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Suzuki T. Overview of single-cell RNA sequencing analysis and its application to spermatogenesis research. Reprod Med Biol 2023; 22:e12502. [PMID: 36726594 PMCID: PMC9884325 DOI: 10.1002/rmb2.12502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 12/18/2022] [Accepted: 01/10/2023] [Indexed: 01/30/2023] Open
Abstract
Background Single-cell transcriptomics allows parallel analysis of multiple cell types in tissues. Because testes comprise somatic cells and germ cells at various stages of spermatogenesis, single-cell RNA sequencing is a powerful tool for investigating the complex process of spermatogenesis. However, single-cell RNA sequencing analysis needs extensive knowledge of experimental technologies and bioinformatics, making it difficult for many, particularly experimental biologists and clinicians, to use it. Methods Aiming to make single-cell RNA sequencing analysis familiar, this review article presents an overview of experimental and computational methods for single-cell RNA sequencing analysis with a history of transcriptomics. In addition, combining the PubMed search and manual curation, this review also provides a summary of recent novel insights into human and mouse spermatogenesis obtained using single-cell RNA sequencing analyses. Main Findings Single-cell RNA sequencing identified mesenchymal cells and type II innate lymphoid cells as novel testicular cell types in the adult mouse testes, as well as detailed subtypes of germ cells. This review outlines recent discoveries into germ cell development and subtypes, somatic cell development, and cell-cell interactions. Conclusion The findings on spermatogenesis obtained using single-cell RNA sequencing may contribute to a deeper understanding of spermatogenesis and provide new directions for male fertility therapy.
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Affiliation(s)
- Takahiro Suzuki
- RIKEN Center for Integrated Medical Science (IMS)Yokohama CityKanagawaJapan
- Graduate School of Medical Life ScienceYokohama City UniversityYokohama CityKanagawaJapan
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2
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Miętkiewska K, Kordowitzki P, Pareek CS. Effects of Heat Stress on Bovine Oocytes and Early Embryonic Development-An Update. Cells 2022; 11:cells11244073. [PMID: 36552837 PMCID: PMC9776454 DOI: 10.3390/cells11244073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Heat stress is a major threat to cattle reproduction today. It has been shown that the effect of high temperature not only has a negative effect on the hormonal balance, but also directly affects the quality of oocytes, disrupting the function of mitochondria, fragmenting their DNA and changing their maternal transcription. Studies suggest that the induction of HSP70 may reduce the apoptosis of granular layer cells caused by heat stress. It has been shown that the changes at the transcriptome level caused by heat stress are consistent with 46.4% of blastocyst development disorders. Cows from calves exposed to thermal stress in utero have a lower milk yield in their lifetime, exhibit immunological disorders, have a lower birth weight and display a shorter lifespan related to the expedited aging. In order to protect cow reproduction, the effects of heat stress at the intracellular and molecular levels should be tracked step by step, and the impacts of the dysregulation of thermal homeostasis (i.e., hyperthermy) should be taken into account.
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Affiliation(s)
- Klaudia Miętkiewska
- Department of Preclinical and Basic Sciences, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Pawel Kordowitzki
- Department of Preclinical and Basic Sciences, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland
| | - Chandra S. Pareek
- Department of Preclinical and Basic Sciences, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland
- Division of Functional Genomics in Biological and Biomedical Research, Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland
- Correspondence:
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3
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T908 Polymeric Micelles Improved the Uptake of Sgc8-c Aptamer Probe in Tumor-Bearing Mice: A Co-Association Study between the Probe and Preformed Nanostructures. Pharmaceuticals (Basel) 2021; 15:ph15010015. [PMID: 35056072 PMCID: PMC8780797 DOI: 10.3390/ph15010015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022] Open
Abstract
Aptamers are oligonucleotides that have the characteristic of recognizing a target with high affinity and specificity. Based on our previous studies, the aptamer probe Sgc8-c-Alexa647 is a promising tool for molecular imaging of PTK7, which is an interesting biomarker in cancer. In order to improve the delivery of this probe as well as create a novel drug delivery nanosystem targeted to the PTK7 receptor, we evaluate the co-association between the probe and preformed nanostructures. In this work, preformed pegylated liposomes (PPL) and linear and branched pristine polymeric micelles (PMs), based on PEO–PPO–PEO triblock copolymers were used: poloxamer F127® and poloxamines T1307® and T908®. For it, Sgc8-c-Alexa647 and its co-association with the different nanostructures was exhaustively analyzed. DLS analysis showed nanometric sizes, and TEM and AFM showed notable differences between free- and co-associated probe. Likewise, all nanosystems were evaluated on A20 lymphoma cell line overexpressing PTK7, and the confocal microscopy images showed distinctness in cellular uptake. Finally, the biodistribution in BALB/c mice bearing lymphoma-tumor and pharmacokinetic study revealed an encouraging profile for T908-probe. All data obtained from this work suggested that PMs and, more specifically T908 ones, are good candidates to improve the pharmacokinetics and the tumor uptake of aptamer-based probes.
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4
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Tanio A, Saito H, Amisaki M, Hara K, Sugezawa K, Uejima C, Tada Y, Kihara K, Yamamoto M, Nosaka K, Sasaki R, Osaki M, Okada F, Fujiwara Y. AMIGO2 as a novel indicator of liver metastasis in patients with colorectal cancer. Oncol Lett 2021; 21:278. [PMID: 33732354 PMCID: PMC7905583 DOI: 10.3892/ol.2021.12539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/10/2020] [Indexed: 12/19/2022] Open
Abstract
Our previous study showed that adhesion molecule with immunoglobulin like domain 2 (AMIGO2) is a pivotal driver gene of liver metastasis via regulating tumor cell adhesion to liver endothelial cells in mouse models. The aim of the present study was to clarify the role of AMIGO2 in liver metastasis in patients the colorectal cancer (CRC). Two human CRC cell lines, Caco-2 (AMIGO2-low) and HCT116 (AMIGO2-high), were used in this study. AMIGO2-overexpressing Caco-2 and AMIGO2-knockdown HCT116 cells were generated by transfection with an AMIGO2 expression vector or AMIGO2 small interfering RNA, respectively. Cell proliferation, invasion and adhesion to human liver endothelial cells were examined in in vitro studies. Immunohistochemical analysis was also performed to evaluate the association between AMIGO2 expression and liver metastasis in patients with CRC. In vitro studies revealed that cell proliferation, invasion and adhesion to liver endothelial cells were accelerated by upregulation of AMIGO2 expression, but suppressed by downregulation of AMIGO2 expression in human CRC cells. Immunohistochemical analysis using clinical CRC specimens revealed that AMIGO2 expression was associated with the frequency of liver metastasis (P<0.01), but not that of pulmonary metastasis (P=0.611) and peritoneal dissemination (P=0.909). In addition, AMIGO2 expression levels in tumor cells were significantly higher in liver metastatic foci than primary lesions (P=0.012). In conclusion, the present results indicated that AMIGO2 expression may contribute to the formation of liver metastasis in CRC.
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Affiliation(s)
- Akimitsu Tanio
- Division of Gastrointestinal and Pediatric Surgery, Department of Surgery, School of Medicine, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Hiroaki Saito
- Division of Gastrointestinal and Pediatric Surgery, Department of Surgery, School of Medicine, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan.,Department of Surgery, Japanese Red Cross Tottori Hospital, Yonago, Tottori 680-8517, Japan
| | - Masataka Amisaki
- Division of Gastrointestinal and Pediatric Surgery, Department of Surgery, School of Medicine, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Kazushi Hara
- Division of Gastrointestinal and Pediatric Surgery, Department of Surgery, School of Medicine, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Ken Sugezawa
- Division of Gastrointestinal and Pediatric Surgery, Department of Surgery, School of Medicine, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Chihiro Uejima
- Division of Gastrointestinal and Pediatric Surgery, Department of Surgery, School of Medicine, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Yoichiro Tada
- Division of Gastrointestinal and Pediatric Surgery, Department of Surgery, School of Medicine, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Kyoichi Kihara
- Division of Gastrointestinal and Pediatric Surgery, Department of Surgery, School of Medicine, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Manabu Yamamoto
- Division of Gastrointestinal and Pediatric Surgery, Department of Surgery, School of Medicine, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
| | - Kanae Nosaka
- Division of Organ Pathology, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8503, Japan
| | - Ryo Sasaki
- Division of Experimental Pathology, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8503, Japan
| | - Mitsuhiko Osaki
- Division of Experimental Pathology, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8503, Japan.,Chromosome Engineering Research Center, Tottori University, Yonago, Tottori 683-8503, Japan
| | - Futoshi Okada
- Division of Experimental Pathology, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8503, Japan.,Chromosome Engineering Research Center, Tottori University, Yonago, Tottori 683-8503, Japan
| | - Yoshiyuki Fujiwara
- Division of Gastrointestinal and Pediatric Surgery, Department of Surgery, School of Medicine, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8504, Japan
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5
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Mahesh HB, Shirke MD, Wang GL, Gowda M. In planta transcriptome analysis reveals tissue-specific expression of pathogenicity genes and microRNAs during rice-Magnaporthe interactions. Genomics 2020; 113:265-275. [PMID: 33326830 DOI: 10.1016/j.ygeno.2020.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/23/2020] [Accepted: 12/10/2020] [Indexed: 12/17/2022]
Abstract
Transcriptional re-programming in host and pathogen upon leaf and neck infection is an evolving area of research for the rice blast community. Analysis of in planta rice transcriptome in leaf and neck tissues revealed tissue-specific and infection-specific expression of rice and Magnaporthe oryzae genes in host and pathogen. The glycosyl hydrolase, isocitrate lyase, cupin domain containing protein, TF2, CMPG1, CHIT17 and OsCML14 genes were uniquely expressed in leaf infection. Genes like cytochrome P450, inhibitor I family protein, GSTU6, abscisic stress ripening, and cupin domain containing protein were up-regulated during neck infection. In our microRNA sequencing study, Osa-miR166n-3p was highly expressed in upon Magnaporthe leaf infection, whereas osa-miR1661-3p, osa-miR166n-3p and osa-miR159b were overexpressed in neck infection. Here we report several transcripts being targeted by up and down regulated microRNAs during infection. The putative genes expressed upon infection in leaf and neck could be used in understanding the dual-epidemics of blast disease.
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Affiliation(s)
- H B Mahesh
- Genomics Laboratory, Centre for Cellular and Molecular Platforms (C-CAMP), National Centre for Biological Sciences (NCBS), Bengaluru 560065, India; Department of Genetics and Plant Breeding, College of Agriculture, V. C. Farm, Mandya, University of Agricultural Sciences, Bengaluru 560065, India; Centre for Functional Genomics and Bioinformatics, The University of Trans-disciplinary Health Science and Technology, Bengaluru 560064, India.
| | - Meghana Deepak Shirke
- Centre for Functional Genomics and Bioinformatics, The University of Trans-disciplinary Health Science and Technology, Bengaluru 560064, India
| | - Guo-Liang Wang
- Department of Genetics and Plant Breeding, College of Agriculture, V. C. Farm, Mandya, University of Agricultural Sciences, Bengaluru 560065, India
| | - Malali Gowda
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Columbus 43210, USA; Centre for Functional Genomics and Bioinformatics, The University of Trans-disciplinary Health Science and Technology, Bengaluru 560064, India.
