engineering of apomixis and interspecies hybrids.
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Affiliation(s)
- Milica Milutinovic
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Benson E Lindsey
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Asela Wijeratne
- Department of Molecular Genetics, Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - J Marcela Hernandez
- Department of Molecular Genetics, Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Nikolas Grotewold
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Virginia Fernández
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - Erich Grotewold
- Department of Molecular Genetics, Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, 43210, USA.
| | - Jelena Brkljacic
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA.
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Huynh S, Marcussen T, Felber F, Parisod C. Hybridization preceded radiation in diploid wheats. Mol Phylogenet Evol 2019; 139:106554. [PMID: 31288105 DOI: 10.1016/j.ympev.2019.106554] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/03/2019] [Accepted: 07/03/2019] [Indexed: 01/06/2023]
Abstract
Evolutionary relationships among the Aegilops-Triticum relatives of cultivated wheats have been difficult to resolve owing to incomplete lineage sorting and reticulate evolution. Recent studies have suggested that the wheat D-genome lineage (progenitor of Ae. tauschii) originated through homoploid hybridization between the A-genome lineage (progenitor of Triticum s.str.) and the B-genome lineage (progenitor of Ae. speltoides). This scenario of reticulation has been debated, calling for adequate phylogenetic analyses based on comprehensive sampling. To reconstruct the evolution of Aegilops-Triticum diploids, we here combined high-throughput sequencing of 38 nuclear low-copy loci of multiple accessions of all 13 species with inferences of the species phylogeny using the full-parameterized MCMC_SEQ method. Phylogenies recovered a monophyletic Aegilops-Triticum lineage that began diversifying ~6.6 Ma ago and gave rise to four sublineages, i.e. the A- (2 species), B- (1 species), D- (9 species) and T- (Ae. mutica) genome lineage. Full-parameterized phylogenies as well as patterns of tree dilation and tree compression supported a hybrid origin of the D-genome lineage from A and B ~3.0-4.0 Ma ago, and did not indicate additional hybridization events. Conflicting ABBA-BABA tests suggestive of further reticulation were shown here to result from ancestral population structure rather than hybridization. This comprehensive and dated phylogeny of wheat relatives indicates that the origin of the hybrid D-genome was followed by intense diversification into the majority of extant diploid as well as allopolyploid wild wheats.
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Affiliation(s)
- Stella Huynh
- Institute of Biology, University of Neuchâtel, Switzerland
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
| | - François Felber
- Institute of Biology, University of Neuchâtel, Switzerland; Musée et Jardins botaniques cantonaux de Lausanne et Pont-de-Nant, Switzerland
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Badawi MA, Agharbaoui Z, Zayed M, Li Q, Byrns B, Zou J, Fowler DB, Danyluk J, Sarhan F. Genome-Wide Identification and Characterization of the Wheat Remorin ( TaREM) Family during Cold Acclimation. THE PLANT GENOME 2019; 12:180040. [PMID: 31290927 DOI: 10.3835/plantgenome2018.06.0040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Remorins (REMs) are plant-specific proteins that play an essential role in plant-microbe interactions. However, their roles in vernalization and abiotic stress responses remain speculative. Most remorins have a variable proline-rich -half and a more conserved -half that is predicted to form coils. A search of the wheat ( L.) database revealed the existence of 20 different genes, which we classified into six groups on the basis of whether they shared a common phylogenetic and structural origin. Analysis of the physical genomic distributions demonstrated that genes are dispersed in the wheat genome and have one to seven introns. Promoter analysis of genes revealed the presence of putative -elements related to diverse functions like development, hormonal regulation, and biotic and abiotic stress responsiveness. Expression levels of genes were measured in plants grown under field and controlled conditions and in response to hormone treatment. Our analyses revealed that 12 members of the REM family are regulated during cold acclimation in wheat in four different tissues (roots, crowns, stems, and leaves), with the highest expression in roots. Differential gene expression was found between wheat cultivars with contrasting degrees of cold tolerance, suggesting the implication of genes in cold response and tolerance. Additionally, eight genes were induced in response to abscisic acid and methyl jasmonate treatment. This genome-wide analysis of genes provides valuable resources for functional analysis aimed at understanding their role in stress adaptation.
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Shi G, Chen L, Chen G, Zou C, Li J, Li M, Fang C, Li C. Identification and Functional Prediction of Long Intergenic Non-coding RNAs Related to Subcutaneous Adipose Development in Pigs. Front Genet 2019; 10:160. [PMID: 30886630 PMCID: PMC6409335 DOI: 10.3389/fgene.2019.00160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/14/2019] [Indexed: 12/19/2022] Open
Abstract
An increasing number of studies have shown that long intergenic non-coding RNAs (lincRNAs) are a very important class of non-coding RNAs that plays a vital role in many biological processes. Adipose tissue is an important place for storing energy, but few studies on lincRNAs were related to pig subcutaneous fat development. Here, we used published RNA-seq data from subcutaneous adipose tissue of Italian Large White pigs and identified 252 putative lincRNAs, wherein 34 were unannotated. These lincRNAs had relatively shorter length, lower number of exons, and lower expression level compared with protein-coding transcripts. Gene ontology and pathway analysis indicated that the adjacent genes of lincRNAs were involved in lipid metabolism. In addition, differentially expressed lincRNAs (DELs) between low and high backfat thickness pigs were identified. Through the detection of quantitative trait locus (QTL), DELs were mainly located in QTLs related to adipose development. Based on the expression correlation of DEL genes and their differentially expressed potential target genes, we constructed a co-expression network and a potential pathway of DEL's effect on lipid metabolism. Our study identified and analyzed lincRNAs in subcutaneous adipose tissue, and results suggested that lincRNAs may be involved in the regulation of subcutaneous fat development. Our findings provided new insights into the biological function of porcine lincRNAs.