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6
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Exosomal Long Non-coding RNAs: Emerging Players in the Tumor Microenvironment. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 23:1371-1383. [PMID: 33738133 PMCID: PMC7940039 DOI: 10.1016/j.omtn.2020.09.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Recent advances in exosome biology have uncovered a significant role of exosomes in cancer and make them a determining factor in intercellular communication. Exosomes are types of extracellular vesicles that are involved in the communication between cells by exchanging various signaling molecules between the surrounding cells. Among various signaling molecules, long non-coding RNAs (lncRNAs), a type of non-coding RNA having a size of more than 200 nt in length and lacking protein-coding potential, have emerged as crucial regulators of intercellular communication. Tumor-derived exosomes containing various lncRNAs, known as exosomal lncRNAs, reprogram the microenvironment by regulating numerous cellular functions, including the regulation of gene transcription that favors cancer growth and progression, thus significantly determining the biological effects of exosomes. In addition, deregulated expression of lncRNAs is found in various human cancers and serves as a diagnostic biomarker to predict cancer type. The present review discusses the role of exosomal lncRNAs in the crosstalk between tumor cells and the surrounding cells of the microenvironment. Furthermore, we also discuss the involvement of exosomal lncRNAs within the tumor microenvironment in favoring tumor growth, metabolic reprogramming of tumor cells, and tumor-supportive autophagy. Therefore, lncRNAs can be used as a therapeutic target in the treatment of various human cancers.
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7
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Huang T, Yang M, Dong K, Xu M, Liu J, Chen Z, Zhu S, Chen W, Yin J, Jin K, Deng Y, Guan Z, Huang X, Yang J, Han R, Yao M. A transcriptional landscape of 28 porcine tissues obtained by super deepSAGE sequencing. BMC Genomics 2020; 21:229. [PMID: 32171242 PMCID: PMC7071599 DOI: 10.1186/s12864-020-6628-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 02/26/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Gene expression regulators identified in transcriptome profiling experiments may serve as ideal targets for genetic manipulations in farm animals. RESULTS In this study, we developed a gene expression profile of 76,000+ unique transcripts for 224 porcine samples from 28 tissues collected from 32 animals using Super deepSAGE technology. Excellent sequencing depth was achieved for each multiplexed library, and replicated samples from the same tissues clustered together, demonstrating the high quality of Super deepSAGE data. Comparison with previous research indicated that our results not only have good reproducibility but also have greatly extended the coverage of the sample types as well as the number of genes. Clustering analysis revealed ten groups of genes showing distinct expression patterns among these samples. Our analysis of over-represented binding motifs identified 41 regulators, and we demonstrated a potential application of this dataset in infectious diseases and immune biology research by identifying an LPS-dependent transcription factor, runt-related transcription factor 1 (RUNX1), in peripheral blood mononuclear cells (PBMCs). The selected genes are specifically responsible for the transcription of toll-like receptor 2 (TLR2), lymphocyte-specific protein tyrosine kinase (LCK), and vav1 oncogene (VAV1), which belong to the T and B cell signaling pathways. CONCLUSIONS The Super deepSAGE technology and tissue-differential expression profiles are valuable resources for investigating the porcine gene expression regulation. The identified RUNX1 target genes belong to the T and B cell signaling pathways, making them novel potential targets for the diagnosis and therapy of bacterial infections and other immune disorders.
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Affiliation(s)
- Tinghua Huang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Min Yang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Kaihui Dong
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Mingjiang Xu
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jinhui Liu
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Zhi Chen
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Shijia Zhu
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Wang Chen
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jun Yin
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Kai Jin
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Yu Deng
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Zhou Guan
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Xiali Huang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Jun Yang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Rongxun Han
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Min Yao
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China.
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8
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Dougherty SE, Maduka AO, Inada T, Silva GM. Expanding Role of Ubiquitin in Translational Control. Int J Mol Sci 2020; 21:E1151. [PMID: 32050486 PMCID: PMC7037965 DOI: 10.3390/ijms21031151] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic proteome has to be precisely regulated at multiple levels of gene expression, from transcription, translation, and degradation of RNA and protein to adjust to several cellular conditions. Particularly at the translational level, regulation is controlled by a variety of RNA binding proteins, translation and associated factors, numerous enzymes, and by post-translational modifications (PTM). Ubiquitination, a prominent PTM discovered as the signal for protein degradation, has newly emerged as a modulator of protein synthesis by controlling several processes in translation. Advances in proteomics and cryo-electron microscopy have identified ubiquitin modifications of several ribosomal proteins and provided numerous insights on how this modification affects ribosome structure and function. The variety of pathways and functions of translation controlled by ubiquitin are determined by the various enzymes involved in ubiquitin conjugation and removal, by the ubiquitin chain type used, by the target sites of ubiquitination, and by the physiologic signals triggering its accumulation. Current research is now elucidating multiple ubiquitin-mediated mechanisms of translational control, including ribosome biogenesis, ribosome degradation, ribosome-associated protein quality control (RQC), and redox control of translation by ubiquitin (RTU). This review discusses the central role of ubiquitin in modulating the dynamism of the cellular proteome and explores the molecular aspects responsible for the expanding puzzle of ubiquitin signals and functions in translation.
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Affiliation(s)
- Shannon E. Dougherty
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Austin O. Maduka
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
| | - Toshifumi Inada
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan;
| | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, NC 27708-0338, USA; (S.E.D.); (A.O.M.)
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9
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Bie J, Liu K, Song G, Hu X, Xiong R, Zhang X, Shi X, Wang Z. ENST00000489707.5 Is a Preferred Alternative Splicing Variant of PTK7 in Adrenocortical Cancer and Shows Potential Prognostic Value. Med Sci Monit 2019; 25:8326-8334. [PMID: 31689287 PMCID: PMC6857428 DOI: 10.12659/msm.919818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background This study aimed to explore the transcript preference of PTK7 in adrenocortical cancer (ACC), the prognostic value, and the potential underlying genetic alterations. Material/Methods Data from the Cancer Genome Atlas-Adrenocortical Cancer (TCGA-ACC) and the Genotype-Tissue Expression (GTEx)-normal adrenal gland were used for analysis. Results A non-canonical alternative transcript, ENST00000489707.5, which only encodes an extracellular immunoglobulin (Ig)-like domain and an intracellular kinase domain, is the dominant isoform of PTK7 in both ACC and normal adrenal gland. Its expression percentage was significantly higher in ACC than in normal adrenal gland. ACC tissues showed preferred expression of this transcript compared with other cancers with known PTK7 expression. Prognostic analysis showed that ENST00000489707.5 had independent prognostic value in progression-free survival (PFS) (HR: 1.227, 95%CI: 1.077–1.398, p=0.002) and disease-specific survival (DSS) (HR: 1.419, 95%CI: 1.154–1.745, p=0.001) after adjustment of other risk factors. cg20819617 methylation was negatively correlated with both PTK7 and ENST00000489707.5 expression. Conclusions ENST00000489707.5 is a preferred alternative splicing product of PTK7, with a significantly increased proportion in ACC compared with other cancers. Its expression shows potential prognostic value in terms of PFS and DSS in ACC patients. The methylation status of cg20819617 might play a critical role in modulating PTK7 transcription and ENST00000489707.5 expression.
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Affiliation(s)
- Jun Bie
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China (mainland).,Cancer Center, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, Sichuan, China (mainland)
| | - Kang Liu
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, Sichuan, China (mainland)
| | - Guiqin Song
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, Sichuan, China (mainland).,Department of Biology, North Sichuan Medical College, Nanchong, Sichuan, China (mainland)
| | - Xin Hu
- Cancer Center, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, Sichuan, China (mainland)
| | - Rong Xiong
- Institute of Tissue Engineering and Stem Cells, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, Sichuan, China (mainland)
| | - Xinping Zhang
- Cancer Center, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, Sichuan, China (mainland)
| | - Xianwei Shi
- Cancer Center, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, Sichuan, China (mainland)
| | - Ziwei Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China (mainland)
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10
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García-Sánchez M, Jiménez-Pelayo L, Horcajo P, Regidor-Cerrillo J, Collantes-Fernández E, Ortega-Mora LM. Gene Expression Profiling of Neospora caninum in Bovine Macrophages Reveals Differences Between Isolates Associated With Key Parasite Functions. Front Cell Infect Microbiol 2019; 9:354. [PMID: 31681630 PMCID: PMC6803445 DOI: 10.3389/fcimb.2019.00354] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/01/2019] [Indexed: 12/19/2022] Open
Abstract
Intraspecific differences in biological traits between Neospora caninum isolates have been widely described and associated with variations in virulence. However, the molecular basis underlying these differences has been poorly studied. We demonstrated previously that Nc-Spain7 and Nc-Spain1H, high- and low-virulence isolates, respectively, show different invasion, proliferation and survival capabilities in bovine macrophages (boMØs), a key cell in the immune response against Neospora, and modulate the cell immune response in different ways. Here, we demonstrate that these differences are related to specific tachyzoite gene expression profiles. Specifically, the low-virulence Nc-Spain1H isolate showed enhanced expression of genes encoding for surface antigens and genes related to the bradyzoite stage. Among the primary up-regulated genes in Nc-Spain7, genes involved in parasite growth and redox homeostasis are particularly noteworthy because of their correlation with the enhanced proliferation and survival rates of Nc-Spain7 in boMØs relative to Nc-Spain1H. Genes potentially implicated in induction of proinflammatory immune responses were found to be up-regulated in the low-virulence isolate, whereas the high-virulence isolate showed enhanced expression of genes that may be involved in immune evasion. These results represent a further step in understanding the parasite effector molecules that may be associated to virulence and thus to disease traits as abortion and transmission.
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Affiliation(s)
- Marta García-Sánchez
- Saluvet, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - Laura Jiménez-Pelayo
- Saluvet, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - Pilar Horcajo
- Saluvet, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - Javier Regidor-Cerrillo
- Saluvet, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain.,Saluvet-Innova, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - Esther Collantes-Fernández
- Saluvet, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
| | - Luis Miguel Ortega-Mora
- Saluvet, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Madrid, Spain
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11
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Girma G, Natsume S, Carluccio AV, Takagi H, Matsumura H, Uemura A, Muranaka S, Takagi H, Stavolone L, Gedil M, Spillane C, Terauchi R, Tamiru M. Identification of candidate flowering and sex genes in white Guinea yam (D. rotundata Poir.) by SuperSAGE transcriptome profiling. PLoS One 2019; 14:e0216912. [PMID: 31545796 PMCID: PMC6756524 DOI: 10.1371/journal.pone.0216912] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/05/2019] [Indexed: 01/03/2023] Open
Abstract
Dioecy (distinct male and female individuals) and scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are largely unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowering and sex-related genes in white Guinea yam (D. rotundata), generating 20,236 unique tags. Of these, 13,901 were represented by a minimum of 10 tags. A total 88 tags were significantly differentially expressed in male, female and monoecious plants, of which 18 corresponded to genes previously implicated in flower development and sex determination in multiple plant species. We validated the SuperSAGE data with quantitative real-time PCR (qRT-PCR)-based analysis of the expression of three candidate genes. We further investigated the flowering patterns of 1938 D. rotundata accessions representing diverse geographical origins over two consecutive years. Over 85% of accessions were either male or non-flowering, less than 15% were female, while monoecious plants were rare. Intensity of flowering varied between male and female plants, with the former flowering more abundantly than the latter. Candidate genes identified in this study can be targeted for further validation and to induce regular flowering in poor to non-flowering cultivars. Findings of the study provide important inputs for further studies aiming to overcome the challenge of flowering in yams and to improve efficiency of yam breeding.
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Affiliation(s)
- Gezahegn Girma
- Bioscience center, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
- Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Satoshi Natsume
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Anna Vittoria Carluccio
- Bioscience center, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Hiroki Takagi
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Hideo Matsumura
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Aiko Uemura
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Satoru Muranaka
- Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Japan
- * E-mail:
| | - Hiroko Takagi
- Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Japan
| | - Livia Stavolone
- Bioscience center, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Melaku Gedil
- Bioscience center, International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, Nigeria
| | - Charles Spillane
- Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Ryohei Terauchi
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
| | - Muluneh Tamiru
- Department of Genomics and Breeding, Iwate Biotechnology Research Center (IBRC), Kitakami, Iwate, Japan
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12
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GRID-seq for comprehensive analysis of global RNA-chromatin interactions. Nat Protoc 2019; 14:2036-2068. [PMID: 31175345 DOI: 10.1038/s41596-019-0172-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 04/02/2019] [Indexed: 01/29/2023]
Abstract
Chromatin in higher eukaryotic nuclei is extensively bound by various RNA species. We recently developed a method for in situ capture of global RNA interactions with DNA by deep sequencing (GRID-seq) of fixed permeabilized nuclei that allows identification of the entire repertoire of chromatin-associated RNAs in an unbiased manner. The experimental design of GRID-seq is related to those of two recently published strategies (MARGI (mapping RNA-genome interactions) and ChAR-seq (chromatin-associated RNA sequencing)), which also use a bivalent linker to ligate RNA and DNA in proximity. Importantly, however, GRID-seq also implements a combined experimental and computational approach to control nonspecific RNA-DNA interactions that are likely to occur during library construction, which is critical for accurate interpretation of detected RNA-DNA interactions. GRID-seq typically finds both coding and non-coding RNAs (ncRNAs) that interact with tissue-specific promoters and enhancers, especially super-enhancers, from which a global promoter-enhancer connectivity map can be deduced. Here, we provide a detailed protocol for GRID-seq that includes nuclei preparation, chromatin fragmentation, RNA and DNA in situ ligation with a bivalent linker, PCR amplification and high-throughput sequencing. To further enhance the utility of GRID-seq, we include a pipeline for data analysis, called GridTools, into which key steps such as background correction and inference of genomic element proximity are integrated. For researchers experienced in molecular biology with minimal bioinformatics skills, the protocol typically takes 4-5 d from cell fixation to library construction and 2-3 d for data processing.
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Wang B, Kumar V, Olson A, Ware D. Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing. Front Genet 2019; 10:384. [PMID: 31105749 PMCID: PMC6498185 DOI: 10.3389/fgene.2019.00384] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/09/2019] [Indexed: 12/23/2022] Open
Abstract
Advances in transcriptomics have provided an exceptional opportunity to study functional implications of the genetic variability. Technologies such as RNA-Seq have emerged as state-of-the-art techniques for transcriptome analysis that take advantage of high-throughput next-generation sequencing. However, similar to their predecessors, these approaches continue to impose major challenges on full-length transcript structure identification, primarily due to inherent limitations of read length. With the development of single-molecule sequencing (SMS) from PacBio, a growing number of studies on the transcriptome of different organisms have been reported. SMS has emerged as advantageous for comprehensive genome annotation including identification of novel genes/isoforms, long non-coding RNAs and fusion transcripts. This approach can be used across a broad spectrum of species to better interpret the coding information of the genome, and facilitate the biological function study. We provide an overview of SMS platform and its diverse applications in various biological studies, and our perspective on the challenges associated with the transcriptome studies.
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Affiliation(s)
- Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Vivek Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States.,USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
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Wang Z, Luan S, Meng X, Cao B, Luo K, Kong J. Comparative transcriptomic characterization of the eyestalk in Pacific white shrimp (Litopenaeus vannamei) during ovarian maturation. Gen Comp Endocrinol 2019; 274:60-72. [PMID: 30611813 DOI: 10.1016/j.ygcen.2019.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 01/02/2019] [Accepted: 01/02/2019] [Indexed: 12/17/2022]
Abstract
In crustaceans, some of fundamental regulatory processes related to a range of physiological functions, including ovarian maturation, molting, glucose homeostasis, osmoregulation, etc., occur in the organs of the eyestalk. Additionally, reproduction is regulated by neuropeptide hormones and other proteins released from secretory sites (X-organ/sinus gland, XO/SG) within the eyestalk. As unilateral eyestalk ablation was the most common method used to artificially induce ovarian maturation for farmed Litopenaeus vannamei, to better understand the reproductive regulation mechanism in L. vannamei, we have investigated the transcriptomes of the eyestalk during five ovary developmental stages with or without eyestalk ablation by high-throughput Illumina sequencing technology. The raw reads were assembled and clustered into 127,031 unigenes. Meanwhile, the differentially expressed genes (DEGs) between ovarian development stages were identified. We examined, through DEG enrichment analysis, eyestalk gene expression patterns for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, comparing natural to artificially induced ovarian maturation. We also identified a variety of transcripts that appear to be differentially expressed throughout ovarian maturation. These include transcripts that encode G-protein coupled receptors (GPCRs) and neuropeptides, such as the crustacean hyperglycemic hormone (CHH), molt-inhibiting hormone (MIH), and crustacean female sex hormone (CFSH). Furthermore, numerous exoskeleton formation-related genes were found to be down-regulated during ovarian maturation, including cuticle-like proteins, eclosion hormone (EH), and gastrolith-like proteins, of which the latter are the first reported in L. vannamei. Our work is the first reproduction-related investigation of L. vannamei focusing on the eyestalk at the whole transcriptome level. These findings provide novel insight into the function of the eyestalk in reproduction regulation.
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Affiliation(s)
- Zhongkai Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Sheng Luan
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Xianhong Meng
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Baoxiang Cao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Kun Luo
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
| | - Jie Kong
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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15
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Chen HH, Petty LE, Bush W, Naj AC, Below JE. GWAS and Beyond: Using Omics Approaches to Interpret SNP Associations. CURRENT GENETIC MEDICINE REPORTS 2019; 7:30-40. [PMID: 33312764 PMCID: PMC7731888 DOI: 10.1007/s40142-019-0159-z] [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] [Indexed: 10/27/2022]
Abstract
PURPOSE OF REVIEW Neurodegenerative diseases, neuropsychiatric disorders, and related traits have highly complex etiologies but are also highly heritable and identifying the causal genes and biological pathways underlying these traits may advance the development of treatments and preventive strategies. While many genome-wide association studies (GWAS) have successfully identified variants contributing to polygenic neurodegenerative and neuropsychiatric phenotypes including Alzheimer's disease (AD), schizophrenia (SCZ), and bipolar disorder (BPD) amongst others, interpreting the biological roles of significantly-associated variants in the genetic architecture of these traits remains a significant challenge. Here we review several 'omics' approaches which attempt to bridge the gap from associated genetic variants to phenotype by helping define the functional roles of GWAS loci in the development of neuropsychiatric disorders and traits. RECENT FINDINGS Several common 'omics' approaches have been applied to examine neuropsychiatric traits, such as nearest-gene mapping, trans-ethnic fine mapping, annotation enrichment analysis, transcriptomic analysis, and pathway analysis, and each of these approaches has strengths and limitations in providing insight into biological mechanisms. One popular emerging method is the examination of tissue-specific genetically-regulated gene expression (GReX), which aggregates the genetic variants' effects at the gene-level. Furthermore, proteomic, metabolomic, and microbiomic studies and phenome-wide association studies will further enhance our understanding of neuropsychiatric traits. SUMMARY GWAS has been applied to neuropsychiatric traits for a decade, but our understanding about the biological function of identified variants remains limited. Today, technological advancements have created analytical approaches for integrating transcriptomics, metabolomics, proteomics, pharmacology and toxicology as tools for understanding the functional roles of genetics variants. These data, as well as the broader clinical information provided by electronic health records, can provide additional insight and complement genomic analyses.
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Affiliation(s)
- Hung-Hsin Chen
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lauren E. Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - William Bush
- Institute for Computational Biology, Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Adam C. Naj
- Department of Biostatistics, Epidemiology, and Informatics; Department of Pathology and Laboratory Medicine; Center for Clinical Epidemiology and Biostatistics; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer E. Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
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Lopez JV, Kamel B, Medina M, Collins T, Baums IB. Multiple Facets of Marine Invertebrate Conservation Genomics. Annu Rev Anim Biosci 2018; 7:473-497. [PMID: 30485758 DOI: 10.1146/annurev-animal-020518-115034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Conservation genomics aims to preserve the viability of populations and the biodiversity of living organisms. Invertebrate organisms represent 95% of animal biodiversity; however, few genomic resources currently exist for the group. The subset of marine invertebrates includes the most ancient metazoan lineages and possesses codes for unique gene products and possible keys to adaptation. The benefits of supporting invertebrate conservation genomics research (e.g., likely discovery of novel genes, protein regulatory mechanisms, genomic innovations, and transposable elements) outweigh the various hurdles (rare, small, or polymorphic starting materials). Here we review best conservation genomics practices in the laboratory and in silico when applied to marine invertebrates and also showcase unique features in several case studies of acroporid corals, crown-of-thorns starfish, apple snails, and abalone. Marine conservation genomics should also address how diversity can lead to unique marine innovations, the impact of deleterious variation, and how genomic monitoring and profiling could positively affect broader conservation goals (e.g., value of baseline data for in situ/ex situ genomic stocks).