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Affiliation(s)
- Gaoli Shi
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Lin Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Guoting Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Cheng Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Jingxuan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Mengxun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Chengchi Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Synthetic lethality guiding selection of drug combinations in ovarian cancer. PLoS One 2019; 14:e0210859. [PMID: 30682083 PMCID: PMC6347359 DOI: 10.1371/journal.pone.0210859] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 01/03/2019] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Synthetic lethality describes a relationship between two genes where single loss of either gene does not trigger significant impact on cell viability, but simultaneous loss of both gene functions results in lethality. Targeting synthetic lethal interactions with drug combinations promises increased efficacy in tumor therapy. MATERIALS AND METHODS We established a set of synthetic lethal interactions using publicly available data from yeast screens which were mapped to their respective human orthologs using information from orthology databases. This set of experimental synthetic lethal interactions was complemented by a set of predicted synthetic lethal interactions based on a set of protein meta-data like e.g. molecular pathway assignment. Based on the combined set, we evaluated drug combinations used in late stage clinical development (clinical phase III and IV trials) or already in clinical use for ovarian cancer with respect to their effect on synthetic lethal interactions. We furthermore identified a set of drug combinations currently not being tested in late stage ovarian cancer clinical trials that however have impact on synthetic lethal interactions thus being worth of further investigations regarding their therapeutic potential in ovarian cancer. RESULTS Twelve of the tested drug combinations addressed a synthetic lethal interaction with the anti-VEGF inhibitor bevacizumab in combination with paclitaxel being the most studied drug combination addressing the synthetic lethal pair between VEGFA and BCL2. The set of 84 predicted drug combinations for example holds the combination of the PARP inhibitor olaparib and paclitaxel, which showed efficacy in phase II clinical studies. CONCLUSION A set of drug combinations currently not tested in late stage ovarian cancer clinical trials was identified having impact on synthetic lethal interactions thus being worth of further investigations regarding their therapeutic potential in ovarian cancer.
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Abstract
Regulation of plant root angle is critical for obtaining nutrients and water and is an important trait for plant breeding. A plant’s final, long-term root angle is the net result of a complex series of decisions made by a root tip in response to changes in nutrient availability, impediments, the gravity vector and other stimuli. When a root tip is displaced from the gravity vector, the short-term process of gravitropism results in rapid reorientation of the root toward the vertical. Here, we explore both short- and long-term regulation of root growth angle, using natural variation in tomato to identify shared and separate genetic features of the two responses. Mapping of expression quantitative trait loci mapping and leveraging natural variation between and within species including Arabidopsis suggest a role for PURPLE ACID PHOSPHATASE 27 and CELL DIVISION CYCLE 73 in determining root angle.
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Synthetic lethal combinations of low-toxicity drugs for breast cancer identified in silico by genetic screens in yeast. Oncotarget 2018; 9:36379-36391. [PMID: 30555636 PMCID: PMC6284748 DOI: 10.18632/oncotarget.26372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 10/21/2018] [Indexed: 12/20/2022] Open
Abstract
In recent years, the concept of synthetic lethality, describing a cellular state where loss of two genes leads to a non-viable phenotype while loss of one gene can be compensated, has emerged as a novel strategy for cancer therapy. Various compounds targeting synthetic lethal pathways are either under clinical investigation or are already routinely used in multiple cancer entities such as breast cancer. Most of them target the well-described synthetic lethal interplay between PARP1 and BRCA1/2. In our study, we investigated, using an in silico methodological approach, clinically utilized drug combinations for breast cancer treatment, by correlating their known molecular targets with known homologous interaction partners that cause synthetic lethality in yeast. Further, by creating a machine-learning algorithm, we were able to suggest novel synthetic lethal drug combinations of low-toxicity drugs in breast cancer and showed their negative effects on cancer cell viability in vitro. Our findings foster the understanding of evolutionarily conserved synthetic lethality in breast cancer cells and might lead to new drug combinations with favorable toxicity profile in this entity.
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Ying H, Cooke I, Sprungala S, Wang W, Hayward DC, Tang Y, Huttley G, Ball EE, Forêt S, Miller DJ. Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages. Genome Biol 2018; 19:175. [PMID: 30384840 PMCID: PMC6214176 DOI: 10.1186/s13059-018-1552-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/28/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there are two major clades, Complexa and Robusta, but the genomic bases of significant differences between them remain unclear. RESULTS Draft genome assemblies and annotations were generated for three coral species: Galaxea fascicularis (Complexa), Fungia sp., and Goniastrea aspera (Robusta). Whilst phylogenetic analyses strongly support a deep split between Complexa and Robusta, synteny analyses reveal a high level of gene order conservation between all corals, but not between corals and sea anemones or between sea anemones. HOX-related gene clusters are, however, well preserved across all of these combinations. Differences between species are apparent in the distribution and numbers of protein domains and an apparent correlation between number of HSP20 proteins and stress tolerance. Uniquely amongst animals, a complete histidine biosynthesis pathway is present in robust corals but not in complex corals or sea anemones. This pathway appears to be ancestral, and its retention in the robust coral lineage has important implications for coral nutrition and symbiosis. CONCLUSIONS The availability of three new coral genomes enabled recognition of a de novo histidine biosynthesis pathway in robust corals which is only the second identified biosynthetic difference between corals. These datasets provide a platform for understanding many aspects of coral biology, particularly the interactions of corals with their endosymbionts.