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Affiliation(s)
- Jose V Lopez
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida 33004, USA;
| | - Bishoy Kamel
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, New Mexico 87131, USA;
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
| | - Timothy Collins
- Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA;
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
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17
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Liu W, Bai S, Zhao N, Jia S, Li W, Zhang L, Wang J. Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.). BMC PLANT BIOLOGY 2018; 18:225. [PMID: 30305027 PMCID: PMC6180388 DOI: 10.1186/s12870-018-1451-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 09/27/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND Water chickweed (Myosoton aquaticum (L.)) is a dicot broadleaf weed that is widespread in winter fields in China, and has evolved serious resistance to acetolactate synthase (ALS) inhibiting herbicides. RESULTS We identified a M. aquaticum population exhibiting moderate (6.15-fold) resistance to tribenuron-methyl (TM). Target-site ALS gene sequencing revealed no known resistance mutations in these plants, and the in vitro ALS activity assays showed no differences in enzyme sensitivity between susceptible and resistant populations; however, resistance was reversed by pretreatment with the cytochrome P450 (CYP) monooxygenase inhibitor malathion. An RNA sequencing transcriptome analysis was performed to identify candidate genes involved in metabolic resistance, and the unigenes obtained by de novo transcriptome assembly were annotated across seven databases. In total, 34 differentially expressed genes selected by digital gene expression analysis were validated by quantitative real-time (qRT)-PCR. Ten consistently overexpressed contigs, including four for CYP, four for ATP-binding cassette (ABC) transporter, and two for peroxidase were further validated by qRT-PCR using additional plants from resistant and susceptible populations. Three CYP genes (with homology to CYP734A1, CYP76C1, and CYP86B1) and one ABC transporter gene (with homology to ABCC10) were highly expressed in all resistant plants. CONCLUSION The mechanism of TM resistance in M. aquaticum is controlled by NTSR rather than TSR. Four genes, CYP734A1, CYP76C1, CYP86B1, and ABCC10 could play essential role in metabolic resistance to TM and justify further functional studies. To our knowledge, this is the first large-scale transcriptome analysis of genes associated with NTSR in M. aquaticum using the Illumina platform. Our data provide resource for M. aquaticum biology, and will facilitate the study of herbicide resistance mechanism at the molecular level in this species as well as in other weeds.
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Affiliation(s)
- Weitang Liu
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Shuang Bai
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Ning Zhao
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Sisi Jia
- Taian Customs, Taian, 271000 Shandong China
| | - Wei Li
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Lele Zhang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Taian, 271018 Shandong China
| | - Jinxin Wang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Taian, 271018 Shandong China
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De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome. Sci Rep 2018; 8:13553. [PMID: 30202061 PMCID: PMC6131155 DOI: 10.1038/s41598-018-31148-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/12/2018] [Indexed: 12/17/2022] Open
Abstract
The black tiger shrimp (Penaeus monodon) remains the second most widely cultured shrimp species globally; however, issues with disease and domestication have seen production levels stagnate over the past two decades. To help identify innovative solutions needed to resolve bottlenecks hampering the culture of this species, it is important to generate genetic and genomic resources. Towards this aim, we have produced the most complete publicly available P. monodon transcriptome database to date based on nine adult tissues and eight early life-history stages (BUSCO - Complete: 98.2% [Duplicated: 51.3%], Fragmented: 0.8%, Missing: 1.0%). The assembly resulted in 236,388 contigs, which were then further segregated into 99,203 adult tissue specific and 58,678 early life-history stage specific clusters. While annotation rates were low (approximately 30%), as is typical for a non-model organisms, annotated transcript clusters were successfully mapped to several hundred functional KEGG pathways. Transcripts were clustered into groups within tissues and early life-history stages, providing initial evidence for their roles in specific tissue functions, or developmental transitions. We expect the transcriptome to provide an essential resource to investigate the molecular basis of commercially relevant-significant traits in P. monodon and other shrimp species.
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Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
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20
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Yang Y, Han T, Xiao J, Li X, Wang J. Transcriptome analysis reveals carbohydrate-mediated liver immune responses in Epinephelus akaara. Sci Rep 2018; 8:639. [PMID: 29330509 PMCID: PMC5766613 DOI: 10.1038/s41598-017-18990-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 12/20/2017] [Indexed: 11/09/2022] Open
Abstract
As the cheapest energy source, carbohydrates are used in fish feeds to improve physical quality and reduce catabolism of proteins and lipids. The liver is the primary organ for metabolism and is also an important site of immune regulation. Here, we investigated the effect of different dietary carbohydrate levels on growth and health by evaluating the liver transcriptome of Epinephelus akaara. In this study, E. akaara juveniles were fed diets containing few (0% corn starch), moderate (18% corn starch), and high (30% corn starch) levels of dietary carbohydrate. After an 8-week feeding trial, E. akaara fed 30% dietary carbohydrates exhibited poor growth performance compared with those fed 0% and 18% dietary carbohydrates (P > 0.05). Genes related to the immune system, including IL8, TLR9, CXCR4, CCL4, and NFκB inhibitor alpha, were over-expressed in E. akaara fed the highest level of carbohydrate (30%). This general over-expression could indicate activation of inflammatory processes in the liver. The liver transcriptome data of E. akaara reported here indicate that high carbohydrate level of diet can lead to poor growth and inflammatory immune response in E. akaara.
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Affiliation(s)
- Yunxia Yang
- Department of Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Tao Han
- Department of Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Jia Xiao
- Department of Immunobiology, Jinan University, Guangzhou, China
| | - Xinyu Li
- Department of Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Jiteng Wang
- Department of Aquaculture, Zhejiang Ocean University, Zhoushan, China.
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Melouane A, Ghanemi A, Aubé S, Yoshioka M, St-Amand J. Differential gene expression analysis in ageing muscle and drug discovery perspectives. Ageing Res Rev 2018; 41:53-63. [PMID: 29102726 DOI: 10.1016/j.arr.2017.10.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/31/2017] [Accepted: 10/31/2017] [Indexed: 12/12/2022]
Abstract
Identifying therapeutic target genes represents the key step in functional genomics-based therapies. Within this context, the disease heterogeneity, the exogenous factors and the complexity of genomic structure and function represent important challenges. The functional genomics aims to overcome such obstacles via identifying the gene functions and therefore highlight disease-causing genes as therapeutic targets. Genomic technologies promise to reshape the research on ageing muscle, exercise response and drug discovery. Herein, we describe the functional genomics strategies, mainly differential gene expression methods microarray, serial analysis of gene expression (SAGE), massively parallel signature sequence (MPSS), RNA sequencing (RNA seq), representational difference analysis (RDA), and suppression subtractive hybridization (SSH). Furthermore, we review these illustrative approaches that have been used to discover new therapeutic targets for some complex diseases along with the application of these tools to study the modulation of the skeletal muscle transcriptome.
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22
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Tigano A, Sackton TB, Friesen VL. Assembly and RNA-free annotation of highly heterozygous genomes: The case of the thick-billed murre (Uria lomvia). Mol Ecol Resour 2017; 18:79-90. [PMID: 28815912 DOI: 10.1111/1755-0998.12712] [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: 01/31/2017] [Revised: 08/02/2017] [Accepted: 08/08/2017] [Indexed: 11/29/2022]
Abstract
Thanks to a dramatic reduction in sequencing costs followed by a rapid development of bioinformatics tools, genome assembly and annotation have become accessible to many researchers in recent years. Among tetrapods, birds have genomes that display many features that facilitate their assembly and annotation, such as small genome size, low number of repeats and highly conserved genomic structure. However, we found that high genomic heterozygosity could have a great impact on the quality of the genome assembly of the thick-billed murre (Uria lomvia), an arctic colonial seabird. In this study, we tested the performance of three genome assemblers, ray/sscape, soapdenovo2 and platanus, in assembling the highly heterozygous genome of the thick-billed murre. Our results show that platanus, an assembler specifically designed for heterozygous genomes, outperforms the other two approaches and produces a highly contiguous (N50 = 15.8 Mb) and complete genome assembly (93% presence of genes from the Benchmarking Universal Single Copy Ortholog [BUSCO] gene set). Additionally, we annotated the thick-billed murre genome using a homology-based approach that takes advantage of the genomic resources available for birds and other taxa. Our study will be useful for those researchers who are approaching assembly and annotation of highly heterozygous genomes, or genomes of species of conservation concern, and/or who have limited financial resources.
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Affiliation(s)
- Anna Tigano
- Department of Biology, Queen's University, Kingston, ON, Canada
| | | | - Vicki L Friesen
- Department of Biology, Queen's University, Kingston, ON, Canada
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Upasani ML, Limaye BM, Gurjar GS, Kasibhatla SM, Joshi RR, Kadoo NY, Gupta VS. Chickpea-Fusarium oxysporum interaction transcriptome reveals differential modulation of plant defense strategies. Sci Rep 2017; 7:7746. [PMID: 28798320 PMCID: PMC5552786 DOI: 10.1038/s41598-017-07114-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 06/21/2017] [Indexed: 12/22/2022] Open
Abstract
Fusarium wilt is one of the major biotic stresses reducing chickpea productivity. The use of wilt-resistant cultivars is the most appropriate means to combat the disease and secure productivity. As a step towards understanding the molecular basis of wilt resistance in chickpea, we investigated the transcriptomes of wilt-susceptible and wilt-resistant cultivars under both Fusarium oxysporum f.sp. ciceri (Foc) challenged and unchallenged conditions. Transcriptome profiling using LongSAGE provided a valuable insight into the molecular interactions between chickpea and Foc, which revealed several known as well as novel genes with differential or unique expression patterns in chickpea contributing to lignification, hormonal homeostasis, plant defense signaling, ROS homeostasis, R-gene mediated defense, etc. Similarly, several Foc genes characteristically required for survival and growth of the pathogen were expressed only in the susceptible cultivar with null expression of most of these genes in the resistant cultivar. This study provides a rich resource for functional characterization of the genes involved in resistance mechanism and their use in breeding for sustainable wilt-resistance. Additionally, it provides pathogen targets facilitating the development of novel control strategies.
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Affiliation(s)
- Medha L Upasani
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, 411007, India
| | - Bhakti M Limaye
- HPC-Medical and Bioinformatics Applications Group, Center for Development of Advanced Computing, Savitribai Phule Pune University Campus, Pune, 411007, India
| | - Gayatri S Gurjar
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Sunitha M Kasibhatla
- HPC-Medical and Bioinformatics Applications Group, Center for Development of Advanced Computing, Savitribai Phule Pune University Campus, Pune, 411007, India
| | - Rajendra R Joshi
- HPC-Medical and Bioinformatics Applications Group, Center for Development of Advanced Computing, Savitribai Phule Pune University Campus, Pune, 411007, India
| | - Narendra Y Kadoo
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.
| | - Vidya S Gupta
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.