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Affiliation(s)
- Hua Ying
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Ira Cooke
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811 Australia
| | - Susanne Sprungala
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811 Australia
| | - Weiwen Wang
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - David C. Hayward
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Yurong Tang
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
- Computational Biology and Bioinformatics Unit, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Gavin Huttley
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
- Computational Biology and Bioinformatics Unit, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Eldon E. Ball
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - Sylvain Forêt
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601 Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
| | - David J. Miller
- Comparative Genomics Centre, Department of Molecular and Cell Biology, James Cook University, Townsville, QLD 4811 Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811 Australia
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Grobler Y, Yun CY, Kahler DJ, Bergman CM, Lee H, Oliver B, Lehmann R. Whole genome screen reveals a novel relationship between Wolbachia levels and Drosophila host translation. PLoS Pathog 2018; 14:e1007445. [PMID: 30422992 PMCID: PMC6258568 DOI: 10.1371/journal.ppat.1007445] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 11/27/2018] [Accepted: 10/30/2018] [Indexed: 11/29/2022] Open
Abstract
Wolbachia is an intracellular bacterium that infects a remarkable range of insect hosts. Insects such as mosquitos act as vectors for many devastating human viruses such as Dengue, West Nile, and Zika. Remarkably, Wolbachia infection provides insect hosts with resistance to many arboviruses thereby rendering the insects ineffective as vectors. To utilize Wolbachia effectively as a tool against vector-borne viruses a better understanding of the host-Wolbachia relationship is needed. To investigate Wolbachia-insect interactions we used the Wolbachia/Drosophila model that provides a genetically tractable system for studying host-pathogen interactions. We coupled genome-wide RNAi screening with a novel high-throughput fluorescence in situ hybridization (FISH) assay to detect changes in Wolbachia levels in a Wolbachia-infected Drosophila cell line JW18. 1117 genes altered Wolbachia levels when knocked down by RNAi of which 329 genes increased and 788 genes decreased the level of Wolbachia. Validation of hits included in depth secondary screening using in vitro RNAi, Drosophila mutants, and Wolbachia-detection by DNA qPCR. A diverse set of host gene networks was identified to regulate Wolbachia levels and unexpectedly revealed that perturbations of host translation components such as the ribosome and translation initiation factors results in increased Wolbachia levels both in vitro using RNAi and in vivo using mutants and a chemical-based translation inhibition assay. This work provides evidence for Wolbachia-host translation interaction and strengthens our general understanding of the Wolbachia-host intracellular relationship.
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Affiliation(s)
- Yolande Grobler
- Department of Cell Biology, Howard Hughes Medical Institute and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY, United States of America
| | - Chi Y. Yun
- High Throughput Biology Core, Skirball Institute at New York University Langone Medical Center, New York, NY, United States of America
| | - David J. Kahler
- High Throughput Biology Core, Skirball Institute at New York University Langone Medical Center, New York, NY, United States of America
| | - Casey M. Bergman
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Hangnoh Lee
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States of America
| | - Brian Oliver
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, United States of America
| | - Ruth Lehmann
- Department of Cell Biology, Howard Hughes Medical Institute and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY, United States of America
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Agapito-Tenfen SZ, Vilperte V, Traavik TI, Nodari RO. Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism. ENVIRONMENTAL SCIENCES EUROPE 2018; 30:37. [PMID: 30294516 PMCID: PMC6153861 DOI: 10.1186/s12302-018-0168-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND While some genetically modified organisms (GMOs) are created to produce new double-stranded RNA molecules (dsRNA), in others, such molecules may occur as an unintended effect of the genetic engineering process. Furthermore, GMOs might produce naturally occurring dsRNA molecules in higher or lower quantities than its non-transgenic counterpart. This study is the first to use high-throughput technology to characterize the miRNome of commercialized GM maize events and to investigate potential alterations in miRNA regulatory networks. RESULTS Thirteen different conserved miRNAs were found to be dys-regulated in GM samples. The insecticide Bt GM variety had the most distinct miRNome. These miRNAs target a range of endogenous transcripts, such as transcription factors and nucleic acid binding domains, which play key molecular functions in basic genetic regulation. In addition, we have identified 20 potential novel miRNAs with target transcripts involved in lipid metabolism in maize. isomiRs were also found in 96 conserved miRNAs sequences, as well as potential transgenic miRNA sequences, which both can be a source of potential off-target effects in the plant genome. We have also provided information on technical limitations and when to carry on additional in vivo experimental testing. CONCLUSIONS These findings do not reveal hazards per se but show that robust and reproducible miRNA profiling technique can strengthen the assessment of risk by detecting any new intended and unintended dsRNA molecules, regardless of the outcome, at any stage of GMO development.
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Affiliation(s)
| | - Vinicius Vilperte
- Departamento de Fitotecnia, Universidade Federal de Santa Catarina, Florianópolis, 88034000 Brazil
- Present Address: Institute for Plant Genetics, Faculty of Natural Sciences, Leibniz University of Hannover, 30419 Hannover, Germany
| | - Terje Ingemar Traavik
- GenØk–Centre for Biosafety, Forskningsparken i Breivika, Sykehusveien 23, 9294 Tromsø, Norway
| | - Rubens Onofre Nodari
- Departamento de Fitotecnia, Universidade Federal de Santa Catarina, Florianópolis, 88034000 Brazil
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Hou Y, Liang W, Zhang J, Li Q, Ou H, Wang Z, Li S, Huang X, Zhao C. Schizophrenia-associated rs4702 G allele-specific downregulation of FURIN expression by miR-338-3p reduces BDNF production. Schizophr Res 2018; 199:176-180. [PMID: 29499969 DOI: 10.1016/j.schres.2018.02.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 02/21/2018] [Accepted: 02/21/2018] [Indexed: 12/13/2022]
Abstract
Genome-wide association studies (GWAS) reveal numerous schizophrenia (SCZ)-associated single-nucleotide polymorphisms (SNPs); however, functional characterizations of the risk variants remain to be established. Using data from 108 SCZ GWAS loci, we performed systematic miRNA binding site screening of 128 SCZ-associated SNPs and found that 2 out of 3 SNPs located in the 3'UTR were predicted to alter 3 miRNAs' binding sites in 2 target genes. Of the identified SNPs, the most genome-wide significant SNP rs4702 (A/G) in the FURIN 3'UTR, previously identified as an SCZ-associated cis-expression quantitative trait loci (downregulated by the risk G allele), is located in the binding site of miR-338-3p in the presence of the risk G allele. Allele-specific downregulation of FURIN by miR-338-3p was validated with a luciferase reporter assay. Furthermore, we demonstrated that miR-338-3p-mediated FURIN inhibition reduced brain-derived neurotrophic factor (BDNF) maturation and secretion in human embryonic kidney 293T cells. Our data reveal that schizophrenia-associated rs4702 G allele-specific downregulation of FURIN by miR-338-3p reduces mature BDNF production. These data help elucidate the mechanism of genetic predisposition toward schizophrenia or other neurodevelopmental diseases.
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Affiliation(s)
- Yu Hou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Department of Pediatric Neurology, Affiliated BaYi Children's Hospital, PLA Army General Hospital, Beijing, China
| | - Wenquan Liang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Psychiatric Disorders, Guangzhou, Guangdong, China
| | - Jian Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China
| | - Qiyang Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China
| | - Haiyan Ou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China
| | - Zhongju Wang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China
| | - Shufen Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Psychiatric Disorders, Guangzhou, Guangdong, China
| | - Xingbing Huang
- Department of Psychiatry, The Affiliated Brain Hospital of Guangzhou Medical University (Guangzhou Huiai Hospital), Guangzhou, Guangdong, China
| | - Cunyou Zhao
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Guangdong Province Key Laboratory of Psychiatric Disorders, Guangzhou, Guangdong, China.
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Mukherjee D, Saha D, Acharya D, Mukherjee A, Chakraborty S, Ghosh TC. The role of introns in the conservation of the metabolic genes of Arabidopsis thaliana. Genomics 2018; 110:310-317. [DOI: 10.1016/j.ygeno.2017.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/06/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
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Pei L, Tian X, Long Y, Nan W, Jia M, Qiao R, Zhang J. Establishment of a Han Chinese-specific pharmacogenetic-guided warfarin dosing algorithm. Medicine (Baltimore) 2018; 97:e12178. [PMID: 30200121 PMCID: PMC6133597 DOI: 10.1097/md.0000000000012178] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Warfarin is the most common oral anticoagulant. Because of a narrow therapeutic range, interindividual differences in drug responses, and the risk of bleeding, there are many challenges in using warfarin. We need to predict the warfarin maintenance dose. However, ethnic-specific algorithms may be required, and some Chinese algorithms do not perform adequately. Therefore, we aimed to establish a Han Chinese appropriate algorithm.We recruited a study group consisting of 361 Han Chinese patients receiving warfarin treatment who had heart valve replacements. Genotyping of 38 single nucleotide polymorphisms (SNPs) in 13 candidate genes was carried out using the MassARRAY. In the derivation cohort, a multiple linear regression model was constructed to predict the warfarin dosage. We evaluated the accuracy of our algorithm in the validation cohort and compared it with the other 5 algorithms based on Han Chinese and other races.We established a Han Chinese-specific pharmacogenetic-guided warfarin dosing algorithm. Warfarin maintenance dosage (mg/day) = 1.787 - 0.023 × (Age) + 1.151 × (BSA [m]) + 0.917 × (VKORC1 AG) + 4.619 × (VKORC1 GG) + 0.595 × (CYP4F2 TT) + 0.707 × (CYP2C19 CC). It explained 58.3% of the variance in warfarin doses in Han Chinese patients and was superior to the other 5 algorithms. The ability of the 6 algorithms which estimate the required dose correctly was tested. Our model had a mean absolute error of 0.74 mg/day, the other 5 models have mean absolute error of 0.81 mg/day,1.05 mg/day, 1.24 mg/day, 1.18 mg/day, and 0.85 mg/day, respectively. Our model had a mean percentage error of 26.9%, the other 5 models have the mean percentage error of 27.7%, 27.2%, 52.3%, 45.7%, and 29.3%, respectively.Physicians can not adopt algorithm from other race directly to predict warfarin dose in patients with heart valve replacements, they should establish a new algorithm or adjust another algorithm to fit their patients. The algorithm established in this study has the potential to assist physicians in determining warfarin doses that are close to the appropriate doses.