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Kannan M, Li J, Fritz SE, Husarek KE, Sanford JC, Sullivan TL, Tiwary PK, An W, Boeke JD, Symer DE. Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration. Mob DNA 2017; 8:8. [PMID: 28491150 PMCID: PMC5424313 DOI: 10.1186/s13100-017-0091-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/03/2017] [Indexed: 02/15/2023] Open
Abstract
Background The ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive, real-time L1 retrotransposon reporter constructs. Results Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human cancer cells, mouse embryonic stem cells, and tissues of pseudofounder transgenic mice and their progeny. In cancer cell lines, the newly inserted sequences typically underwent rapid transcriptional gene silencing, but they lacked cytosine methylation even after many cell divisions. L1 reporter expression was reversible and oscillated frequently. Silenced or variegated reporter expression was strongly and uniformly reactivated by treatment with inhibitors of histone deacetylation, revealing the mechanism for their silencing. By contrast, de novo integrants retrotransposed by L1 in pluripotent mouse embryonic stem (ES) cells underwent rapid silencing by dense cytosine methylation. Similarly, de novo cytosine methylation also was identified at new integrants when studied in several distinct somatic tissues of adult founder mice. Pre-existing L1 elements in cultured human cancer cells were stably silenced by dense cytosine methylation, whereas their transcription modestly increased when cytosine methylation was experimentally reduced in cells lacking DNA methyltransferases DNMT1 and DNMT3b. As a control, reporter genes mobilized by piggyBac (PB), a DNA transposon, revealed relatively stable and robust expression without apparent silencing in both cultured cancer cells and ES cells. Conclusions We hypothesize that the de novo methylation marks at newly inserted sequences retrotransposed by L1 in early pre-implantation development are maintained or re-established in adult somatic tissues. By contrast, histone deacetylation reversibly silences L1 reporter insertions that had mobilized at later timepoints in somatic development and differentiation, e.g., in cancer cell lines. We conclude that the cellular contexts of L1 retrotransposition can determine expression or silencing of newly integrated sequences. We propose a model whereby reporter expression from somatic TE insertions reflects the timing, molecular mechanism, epigenetic controls and the genomic, cellular and developmental contexts of their integration. Electronic supplementary material The online version of this article (doi:10.1186/s13100-017-0091-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manoj Kannan
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani, 333031 Rajasthan India.,Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Present Address: Birla Institute of Technology and Science, Pilani, Dubai campus, Dubai, United Arab Emirates
| | - Jingfeng Li
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH USA.,Department of Internal Medicine, The Ohio State University, Columbus, OH USA
| | - Sarah E Fritz
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH USA.,Present Address: National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Kathryn E Husarek
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH USA.,Present Address: Aventiv Research, Inc., Columbus, OH USA
| | - Jonathan C Sanford
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH USA.,Present Address: Drug Safety Research and Development, Pfizer, Inc., Groton, CT USA
| | - Teresa L Sullivan
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA
| | - Pawan Kumar Tiwary
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Present Address: Biocon, Bangalore, India
| | - Wenfeng An
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD USA.,Present Address: Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD USA
| | - Jef D Boeke
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD USA.,Present Address: Institute for Systems Genetics, New York University Langone Medical Center, New York, NY USA
| | - David E Symer
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH USA.,Human Cancer Genetics Program, and Department of Biomedical Informatics, The Ohio State University, Columbus, OH USA.,Human Cancer Genetics Program, Department of Cancer Biology and Genetics, and Department of Biomedical Informatics, The Ohio State University, Tzagournis Research Facility, Room 440, 420 West 12th Ave, Columbus, OH 43210 USA
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Zhao N, Li W, Bai S, Guo W, Yuan G, Wang F, Liu W, Wang J. Transcriptome Profiling to Identify Genes Involved in Mesosulfuron-Methyl Resistance in Alopecurus aequalis. FRONTIERS IN PLANT SCIENCE 2017; 8:1391. [PMID: 28848590 PMCID: PMC5552757 DOI: 10.3389/fpls.2017.01391] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/26/2017] [Indexed: 05/04/2023]
Abstract
Non-target-site resistance (NTSR) to herbicides is a worldwide concern for weed control. However, as the dominant NTSR mechanism in weeds, metabolic resistance is not yet well-characterized at the genetic level. For this study, we have identified a shortawn foxtail (Alopecurus aequalis Sobol.) population displaying both TSR and NTSR to mesosulfuron-methyl and fenoxaprop-P-ethyl, yet the molecular basis for this NTSR remains unclear. To investigate the mechanisms of metabolic resistance, an RNA-Seq transcriptome analysis was used to find candidate genes that may confer metabolic resistance to the herbicide mesosulfuron-methyl in this plant population. The RNA-Seq libraries generated 831,846,736 clean reads. The de novo transcriptome assembly yielded 95,479 unigenes (averaging 944 bp in length) that were assigned putative annotations. Among these, a total of 29,889 unigenes were assigned to 67 GO terms that contained three main categories, and 14,246 unigenes assigned to 32 predicted KEGG metabolic pathways. Global gene expression was measured using the reads generated from the untreated control (CK), water-only control (WCK), and mesosulfuron-methyl treatment (T) of R and susceptible (S). Contigs that showed expression differences between mesosulfuron-methyl-treated R and S biotypes, and between mesosulfuron-methyl-treated, water-treated and untreated R plants were selected for further quantitative real-time PCR (qRT-PCR) validation analyses. Seventeen contigs were consistently highly expressed in the resistant A. aequalis plants, including four cytochrome P450 monooxygenase (CytP450) genes, two glutathione S-transferase (GST) genes, two glucosyltransferase (GT) genes, two ATP-binding cassette (ABC) transporter genes, and seven additional contigs with functional annotations related to oxidation, hydrolysis, and plant stress physiology. These 17 contigs could serve as major candidate genes for contributing to metabolic mesosulfuron-methyl resistance; hence they deserve further functional study. This is the first large-scale transcriptome-sequencing study to identify NTSR genes in A. aequalis that uses the Illumina platform. This work demonstrates that NTSR is likely driven by the differences in the expression patterns of a set of genes. The assembled transcriptome data presented here provide a valuable resource for A. aequalis biology, and should facilitate the study of herbicide resistance at the molecular level in this and other weed species.
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Affiliation(s)
- Ning Zhao
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural UniversityTai'an, China
| | - Wei Li
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural UniversityTai'an, China
| | - Shuang Bai
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural UniversityTai'an, China
| | - Wenlei Guo
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural UniversityTai'an, China
| | - Guohui Yuan
- Eco-environment and Plant Protection Research Institute, Shanghai Academy of Agricultural SciencesShanghai, China
| | - Fan Wang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural UniversityTai'an, China
| | - Weitang Liu
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural UniversityTai'an, China
| | - Jinxin Wang
- Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural UniversityTai'an, China
- *Correspondence: Jinxin Wang
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26
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Yu SY, Paul S, Hwang SY. Application of the emerging technologies in toxicogenomics: An overview. BIOCHIP JOURNAL 2016. [DOI: 10.1007/s13206-016-0405-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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27
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Liu X, Meng H, Jiang C, Yang S, Cui F, Yang P. Differential microRNA Expression and Regulation in the Rat Model of Post-Infarction Heart Failure. PLoS One 2016; 11:e0160920. [PMID: 27504893 PMCID: PMC4978447 DOI: 10.1371/journal.pone.0160920] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 07/27/2016] [Indexed: 12/21/2022] Open
Abstract
Background Heart failure is a complex end stage of various cardiovascular diseases with a poor prognosis, and the mechanisms for development and progression of heart failure have always been a hot point. However, the molecular mechanisms underlying the post transcriptional regulation of heart failure have not been fully elucidated. Current data suggest that microRNAs (miRNAs) are involved in the pathogenesis of heart failure and could serve as a new biomarker, but the precise regulatory mechanisms are still unclear. Methods The differential miRNA profile in a rat model of post-infarction heart failure was determined using high throughout sequencing and analyzed through bioinformatics approaches. The results were validated using qRT-PCR for 8 selected miRNAs. Then the expression patterns of 4 miRNAs were analyzed in different periods after myocardial infarction. Finally, gain- and loss-of-function experiments of rno-miR-122-5p and rno-miR-184 were analyzed in H2O2 treated H9c2 cells. Results In the heart failure sample, 78 miRNAs were significantly upregulated and 28 were downregulated compared to the controls. GO and KEGG pathway analysis further indicated the likely roles of these miRNAs in heart failure. Time-course analysis revealed different expression patterns of 4 miRNAs: rno-miR-122-5p, rno-miR-199a-5p, rno-miR-184 and rno-miR-208a-3p. Additionally, rno-miR-122-5p and rno-miR-184 were proved to promote apoptosis in vitro. Conclusions Differential profile and expression patterns of miRNAs in the rats model of post-infarction heart failure were found, and the pro-apoptotic roles of rno-miR-122-5p and rno-miR-184 were revealed. These findings may provide a novel way that may assist in heart failure diagnosis and treatment.
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Affiliation(s)
- Xueyan Liu
- Department of Internal Medicine and Cardiology, China–Japan Union Hospital of Jilin University, Changchun, China
| | - Heyu Meng
- Clinical Medicine, Yanbian University, Yanji, China
| | - Chao Jiang
- Department of Hepatobiliary Pancreatic Surgery, First Hospital of Jilin University, Changchun, China
| | - Sibao Yang
- Department of Internal Medicine and Cardiology, China–Japan Union Hospital of Jilin University, Changchun, China
| | - Fengwen Cui
- Department of Internal Medicine and Cardiology, China–Japan Union Hospital of Jilin University, Changchun, China
| | - Ping Yang
- Department of Internal Medicine and Cardiology, China–Japan Union Hospital of Jilin University, Changchun, China
- * E-mail:
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Mirvish ED, Shuda M. Strategies for Human Tumor Virus Discoveries: From Microscopic Observation to Digital Transcriptome Subtraction. Front Microbiol 2016; 7:676. [PMID: 27242703 PMCID: PMC4865503 DOI: 10.3389/fmicb.2016.00676] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/26/2016] [Indexed: 01/07/2023] Open
Abstract
Over 20% of human cancers worldwide are associated with infectious agents, including viruses, bacteria, and parasites. Various methods have been used to identify human tumor viruses, including electron microscopic observations of viral particles, immunologic screening, cDNA library screening, nucleic acid hybridization, consensus PCR, viral DNA array chip, and representational difference analysis. With the Human Genome Project, a large amount of genetic information from humans and other organisms has accumulated over the last decade. Utilizing the available genetic databases, Feng et al. (2007) developed digital transcriptome subtraction (DTS), an in silico method to sequentially subtract human sequences from tissue or cellular transcriptome, and discovered Merkel cell polyomavirus (MCV) from Merkel cell carcinoma. Here, we review the background and methods underlying the human tumor virus discoveries and explain how DTS was developed and used for the discovery of MCV.