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Affiliation(s)
- Lin Pei
- The Department of Laboratory Medicine, Peking University Third Hospital
| | - Xiaoyi Tian
- The Department of Clinical Laboratory Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health
| | - Yan Long
- The Department of Laboratory Medicine, Peking University People's Hospital, Beijing, PR China
| | - Wenhui Nan
- The Department of Laboratory Medicine, Peking University People's Hospital, Beijing, PR China
| | - Mei Jia
- The Department of Laboratory Medicine, Peking University People's Hospital, Beijing, PR China
| | - Rui Qiao
- The Department of Laboratory Medicine, Peking University Third Hospital
| | - Jie Zhang
- The Department of Laboratory Medicine, Peking University Third Hospital
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Duffy EE, Canzio D, Maniatis T, Simon MD. Solid phase chemistry to covalently and reversibly capture thiolated RNA. Nucleic Acids Res 2018; 46:6996-7005. [PMID: 29986098 PMCID: PMC6101502 DOI: 10.1093/nar/gky556] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/04/2018] [Accepted: 06/14/2018] [Indexed: 12/26/2022] Open
Abstract
Here, we describe an approach to enrich newly transcribed RNAs from primary mouse neurons using 4-thiouridine (s4U) metabolic labeling and solid phase chemistry. This one-step enrichment procedure captures s4U-RNA by using highly efficient methane thiosulfonate (MTS) chemistry in an immobilized format. Like solution-based methods, this solid-phase enrichment can distinguish mature RNAs (mRNA) with differential stability, and can be used to reveal transient RNAs such as enhancer RNAs (eRNAs) and primary microRNAs (pri-miRNAs) from short metabolic labeling. Most importantly, the efficiency of this solid-phase chemistry made possible the first large scale measurements of RNA polymerase II (RNAPII) elongation rates in mouse cortical neurons. Thus, our approach provides the means to study regulation of RNA metabolism in specific tissue contexts as a means to better understand gene expression in vivo.
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Affiliation(s)
- Erin E Duffy
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Daniele Canzio
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Matthew D Simon
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
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Nevalainen H, Kaur J, Han Z, Kautto L, Ramsperger M, Meyer W, Chen SCA. Biological, biochemical and molecular aspects of Scedosporium aurantiacum, a primary and opportunistic fungal pathogen. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2018.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Segev E, Pasternak Z, Ben Sasson T, Jurkevitch E, Gonen M. Automatic identification of optimal marker genes for phenotypic and taxonomic groups of microorganisms. PLoS One 2018; 13:e0195537. [PMID: 29718935 PMCID: PMC5931505 DOI: 10.1371/journal.pone.0195537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/23/2018] [Indexed: 11/18/2022] Open
Abstract
Finding optimal markers for microorganisms important in the medical, agricultural, environmental or ecological fields is of great importance. Thousands of complete microbial genomes now available allow us, for the first time, to exhaustively identify marker proteins for groups of microbial organisms. In this work, we model the biological task as the well-known mathematical “hitting set” problem, solving it based on both greedy and randomized approximation algorithms. We identify unique markers for 17 phenotypic and taxonomic microbial groups, including proteins related to the nitrite reductase enzyme as markers for the non-anammox nitrifying bacteria group, and two transcription regulation proteins, nusG and yhiF, as markers for the Archaea and Escherichia/Shigella taxonomic groups, respectively. Additionally, we identify marker proteins for three subtypes of pathogenic E. coli, which previously had no known optimal markers. Practically, depending on the completeness of the database this algorithm can be used for identification of marker genes for any microbial group, these marker genes may be prime candidates for the understanding of the genetic basis of the group's phenotype or to help discover novel functions which are uniquely shared among a group of microbes. We show that our method is both theoretically and practically efficient, while establishing an upper bound on its time complexity and approximation ratio; thus, it promises to remain efficient and permit the identification of marker proteins that are specific to phenotypic or taxonomic groups, even as more and more bacterial genomes are being sequenced.
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Affiliation(s)
- Elad Segev
- Department of Mathematics, Holon Institute of Technology, Holon, Israel
- * E-mail:
| | - Zohar Pasternak
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tom Ben Sasson
- Department of Mathematics and Computer Science, The Open University of Israel, Raanana, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Mira Gonen
- Department of Computer Science, Ariel University, Ariel, Israel
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Petryszak R, Fonseca NA, Füllgrabe A, Huerta L, Keays M, Tang YA, Brazma A. The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data. Bioinformatics 2018; 33:2218-2220. [PMID: 28369191 PMCID: PMC5870697 DOI: 10.1093/bioinformatics/btx143] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 03/20/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation The exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those based in institutions with limited computational resources. EMBL-EBI is in an ideal position to address these challenges and to allow the scientific community easy access to not just raw, but also processed RNA-Seq data. We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer. Results The RNASeq-er API (Application Programming Interface) enables ontology-powered search for and retrieval of CRAM, bigwig and bedGraph files, gene and exon expression quantification matrices (Fragments Per Kilobase Of Exon Per Million Fragments Mapped, Transcripts Per Million, raw counts) as well as sample attributes annotated with ontology terms. To date over 270 00 RNA-Seq runs in nearly 10 000 studies (1PB of raw FASTQ data) in 264 species in ENA have been processed and made available via the API. Availability and Implementation The RNASeq-er API can be accessed at http://www.ebi.ac.uk/fg/rnaseq/api . The commands used to analyse the data are available in supplementary materials and at https://github.com/nunofonseca/irap/wiki/iRAP-single-library . Contact rnaseq@ebi.ac.uk ; rpetry@ebi.ac.uk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Robert Petryszak
- Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Nuno A Fonseca
- Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Anja Füllgrabe
- Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Laura Huerta
- Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Maria Keays
- Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Y Amy Tang
- Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Alvis Brazma
- Functional Genomics Group, European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
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Zhang H, Vieira Resende e Silva B, Cui J. miRDis: a Web tool for endogenous and exogenous microRNA discovery based on deep-sequencing data analysis. Brief Bioinform 2018; 19:415-424. [PMID: 28073746 PMCID: PMC5952930 DOI: 10.1093/bib/bbw140] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 12/07/2016] [Indexed: 01/09/2023] Open
Abstract
Small RNA sequencing is the most widely used tool for microRNA (miRNA) discovery, and shows great potential for the efficient study of miRNA cross-species transport, i.e., by detecting the presence of exogenous miRNA sequences in the host species. Because of the increased appreciation of dietary miRNAs and their far-reaching implication in human health, research interests are currently growing with regard to exogenous miRNAs bioavailability, mechanisms of cross-species transport and miRNA function in cellular biological processes. In this article, we present microRNA Discovery (miRDis), a new small RNA sequencing data analysis pipeline for both endogenous and exogenous miRNA detection. Specifically, we developed and deployed a Web service that supports the annotation and expression profiling data of known host miRNAs and the detection of novel miRNAs, other noncoding RNAs, and the exogenous miRNAs from dietary species. As a proof-of-concept, we analyzed a set of human plasma sequencing data from a milk-feeding study where 225 human miRNAs were detected in the plasma samples and 44 show elevated expression after milk intake. By examining the bovine-specific sequences, data indicate that three bovine miRNAs (bta-miR-378, -181* and -150) are present in human plasma possibly because of the dietary uptake. Further evaluation based on different sets of public data demonstrates that miRDis outperforms other state-of-the-art tools in both detection and quantification of miRNA from either animal or plant sources. The miRDis Web server is available at: http://sbbi.unl.edu/miRDis/index.php.
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Affiliation(s)
- Hanyuan Zhang
- Systems Biology and Biomedical Informatics (SBBI) Laboratory, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Bruno Vieira Resende e Silva
- Systems Biology and Biomedical Informatics (SBBI) Laboratory, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Juan Cui
- Systems Biology and Biomedical Informatics (SBBI) Laboratory, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
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Abstract
The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute's Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.
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Chen F, Dong W, Zhang J, Guo X, Chen J, Wang Z, Lin Z, Tang H, Zhang L. The Sequenced Angiosperm Genomes and Genome Databases. FRONTIERS IN PLANT SCIENCE 2018; 9:418. [PMID: 29706973 PMCID: PMC5909171 DOI: 10.3389/fpls.2018.00418] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/15/2018] [Indexed: 05/18/2023]
Abstract
Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.
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Affiliation(s)
- Fei Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Dong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiawei Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinyue Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junhao Chen
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Zhengjia Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Haibao Tang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liangsheng Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Liangsheng Zhang
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Scott Chialvo CH, Chialvo P, Holland JD, Anderson TJ, Breinholt JW, Kawahara AY, Zhou X, Liu S, Zaspel JM. A phylogenomic analysis of lichen-feeding tiger moths uncovers evolutionary origins of host chemical sequestration. Mol Phylogenet Evol 2017; 121:23-34. [PMID: 29274497 DOI: 10.1016/j.ympev.2017.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 11/29/2022]
Abstract
Host species utilize a variety of defenses to deter feeding, including secondary chemicals. Some phytophagous insects have evolved tolerance to these chemical defenses, and can sequester secondary defense compounds for use against their own predators and parasitoids. While numerous studies have examined plant-insect interactions, little is known about lichen-insect interactions. Our study focused on reconstructing the evolution of lichen phenolic sequestration in the tiger moth tribe Lithosiini (Lepidoptera: Erebidae: Arctiinae), the most diverse lineage of lichen-feeding moths, with 3000 described species. We built an RNA-Seq dataset and examined the adult metabolome for the presence of lichen-derived phenolics. Using the transcriptomic dataset, we recover a well-resolved phylogeny of the Lithosiini, and determine that the metabolomes within species are more similar than those among species. Results from an initial ancestral state reconstruction suggest that the ability to sequester phenolics produced by a single chemical pathway preceded generalist sequestration of phenolics produced by multiple chemical pathways. We conclude that phenolics are consistently and selectively sequestered within Lithosiini. Furthermore, sequestration of compounds from a single chemical pathway may represent a synapomorphy of the tribe, and the ability to sequester phenolics produced by multiple pathways arose later. These findings expand on our understanding of the interactions between Lepidoptera and their lichen hosts.
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Affiliation(s)
- Clare H Scott Chialvo
- Department of Biological Sciences, PO Box 870344, University of Alabama, Tuscaloosa, AL 35487, USA.