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Affiliation(s)
- Ezra D Mirvish
- Department of Dermatology, University of Pittsburgh Medical Center, Pittsburgh PA, USA
| | - Masahiro Shuda
- Cancer Virology Program, University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh PA, USA
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Liao C, Xie G, Zhu L, Chen X, Li X, Lu H, Xu B, Ramot Y, Paus R, Yue Z. p53 Is a Direct Transcriptional Repressor of Keratin 17: Lessons from a Rat Model of Radiation Dermatitis. J Invest Dermatol 2016; 136:680-689. [DOI: 10.1016/j.jid.2015.12.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 11/15/2022]
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30
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Achieving Crop Stress Tolerance and Improvement—an Overview of Genomic Techniques. Appl Biochem Biotechnol 2015; 177:1395-408. [DOI: 10.1007/s12010-015-1830-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 09/02/2015] [Indexed: 01/09/2023]
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Ovarian Transcriptome Analysis of Portunus trituberculatus Provides Insights into Genes Expressed during Phase III and IV Development. PLoS One 2015; 10:e0138862. [PMID: 26431399 PMCID: PMC4591999 DOI: 10.1371/journal.pone.0138862] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/04/2015] [Indexed: 12/24/2022] Open
Abstract
Enhancing the production of aquatic animals is crucial for fishery management and aquaculture applications. Ovaries are specialized tissues that play critical roles in producing oocytes and hormones. Significant biochemical changes take place during the sexual maturation of Portunus trituberculatus, but the genetics of this process has not been extensively studied. Transcriptome sequencing can be used to determine gene expression changes within specific periods. In the current study, we used transcriptome sequencing to produce a comprehensive transcript dataset for the ovarian development of P. trituberculatus. Approximately 100 million sequencing reads were generated, and 126,075 transcripts were assembled. Functional annotation of the obtained transcripts revealed important pathways in ovarian development, such as those involving the vitellogenin gene. Also, we performed deep sequencing of ovaries in phases III and IV of sexual maturation in P. trituberculatus. Differential analysis of gene expression identified 506 significantly differentially expressed genes, which belong to 20 pathway, transporters, development, transcription factors, metabolism of other amino acids, carbohydrate and lipid, solute carrier family members, and enzymes. Taken together, our study provides the first comprehensive transcriptomic resource for P. trituberculatus ovaries, which will strengthen understanding of the molecular mechanisms underlying the sexual maturation process and advance molecular nutritional studies of P. trituberculatus.
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Singhal P, Jan AT, Azam M, Haq QMR. Plant abiotic stress: a prospective strategy of exploiting promoters as alternative to overcome the escalating burden. FRONTIERS IN LIFE SCIENCE 2015. [DOI: 10.1080/21553769.2015.1077478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Whole transcriptome analysis with sequencing: methods, challenges and potential solutions. Cell Mol Life Sci 2015; 72:3425-39. [PMID: 26018601 DOI: 10.1007/s00018-015-1934-y] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/25/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
Abstract
Whole transcriptome analysis plays an essential role in deciphering genome structure and function, identifying genetic networks underlying cellular, physiological, biochemical and biological systems and establishing molecular biomarkers that respond to diseases, pathogens and environmental challenges. Here, we review transcriptome analysis methods and technologies that have been used to conduct whole transcriptome shotgun sequencing or whole transcriptome tag/target sequencing analyses. We focus on how adaptors/linkers are added to both 5' and 3' ends of mRNA molecules for cloning or PCR amplification before sequencing. Challenges and potential solutions are also discussed. In brief, next generation sequencing platforms have accelerated releases of the large amounts of gene expression data. It is now time for the genome research community to assemble whole transcriptomes of all species and collect signature targets for each gene/transcript, and thus use known genes/transcripts to determine known transcriptomes directly in the near future.
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Rodríguez-Esteban G, González-Sastre A, Rojo-Laguna JI, Saló E, Abril JF. Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea. BMC Genomics 2015; 16:361. [PMID: 25952370 PMCID: PMC4494696 DOI: 10.1186/s12864-015-1533-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/13/2015] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The freshwater planarian Schmidtea mediterranea is recognised as a valuable model for research into adult stem cells and regeneration. With the advent of the high-throughput sequencing technologies, it has become feasible to undertake detailed transcriptional analysis of its unique stem cell population, the neoblasts. Nonetheless, a reliable reference for this type of studies is still lacking. RESULTS Taking advantage of digital gene expression (DGE) sequencing technology we compare all the available transcriptomes for S. mediterranea and improve their annotation. These results are accessible via web for the community of researchers. Using the quantitative nature of DGE, we describe the transcriptional profile of neoblasts and present 42 new neoblast genes, including several cancer-related genes and transcription factors. Furthermore, we describe in detail the Smed-meis-like gene and the three Nuclear Factor Y subunits Smed-nf-YA, Smed-nf-YB-2 and Smed-nf-YC. CONCLUSIONS DGE is a valuable tool for gene discovery, quantification and annotation. The application of DGE in S. mediterranea confirms the planarian stem cells or neoblasts as a complex population of pluripotent and multipotent cells regulated by a mixture of transcription factors and cancer-related genes.
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Affiliation(s)
- Gustavo Rodríguez-Esteban
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain.
| | - Alejandro González-Sastre
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain.
| | - José Ignacio Rojo-Laguna
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain.
| | - Emili Saló
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain.
| | - Josep F Abril
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona (UB), and Institut de Biomedicina de la Universitat de Barcelona (IBUB), Av. Diagonal 643, Barcelona, 08028, Catalonia, Spain.
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Almeida NF, Krezdorn N, Rotter B, Winter P, Rubiales D, Vaz Patto MC. Lathyrus sativus transcriptome resistance response to Ascochyta lathyri investigated by deepSuperSAGE analysis. FRONTIERS IN PLANT SCIENCE 2015; 6:178. [PMID: 25852725 PMCID: PMC4367168 DOI: 10.3389/fpls.2015.00178] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/05/2015] [Indexed: 05/07/2023]
Abstract
Lathyrus sativus (grass pea) is a temperate grain legume crop with a great potential for expansion in dry areas or zones that are becoming more drought-prone. It is also recognized as a potential source of resistance to several important diseases in legumes, such as ascochyta blight. Nevertheless, the lack of detailed genomic and/or transcriptomic information hampers further exploitation of grass pea resistance-related genes in precision breeding. To elucidate the pathways differentially regulated during ascochyta-grass pea interaction and to identify resistance candidate genes, we compared the early response of the leaf gene expression profile of a resistant L. sativus genotype to Ascochyta lathyri infection with a non-inoculated control sample from the same genotype employing deepSuperSAGE. This analysis generated 14.387 UniTags of which 95.7% mapped to a reference grass pea/rust interaction transcriptome. From the total mapped UniTags, 738 were significantly differentially expressed between control and inoculated leaves. The results indicate that several gene classes acting in different phases of the plant/pathogen interaction are involved in the L. sativus response to A. lathyri infection. Most notably a clear up-regulation of defense-related genes involved in and/or regulated by the ethylene pathway was observed. There was also evidence of alterations in cell wall metabolism indicated by overexpression of cellulose synthase and lignin biosynthesis genes. This first genome-wide overview of the gene expression profile of the L. sativus response to ascochyta infection delivered a valuable set of candidate resistance genes for future use in precision breeding.
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Affiliation(s)
- Nuno F. Almeida
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB, Universidade Nova de LisboaOeiras, Portugal
| | | | | | | | - Diego Rubiales
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Maria C. Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB, Universidade Nova de LisboaOeiras, Portugal
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Omura M, Mombaerts P. Trpc2-expressing sensory neurons in the mouse main olfactory epithelium of type B express the soluble guanylate cyclase Gucy1b2. Mol Cell Neurosci 2015; 65:114-24. [PMID: 25701815 PMCID: PMC4396857 DOI: 10.1016/j.mcn.2015.02.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 02/06/2015] [Accepted: 02/17/2015] [Indexed: 01/20/2023] Open
Abstract
Chemoreception in the mouse olfactory system occurs primarily at two chemosensory epithelia in the nasal cavity: the main olfactory epithelium (MOE) and the vomeronasal epithelium. The canonical chemosensory neurons in the MOE, the olfactory sensory neurons (OSNs), express the odorant receptor (OR) gene repertoire, and depend on Adcy3 and Cnga2 for chemosensory signal transduction. The canonical chemosensory neurons in the vomeronasal epithelium, the vomeronasal sensory neurons (VSNs), express two unrelated vomeronasal receptor (VR) gene repertoires, and involve Trpc2 for chemosensory signal transduction. Recently we reported the discovery of two types of neurons in the mouse MOE that express Trcp2 in addition to Cnga2. These cell types can be distinguished at the single-cell level by expression of Adcy3: positive, type A and negative, type B. Some type A cells express OR genes. Thus far there is no specific gene or marker for type B cells, hampering further analyses such as physiological recordings. Here, we show that among MOE cells, type B cells are unique in their expression of the soluble guanylate cyclase Gucy1b2. We came across Gucy1b2 in an explorative approach based on Long Serial Analysis of Gene Expression (LongSAGE) that we applied to single red-fluorescent cells isolated from whole olfactory mucosa and vomeronasal organ of mice of a novel Trcp2-IRES-taumCherry gene-targeted strain. The generation of a novel Gucy1b2-IRES-tauGFP gene-targeted strain enabled us to visualize coalescence of axons of type B cells into glomeruli in the main olfactory bulb. Our molecular and anatomical analyses define Gucy1b2 as a marker for type B cells within the MOE. The Gucy1b2-IRES-tauGFP strain will be useful for physiological, molecular, cellular, and anatomical studies of this newly described chemosensory subsystem. Trpc2 + cells exist as type A and type B in the mouse main olfactory epithelium. We find no evidence for expression of chemosensory GPCR genes in type B cells. We identify the soluble guanylate cyclase Gucy1b2 as a marker for type B cells. Gucy1b2-IRES-tauGFP knockin mice will be useful for physiological studies.
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Affiliation(s)
- Masayo Omura
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany
| | - Peter Mombaerts
- Max Planck Research Unit for Neurogenetics, Frankfurt, Germany.
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Khudyakov JI, Preeyanon L, Champagne CD, Ortiz RM, Crocker DE. Transcriptome analysis of northern elephant seal (Mirounga angustirostris) muscle tissue provides a novel molecular resource and physiological insights. BMC Genomics 2015; 16:64. [PMID: 25758323 PMCID: PMC4328371 DOI: 10.1186/s12864-015-1253-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/16/2015] [Indexed: 11/10/2022] Open
Abstract
Background The northern elephant seal, Mirounga angustirostris, is a valuable animal model of fasting adaptation and hypoxic stress tolerance. However, no reference sequence is currently available for this and many other marine mammal study systems, hindering molecular understanding of marine adaptations and unique physiology. Results We sequenced a transcriptome of M. angustirostris derived from muscle sampled during an acute stress challenge experiment to identify species-specific markers of stress axis activation and recovery. De novo assembly generated 164,966 contigs and a total of 522,699 transcripts, of which 68.70% were annotated using mouse, human, and domestic dog reference protein sequences. To reduce transcript redundancy, we removed highly similar isoforms in large gene families and produced a filtered assembly containing 336,657 transcripts. We found that a large number of annotated genes are associated with metabolic signaling, immune and stress responses, and muscle function. Preliminary differential expression analysis suggests a limited transcriptional response to acute stress involving alterations in metabolic and immune pathways and muscle tissue maintenance, potentially driven by early response transcription factors such as Cebpd. Conclusions We present the first reference sequence for Mirounga angustirostris produced by RNA sequencing of muscle tissue and cloud-based de novo transcriptome assembly. We annotated 395,102 transcripts, some of which may be novel isoforms, and have identified thousands of genes involved in key physiological processes. This resource provides elephant seal-specific gene sequences, complementing existing metabolite and protein expression studies and enabling future work on molecular pathways regulating adaptations such as fasting, hypoxia, and environmental stress responses in marine mammals. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1253-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jane I Khudyakov
- Department of Biology, Sonoma State University, 1801 E Cotati Ave, Rohnert Park, CA, 94928, USA.
| | - Likit Preeyanon
- Michigan State University, Microbiology and Molecular Genetics, 567 Wilson Rd, East Lansing, MI, 48824, USA.
| | - Cory D Champagne
- National Marine Mammal Foundation, Conservation and Biological Research Program, 224 0Shelter Island Drive, San Diego, CA, 92106, USA.
| | - Rudy M Ortiz
- University of California, Merced, School of Natural Sciences, 5200 North Lake Rd, Merced, CA, 95343, USA.
| | - Daniel E Crocker
- Department of Biology, Sonoma State University, 1801 E Cotati Ave, Rohnert Park, CA, 94928, USA.