| | - Pablo Chialvo
- Department of Biology, 320 Stanley Avenue, Lander University, Greenwood, SC 29649, USA
| | - Jeffrey D Holland
- Department of Entomology, 901 West State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Timothy J Anderson
- Department of Entomology, 901 West State Street, Purdue University, West Lafayette, IN 47907, USA
| | - Jesse W Breinholt
- Florida Museum of Natural History, 3215 Hull Road, University of Florida, Gainesville, FL 32611, USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, 3215 Hull Road, University of Florida, Gainesville, FL 32611, USA
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100193, People's Republic of China; Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Shanlin Liu
- China National GeneBank, 8/F, Beishan Industrial Zone, Yantian District, BGI-Shenzhen, People's Republic of China; BGI-Shenzhen, Beishan Industrial Zone, Yantian District, People's Republic of China
| | - Jennifer M Zaspel
- Department of Entomology, 901 West State Street, Purdue University, West Lafayette, IN 47907, USA; Milwaukee Public Museum, 800 W Wells St, Milwaukee, WI 53233, USA
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Zhang M, Yang L, Su Z, Zhu M, Li W, Wu K, Deng X. Genome-wide scan and analysis of positive selective signatures in Dwarf Brown-egg Layers and Silky Fowl chickens. Poult Sci 2017; 96:4158-4171. [DOI: 10.3382/ps/pex239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/11/2017] [Indexed: 12/18/2022] Open
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An overview of posttraumatic stress disorder genetic studies by analyzing and integrating genetic data into genetic database PTSDgene. Neurosci Biobehav Rev 2017; 83:647-656. [DOI: 10.1016/j.neubiorev.2017.08.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 07/08/2017] [Accepted: 08/30/2017] [Indexed: 01/08/2023]
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Mattila TM, Tyrmi J, Pyhäjärvi T, Savolainen O. Genome-Wide Analysis of Colonization History and Concomitant Selection in Arabidopsis lyrata. Mol Biol Evol 2017; 34:2665-2677. [PMID: 28957505 DOI: 10.1093/molbev/msx193] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The high climatic variability in the past hundred thousand years has affected the demographic and adaptive processes in many species, especially in boreal and temperate regions undergoing glacial cycles. This has also influenced the patterns of genome-wide nucleotide variation, but the details of these effects are largely unknown. Here we study the patterns of genome-wide variation to infer colonization history and patterns of selection of the perennial herb species Arabidopsis lyrata, in locally adapted populations from different parts of its distribution range (Germany, UK, Norway, Sweden, and USA) representing different environmental conditions. Using site frequency spectra based demographic modeling, we found strong reduction in the effective population size of the species in general within the past 100,000 years, with more pronounced effects in the colonizing populations. We further found that the northwestern European A. lyrata populations (UK and Scandinavian) are more closely related to each other than with the Central European populations, and coalescent based population split modeling suggests that western European and Scandinavian populations became isolated relatively recently after the glacial retreat. We also highlighted loci showing evidence for local selection associated with the Scandinavian colonization. The results presented here give new insights into postglacial Scandinavian colonization history and its genome-wide effects.
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Affiliation(s)
- Tiina M Mattila
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Jaakko Tyrmi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Tanja Pyhäjärvi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
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Hindt MN, Akmakjian GZ, Pivarski KL, Punshon T, Baxter I, Salt DE, Guerinot ML. BRUTUS and its paralogs, BTS LIKE1 and BTS LIKE2, encode important negative regulators of the iron deficiency response in Arabidopsis thaliana. Metallomics 2017; 9:876-890. [PMID: 28620661 PMCID: PMC5558852 DOI: 10.1039/c7mt00152e] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Iron (Fe) is required for plant health, but it can also be toxic when present in excess. Therefore, Fe levels must be tightly controlled. The Arabidopsis thaliana E3 ligase BRUTUS (BTS) is involved in the negative regulation of the Fe deficiency response and we show here that the two A. thaliana BTS paralogs, BTS LIKE1 (BTSL1) and BTS LIKE2 (BTSL2) encode proteins that act redundantly as negative regulators of the Fe deficiency response. Loss of both of these E3 ligases enhances tolerance to Fe deficiency. We further generated a triple mutant with loss of both BTS paralogs and a partial loss of BTS expression that exhibits even greater tolerance to Fe-deficient conditions and increased Fe accumulation without any resulting Fe toxicity effects. Finally, we identified a mutant carrying a novel missense mutation of BTS that exhibits an Fe deficiency response in the root when grown under both Fe-deficient and Fe-sufficient conditions, leading to Fe toxicity when plants are grown under Fe-sufficient conditions.
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Affiliation(s)
- Maria N Hindt
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
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46
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Chen D, Zuo Y, Zhang X, Ye Y, Bao X, Huang H, Tepakhan W, Wang L, Ju J, Chen G, Zheng M, Liu D, Huang S, Zong L, Li C, Chen Y, Zheng C, Shi L, Zhao Q, Wu Q, Fucharoen S, Zhao C, Xu X. A Genetic Variant Ameliorates β-Thalassemia Severity by Epigenetic-Mediated Elevation of Human Fetal Hemoglobin Expression. Am J Hum Genet 2017; 101:130-138. [PMID: 28669403 DOI: 10.1016/j.ajhg.2017.05.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 05/18/2017] [Indexed: 12/15/2022] Open
Abstract
A delayed fetal-to-adult hemoglobin (Hb) switch ameliorates the severity of β-thalassemia and sickle cell disease. The molecular mechanism underlying the epigenetic dysregulation of the switch is unclear. To explore the potential cis-variants responsible for the Hb switching, we systematically analyzed an 80-kb region spanning the β-globin cluster using capture-based next-generation sequencing of 1142 Chinese β-thalassemia persons and identified 31 fetal hemoglobin (HbF)-associated haplotypes of the selected 28 tag regulatory single-nucleotide polymorphisms (rSNPs) in seven linkage disequilibrium (LD) blocks. A Ly1 antibody reactive (LYAR)-binding motif disruptive rSNP rs368698783 (G/A) from LD block 5 in the proximal promoter of hemoglobin subunit gamma 1 (HBG1) was found to be a significant predictor for β-thalassemia clinical severity by epigenetic-mediated variant-dependent HbF elevation. We found this rSNP accounted for 41.6% of β-hemoglobinopathy individuals as an ameliorating factor in a total of 2,738 individuals from southern China and Thailand. We uncovered that the minor allele of the rSNP triggers the attenuation of LYAR and two repressive epigenetic regulators DNA methyltransferase 3 alpha (DNMT3A) and protein arginine methyltransferase 5 (PRMT5) from the HBG promoters, mediating allele-biased γ-globin elevation by facilitating demethylation of HBG core promoter CpG sites in erythroid progenitor cells from β-thalassemia persons. The present study demonstrates that this common rSNP in the proximal Aγ-promoter is a major genetic modifier capable of ameliorating the severity of thalassemia major through the epigenetic-mediated regulation of the delayed fetal-to-adult Hb switch and provides potential targets for the treatment of β-hemoglobinopathy.