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Lundin S, Jemt A, Terje-Hegge F, Foam N, Pettersson E, Käller M, Wirta V, Lexow P, Lundeberg J. Endonuclease specificity and sequence dependence of type IIS restriction enzymes. PLoS One 2015; 10:e0117059. [PMID: 25629514 PMCID: PMC4309577 DOI: 10.1371/journal.pone.0117059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 12/17/2014] [Indexed: 11/23/2022] Open
Abstract
Restriction enzymes that recognize specific sequences but cleave unknown sequence outside the recognition site are extensively utilized tools in molecular biology. Despite this, systematic functional categorization of cleavage performance has largely been lacking. We established a simple and automatable model system to assay cleavage distance variation (termed slippage) and the sequence dependence thereof. We coupled this to massively parallel sequencing in order to provide sensitive and accurate measurement. With this system 14 enzymes were assayed (AcuI, BbvI, BpmI, BpuEI, BseRI, BsgI, Eco57I, Eco57MI, EcoP15I, FauI, FokI, GsuI, MmeI and SmuI). We report significant variation of slippage ranging from 1–54%, variations in sequence context dependence, as well as variation between isoschizomers. We believe this largely overlooked property of enzymes with shifted cleavage would benefit from further large scale classification and engineering efforts seeking to improve performance. The gained insights of in-vitro performance may also aid the in-vivo understanding of these enzymes.
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Affiliation(s)
- Sverker Lundin
- Science for Life Laboratory, KTH, Gene Technology, Solna, 171 65, Sweden
| | - Anders Jemt
- Science for Life Laboratory, KTH, Gene Technology, Solna, 171 65, Sweden
| | | | | | | | | | | | | | - Joakim Lundeberg
- Science for Life Laboratory, KTH, Gene Technology, Solna, 171 65, Sweden
- * E-mail:
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Obermeier C, Salazar-Colqui BM, Spamer V, Snowdon R. Multiplexed digital gene expression analysis for genetical genomics in large plant populations. Methods Mol Biol 2015; 1245:119-140. [PMID: 25373753 DOI: 10.1007/978-1-4939-1966-6_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Digital gene expression (DGE) analysis is a cost-effective method for large-scale quantitative transcriptome analysis using second generation sequencing. Here we describe how adaptation of DGE with barcode indexing in large segregating plant populations of over 100 genotypes can be applied for successful expression QTL (eQTL) and gene expression network analysis to develop transcript-based markers for breeding.
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Affiliation(s)
- Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany,
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Remmers EF, Ombrello MJ, Siegel RM. Principles and techniques in molecular biology. Rheumatology (Oxford) 2015. [DOI: 10.1016/b978-0-323-09138-1.00012-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Complete mitogenome of the edible sea urchin Loxechinus albus: genetic structure and comparative genomics within Echinozoa. Mol Biol Rep 2014; 42:1081-9. [DOI: 10.1007/s11033-014-3847-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 11/25/2014] [Indexed: 10/24/2022]
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Wickramasinghe S, Cánovas A, Rincón G, Medrano JF. RNA-Sequencing: A tool to explore new frontiers in animal genetics. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.06.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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43
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Scheider J, Afonso-Grunz F, Hoffmeier K, Horres R, Groher F, Rycak L, Oehlmann J, Winter P. Gene expression of chicken gonads is sex- and side-specific. Sex Dev 2014; 8:178-91. [PMID: 24820130 DOI: 10.1159/000362259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2013] [Indexed: 11/19/2022] Open
Abstract
In chicken, the left and right female gonads undergo a completely different program during development. To learn more about the molecular factors underlying side-specific development and to identify potential sex- and side-specific genes in developing gonads, we separately performed next-generation sequencing-based deepSuperSAGE transcription profiling from left and right, female and male gonads of 19-day-old chicken embryos. A total of 836 transcript variants were significantly differentially expressed (p < 10(-5)) between combined male and female gonads. Left-right comparison revealed 1,056 and 822 differentially (p < 10(-5)) expressed transcript variants for male and female gonads, respectively, of which 72 are side-specific in both sexes. At least some of these may represent key players for lateral development in birds. Additionally, several genes with laterally differential expression in the ovaries seem to determine female gonads for growth or regression, whereas right-left differences in testes are mostly limited to the differentially expressed genes present in both sexes. With a few exceptions, side-specific genes are not located on the sex chromosomes. The large differences in lateral gene expression in the ovaries in almost all metabolic pathways suggest that the regressing right gonad might have undergone a change of function during evolution.
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Affiliation(s)
- Jessica Scheider
- Institute for Ecology, Evolution and Diversity, Goethe University Frankfurt am Main, Frankfurt/M., Germany
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Rallapalli G, Kemen EM, Robert-Seilaniantz A, Segonzac C, Etherington GJ, Sohn KH, MacLean D, Jones JDG. EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics. BMC Genomics 2014; 15:341. [PMID: 24884414 PMCID: PMC4035070 DOI: 10.1186/1471-2164-15-341] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/31/2014] [Indexed: 01/19/2023] Open
Abstract
Background Next Generation Sequencing technologies have facilitated differential gene expression analysis through RNA-seq and Tag-seq methods. RNA-seq has biases associated with transcript lengths, lacks uniform coverage of regions in mRNA and requires 10–20 times more reads than a typical Tag-seq. Most existing Tag-seq methods either have biases or not high throughput due to use of restriction enzymes or enzymatic manipulation of 5’ ends of mRNA or use of RNA ligations. Results We have developed EXpression Profiling through Randomly Sheared cDNA tag Sequencing (EXPRSS) that employs acoustic waves to randomly shear cDNA and generate sequence tags at a relatively defined position (~150-200 bp) from the 3′ end of each mRNA. Implementation of the method was verified through comparative analysis of expression data generated from EXPRSS, NlaIII-DGE and Affymetrix microarray and through qPCR quantification of selected genes. EXPRSS is a strand specific and restriction enzyme independent tag sequencing method that does not require cDNA length-based data transformations. EXPRSS is highly reproducible, is high-throughput and it also reveals alternative polyadenylation and polyadenylated antisense transcripts. It is cost-effective using barcoded multiplexing, avoids the biases of existing SAGE and derivative methods and can reveal polyadenylation position from paired-end sequencing. Conclusions EXPRSS Tag-seq provides sensitive and reliable gene expression data and enables high-throughput expression profiling with relatively simple downstream analysis. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-341) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Jonathan D G Jones
- The Sainsbury Laboratory, Norwich Research Park, Colney, Norwich, UK NR4 7UH.
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Marie-Nelly H, Marbouty M, Cournac A, Liti G, Fischer G, Zimmer C, Koszul R. Filling annotation gaps in yeast genomes using genome-wide contact maps. ACTA ACUST UNITED AC 2014; 30:2105-13. [PMID: 24711652 DOI: 10.1093/bioinformatics/btu162] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATIONS De novo sequencing of genomes is followed by annotation analyses aiming at identifying functional genomic features such as genes, non-coding RNAs or regulatory sequences, taking advantage of diverse datasets. These steps sometimes fail at detecting non-coding functional sequences: for example, origins of replication, centromeres and rDNA positions have proven difficult to annotate with high confidence. Here, we demonstrate an unconventional application of Chromosome Conformation Capture (3C) technique, which typically aims at deciphering the average 3D organization of genomes, by showing how functional information about the sequence can be extracted solely from the chromosome contact map. RESULTS Specifically, we describe a combined experimental and bioinformatic procedure that determines the genomic positions of centromeres and ribosomal DNA clusters in yeasts, including species where classical computational approaches fail. For instance, we determined the centromere positions in Naumovozyma castellii, where these coordinates could not be obtained previously. Although computed centromere positions were characterized by conserved synteny with neighboring species, no consensus sequences could be found, suggesting that centromeric binding proteins or mechanisms have significantly diverged. We also used our approach to refine centromere positions in Kuraishia capsulata and to identify rDNA positions in Debaryomyces hansenii. Our study demonstrates how 3C data can be used to complete the functional annotation of eukaryotic genomes. AVAILABILITY AND IMPLEMENTATION The source code is provided in the Supplementary Material. This includes a zipped file with the Python code and a contact matrix of Saccharomyces cerevisiae. CONTACT romain.koszul@pasteur.fr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hervé Marie-Nelly
- Institut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, FranceInstitut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, FranceInstitut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, FranceInstitut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Agein
| | - Martial Marbouty
- Institut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, FranceInstitut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, France
| | - Axel Cournac
- Institut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, FranceInstitut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, France
| | - Gianni Liti
- Institut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, France
| | - Gilles Fischer
- Institut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, FranceInstitut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, France
| | - Christophe Zimmer
- Institut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, FranceInstitut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, France
| | - Romain Koszul
- Institut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, FranceInstitut Pasteur, Groupe Régulation Spatiale des Génomes, Department of Genomes and Genetics, CNRS, UMR 3525, Institut Pasteur, Unité Imagerie et Modélisation, Department of Cell Biology and Infection, CNRS, URA 2582, F-75015 Paris, France, Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284 - INSERM U108, Université de Nice Sophia Antipolis, 06107 Nice, France, CNRS, UMR7238, Biologie Computationnelle et Quantitative and Sorbonne Universités, UPMC Univ Paris 06, UMR7238, Biologie Computationnelle et Quantitative, F-75005, Paris, France
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Chu Q, Cai L, Fu Y, Chen X, Yan Z, Lin X, Zhou G, Han H, Widelitz RB, Chuong CM, Wu W, Yue Z. Dkk2/Frzb in the dermal papillae regulates feather regeneration. Dev Biol 2014; 387:167-78. [PMID: 24463139 DOI: 10.1016/j.ydbio.2014.01.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 12/20/2013] [Accepted: 01/13/2014] [Indexed: 01/06/2023]
Abstract
Avian feathers have robust growth and regeneration capability. To evaluate the contribution of signaling molecules and pathways in these processes, we profiled gene expression in the feather follicle using an absolute quantification approach. We identified hundreds of genes that mark specific components of the feather follicle: the dermal papillae (DP) which controls feather regeneration and axis formation, the pulp mesenchyme (Pp) which is derived from DP cells and nourishes the feather follicle, and the ramogenic zone epithelium (Erz) where a feather starts to branch. The feather DP is enriched in BMP/TGF-β signaling molecules and inhibitors for Wnt signaling including Dkk2/Frzb. Wnt ligands are mainly expressed in the feather epithelium and pulp. We find that while Wnt signaling is required for the maintenance of DP marker gene expression and feather regeneration, excessive Wnt signaling delays regeneration and reduces pulp formation. Manipulating Dkk2/Frzb expression by lentiviral-mediated overexpression, shRNA-knockdown, or by antibody neutralization resulted in dual feather axes formation. Our results suggest that the Wnt signaling in the proximal feather follicle is fine-tuned to accommodate feather regeneration and axis formation.