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Abstract
We report data associated with the identification of 242 disease resistance genes (R-genes) in the genome of Setaria italica as presented in “Genetic diversity of disease resistance genes in foxtail millet (Setaria italica L.)” (Andersen and Nepal, 2017) [1]. Our data describe the structure and evolution of the Coiled-coil, Nucleotide-binding site, Leucine-rich repeat (CNL) R-genes in foxtail millet. The CNL genes were identified through rigorous extraction and analysis of recently available plant genome sequences using cutting-edge analytical software. Data visualization includes gene structure diagrams, chromosomal syntenic maps, a chromosomal density plot, and a maximum-likelihood phylogenetic tree comparing Sorghum bicolor, Panicum virgatum, Setaria italica, and Arabidopsis thaliana. Compilation of InterProScan annotations, Gene Ontology (GO) annotations, and Basic Local Alignment Search Tool (BLAST) results for the 242 R-genes identified in the foxtail millet genome are also included in tabular format.
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Affiliation(s)
- Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
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Chorev M, Joseph Bekker A, Goldberger J, Carmel L. Identification of introns harboring functional sequence elements through positional conservation. Sci Rep 2017. [PMID: 28646210 PMCID: PMC5482813 DOI: 10.1038/s41598-017-04476-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Many human introns carry out a function, in the sense that they are critical to maintain normal cellular activity. Their identification is fundamental to understanding cellular processes and disease. However, being noncoding elements, such functional introns are poorly predicted based on traditional approaches of sequence and structure conservation. Here, we generated a dataset of human functional introns that carry out different types of functions. We showed that functional introns share common characteristics, such as higher positional conservation along the coding sequence and reduced loss rates, regardless of their specific function. A unique property of the data is that if an intron is unknown to be functional, it still does not mean that it is indeed non-functional. We developed a probabilistic framework that explicitly accounts for this unique property, and predicts which specific human introns are functional. We show that we successfully predict function even when the algorithm is trained on introns with a different type of function. This ability has many implications in studying regulatory networks, gene regulation, the effect of mutations outside exons on human disease, and on our general understanding of intron evolution and their functional exaptation in mammals.
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Affiliation(s)
- Michal Chorev
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel.,The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 91904, Israel
| | | | - Jacob Goldberger
- Faculty of Engineering, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel.
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Vahdati Nia B, Kang C, Tran MG, Lee D, Murakami S. Meta Analysis of Human AlzGene Database: Benefits and Limitations of Using C. elegans for the Study of Alzheimer's Disease and Co-morbid Conditions. Front Genet 2017; 8:55. [PMID: 28553317 PMCID: PMC5427079 DOI: 10.3389/fgene.2017.00055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/19/2017] [Indexed: 11/21/2022] Open
Abstract
Human genome-wide association studies (GWAS) and linkage studies have identified 695 genes associated with Alzheimer's disease (AD), the vast majority of which are associated with late-onset AD. Although orthologs of these AD genes have been studied in several model species, orthologs in the nematode, Caenorhabditis elegans, remain incompletely identified, with orthologs to only 17 AD-related genes identified in the C. elegans database, WormBase. Therefore, we performed a comprehensive search for additional C. elegans orthologs of AD genes using well-established programs, including OrthoList, which utilizes four ontology prediction programs. We also validated 680 of the AD genes as a unique gene from the AlzGene database, including 431 genes (63%) that are predicted to have orthologs in C. elegans. Another 178 human AD genes (26%) were associated with one or more other neurological diseases, including amyotrophic lateral sclerosis, multiple sclerosis, Parkinson's disease, and schizophrenia. Of these, there were 105 genes (59%) with orthologs in C. elegans. Interestingly, three AD genes (ACE, TNF, and MTHFR) were associated with all four of the other neurological diseases. The human AD genes were enriched in three major ontology pathway groups, including lipoprotein metabolism, hemostasis, and extracellular matrix organizations, as well as in pathways that are amyloid related (NOTCH signaling) and associated with neural (neurotransmitter clearance) and immune (advanced glycation end-product receptor signaling and TRAF6-NF-kappaB) systems. Thus, the results from this study provide a potentially useful system for assessing comorbidities that may be associated with late-onset AD and other neurological conditions. The technical advantages and limitations of the ortholog searches are further discussed.
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Affiliation(s)
- Behrad Vahdati Nia
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University CaliforniaVallejo, CA, USA
| | - Christine Kang
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University CaliforniaVallejo, CA, USA
| | - Michelle G Tran
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University CaliforniaVallejo, CA, USA
| | - Deborah Lee
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University CaliforniaVallejo, CA, USA
| | - Shin Murakami
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University CaliforniaVallejo, CA, USA
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