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Affiliation(s)
- Qiqi Chu
- Institute of Life Sciences, Fuzhou University, Fuzhou, # 2 Xue Yuan Road, University Campus, Fujian 350108, China
| | - Linyan Cai
- Institute of Life Sciences, Fuzhou University, Fuzhou, # 2 Xue Yuan Road, University Campus, Fujian 350108, China
| | - Yu Fu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xi Chen
- Institute of Life Sciences, Fuzhou University, Fuzhou, # 2 Xue Yuan Road, University Campus, Fujian 350108, China
| | - Zhipeng Yan
- Institute of Life Sciences, Fuzhou University, Fuzhou, # 2 Xue Yuan Road, University Campus, Fujian 350108, China
| | - Xiang Lin
- Institute of Life Sciences, Fuzhou University, Fuzhou, # 2 Xue Yuan Road, University Campus, Fujian 350108, China
| | - Guixuan Zhou
- Institute of Life Sciences, Fuzhou University, Fuzhou, # 2 Xue Yuan Road, University Campus, Fujian 350108, China
| | - Hao Han
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Randall B Widelitz
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA
| | - Cheng-ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA 90033, USA
| | - Wei Wu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhicao Yue
- Institute of Life Sciences, Fuzhou University, Fuzhou, # 2 Xue Yuan Road, University Campus, Fujian 350108, China.
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Fan P, Nie L, Jiang P, Feng J, Lv S, Chen X, Bao H, Guo J, Tai F, Wang J, Jia W, Li Y. Transcriptome analysis of Salicornia europaea under saline conditions revealed the adaptive primary metabolic pathways as early events to facilitate salt adaptation. PLoS One 2013; 8:e80595. [PMID: 24265831 PMCID: PMC3827210 DOI: 10.1371/journal.pone.0080595] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 10/04/2013] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Halophytes such as Salicornia europaea have evolved to exhibit unique mechanisms controlled by complex networks and regulated by numerous genes and interactions to adapt to habitats with high salinity. However, these mechanisms remain unknown. METHODS To investigate the mechanism by which halophytes tolerate salt based on changes in the whole transcriptome, we performed transcriptome sequencing and functional annotation by database search. Using the unigene database, we conducted digital gene expression analysis of S. europaea at various time points after these materials were treated with NaCl. We also quantified ion uptakes. Gene functional enrichment analysis was performed to determine the important pathways involved in this process. RESULTS A total of 57,151 unigenes with lengths of >300 bp were assembled, in which 57.5% of these unigenes were functionally annotated. Differentially expressed genes indicated that cell wall metabolism and lignin biosynthetic pathways were significantly enriched in S. europaea to promote the development of the xylem under saline conditions. This result is consistent with the increase in sodium uptake as ions pass through the xylem. Given that PSII efficiency remained unaltered, salt treatment activated the expression of electron transfer-related genes encoded by the chloroplast chromosome. Chlorophyll biosynthesis was also inhibited, indicating the energy-efficient state of the electron transfer system of S. europaea. CONCLUSIONS The key function of adjusting important primary metabolic pathways in salt adaption was identified by analyzing the changes in the transcriptome of S. europaea. These pathways could involve unique salt tolerance mechanisms in halophytes. This study also provided information as the basis of future investigations on salt response genes in S. europaea. Ample gene resources were also provided to improve the genes responsible for the salt tolerance ability of crops.
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Affiliation(s)
- Pengxiang Fan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Lingling Nie
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Ping Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Juanjuan Feng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Sulian Lv
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Xianyang Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Hexigeduleng Bao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Jie Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Fang Tai
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Jinhui Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Weitao Jia
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Yinxin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
- * E-mail:
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Bussotti G, Notredame C, Enright AJ. Detecting and comparing non-coding RNAs in the high-throughput era. Int J Mol Sci 2013; 14:15423-58. [PMID: 23887659 PMCID: PMC3759867 DOI: 10.3390/ijms140815423] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/16/2013] [Accepted: 07/17/2013] [Indexed: 02/07/2023] Open
Abstract
In recent years there has been a growing interest in the field of non-coding RNA. This surge is a direct consequence of the discovery of a huge number of new non-coding genes and of the finding that many of these transcripts are involved in key cellular functions. In this context, accurately detecting and comparing RNA sequences has become important. Aligning nucleotide sequences is a key requisite when searching for homologous genes. Accurate alignments reveal evolutionary relationships, conserved regions and more generally any biologically relevant pattern. Comparing RNA molecules is, however, a challenging task. The nucleotide alphabet is simpler and therefore less informative than that of amino-acids. Moreover for many non-coding RNAs, evolution is likely to be mostly constrained at the structural level and not at the sequence level. This results in very poor sequence conservation impeding comparison of these molecules. These difficulties define a context where new methods are urgently needed in order to exploit experimental results to their full potential. This review focuses on the comparative genomics of non-coding RNAs in the context of new sequencing technologies and especially dealing with two extremely important and timely research aspects: the development of new methods to align RNAs and the analysis of high-throughput data.
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Affiliation(s)
- Giovanni Bussotti
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; E-Mail:
| | - Cedric Notredame
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Aiguader, 88, 08003 Barcelona, Spain; E-Mail:
| | - Anton J. Enright
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; E-Mail:
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Zhernakova DV, de Klerk E, Westra HJ, Mastrokolias A, Amini S, Ariyurek Y, Jansen R, Penninx BW, Hottenga JJ, Willemsen G, de Geus EJ, Boomsma DI, Veldink JH, van den Berg LH, Wijmenga C, den Dunnen JT, van Ommen GJB, 't Hoen PAC, Franke L. DeepSAGE reveals genetic variants associated with alternative polyadenylation and expression of coding and non-coding transcripts. PLoS Genet 2013; 9:e1003594. [PMID: 23818875 PMCID: PMC3688553 DOI: 10.1371/journal.pgen.1003594] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/10/2013] [Indexed: 11/18/2022] Open
Abstract
Many disease-associated variants affect gene expression levels (expression quantitative trait loci, eQTLs) and expression profiling using next generation sequencing (NGS) technology is a powerful way to detect these eQTLs. We analyzed 94 total blood samples from healthy volunteers with DeepSAGE to gain specific insight into how genetic variants affect the expression of genes and lengths of 3′-untranslated regions (3′-UTRs). We detected previously unknown cis-eQTL effects for GWAS hits in disease- and physiology-associated traits. Apart from cis-eQTLs that are typically easily identifiable using microarrays or RNA-sequencing, DeepSAGE also revealed many cis-eQTLs for antisense and other non-coding transcripts, often in genomic regions containing retrotransposon-derived elements. We also identified and confirmed SNPs that affect the usage of alternative polyadenylation sites, thereby potentially influencing the stability of messenger RNAs (mRNA). We then combined the power of RNA-sequencing with DeepSAGE by performing a meta-analysis of three datasets, leading to the identification of many more cis-eQTLs. Our results indicate that DeepSAGE data is useful for eQTL mapping of known and unknown transcripts, and for identifying SNPs that affect alternative polyadenylation. Because of the inherent differences between DeepSAGE and RNA-sequencing, our complementary, integrative approach leads to greater insight into the molecular consequences of many disease-associated variants. Many genetic variants that are associated with diseases also affect gene expression levels. We used a next generation sequencing approach targeting 3′ transcript ends (DeepSAGE) to gain specific insight into how genetic variants affect the expression of genes and the usage and length of 3′-untranslated regions. We detected many associations for antisense and other non-coding transcripts, often in genomic regions containing retrotransposon-derived elements. Some of these variants are also associated with disease. We also identified and confirmed variants that affect the usage of alternative polyadenylation sites, thereby potentially influencing the stability of mRNAs. We conclude that DeepSAGE is useful for detecting eQTL effects on both known and unknown transcripts, and for identifying variants that affect alternative polyadenylation.
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Affiliation(s)
- Daria V. Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Eleonora de Klerk
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Harm-Jan Westra
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Anastasios Mastrokolias
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Shoaib Amini
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yavuz Ariyurek
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Genome Technology Center, Leiden, The Netherlands
| | - Rick Jansen
- Department of Psychiatry, The Netherlands Study of Depression and Anxiety, VU University Medical Center, Amsterdam, The Netherlands
| | - Brenda W. Penninx
- Department of Psychiatry, The Netherlands Study of Depression and Anxiety, VU University Medical Center, Amsterdam, The Netherlands
| | - Jouke J. Hottenga
- Department of Biological Psychology, Netherlands Twin Registry, VU University, Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Netherlands Twin Registry, VU University, Amsterdam, The Netherlands
| | - Eco J. de Geus
- Department of Biological Psychology, Netherlands Twin Registry, VU University, Amsterdam, The Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, Netherlands Twin Registry, VU University, Amsterdam, The Netherlands
| | - Jan H. Veldink
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Leonard H. van den Berg
- Department of Neurology, Rudolf Magnus Institute of Neuroscience, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Johan T. den Dunnen
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Genome Technology Center, Leiden, The Netherlands
| | - Gert-Jan B. van Ommen
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A. C. 't Hoen
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- * E-mail:
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Wang K, Chen Y. Analysis of a novel protein in human colorectal adenocarcinoma. Mol Med Rep 2013; 8:529-34. [PMID: 23778839 DOI: 10.3892/mmr.2013.1526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/29/2013] [Indexed: 11/05/2022] Open
Abstract
Colorectal adenocarcinoma (CRC) is the third most common type of cancer worldwide with a low 5‑year survival rate. The present study aimed to investigate the structure and function of a novel protein identified from human colorectal adenocarcinoma (CRC). A differentially expressed sequence tag (GenBank accession number, ES274081) was collected from GenBank. Bioinformatics tools were employed to obtain the sequence of the full‑length cDNA in order to localize the open reading frame and to predict the protein sequence. Mass spectro-metry was used to analyze the structure of this novel protein and western blot analysis was used to confirm the expression of this protein in human CRC tissue samples. The full‑length cDNA was composed of 4,283‑bp nucleotides and the sequence information was obtained (GenBank accession number, NM_001013649). The corresponding protein molecule contained 165 amino acids, with a monoisotopic molecular weight of 18.6033 kDa and an isoelectric point of 8.43, determined by mass spectrometry. The protein structure and its function in adenocarcinoma were further explored. In the present study, a novel protein, which may be involved in nuclear signal transduction, was identified using bioinformatics, mass spectrometry and western blot analysis.
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Affiliation(s)
- Kaicheng Wang
- Department of Anatomy, Premedical and Forensic Medical Institute, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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