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Qin T, Sun C, Kazim A, Cui S, Wang Y, Richard D, Yao P, Bi Z, Liu Y, Bai J. Comparative Transcriptome Analysis of Deep-Rooting and Shallow-Rooting Potato ( Solanum tuberosum L.) Genotypes under Drought Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:2024. [PMID: 35956505 PMCID: PMC9370241 DOI: 10.3390/plants11152024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/26/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
The selection and breeding of deep rooting and drought-tolerant varieties has become a promising approach for improving the yield and adaptability of potato (Solanum tuberosum L.) in arid and semiarid areas. Therefore, the discovery of root-development-related genes and drought tolerance signaling pathways in potato is important. In this study, we used deep-rooting (C119) and shallow-rooting (C16) potato genotypes, with different levels of drought tolerance, to achieve this objective. Both genotypes were treated with 150 mM mannitol for 0 h (T0), 2 h (T2), 6 h (T6), 12 h (T12), and 24 h (T24), and their root tissues were subjected to comparative transcriptome analysis. A total of 531, 1571, 1247, and 3540 differentially expressed genes (DEGs) in C16 and 1531, 1108, 674, and 4850 DEGs in C119 were identified in T2 vs. T0, T6 vs. T2, T12 vs. T6, and T24 vs. T12 comparisons, respectively. Gene expression analysis indicated that a delay in the onset of drought-induced transcriptional changes in C16 compared with C119. Functional enrichment analysis revealed genotype-specific biological processes involved in drought stress tolerance. The metabolic pathways of plant hormone transduction and MAPK signaling were heavily involved in the resistance of C16 and C119 to drought, while abscisic acid (ABA), ethylene, and salicylic acid signal transduction pathways likely played more important roles in C119 stress responses. Furthermore, genes involved in root cell elongation and division showed differential expression between the two genotypes under drought stress. Overall, this study provides important information for the marker-assisted selection and breeding of drought-tolerant potato genotypes.
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Affiliation(s)
- Tianyuan Qin
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Chao Sun
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Ali Kazim
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan;
| | - Song Cui
- School of Agriculture, Middle Tennessee State University, Murfreesboro, TN 37132, USA;
| | - Yihao Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Dormatey Richard
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Panfeng Yao
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Zhenzhen Bi
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Yuhui Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
| | - Jiangping Bai
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (T.Q.); (C.S.); (Y.W.); (D.R.); (P.Y.); (Z.B.); (Y.L.)
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Chen W, Yan X, Yang A, Xu A, Huang T, You H. miRNA-150-5p promotes hepatic stellate cell proliferation and sensitizes hepatocyte apoptosis during liver fibrosis. Epigenomics 2019; 12:53-67. [PMID: 31833387 DOI: 10.2217/epi-2019-0104] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aim: To explore the role of miRNA-150-5p (miR-150-5p) in liver fibrosis. Materials & methods: miRNA expression profiles, CCl4-induced liver fibrosis progression and regression rodent models, quantitative real-time PCR, miR-150-5p mimics and inhibitors, cell proliferation and apoptosis detection, RNA sequencing and bioinformatics analysis were employed. Results: Liver tissue miR-150-5p expression was positively associated with liver fibrosis progression and regression; however, miR-150-5p exhibited a cell-specific expression pattern, namely, it was enhanced in hepatocytes but reduced in hepatic stellate cells (HSCs) during liver fibrosis; miR-150-5p overexpression promoted HSC apoptosis and sensitized hepatocyte apoptosis; miR-150-5p mimic had a larger influence on the transcriptomic stability of HSCs than that of hepatocytes; miR-150-5p mediated activation of interferon signaling pathways might be responsible for HSC apoptosis. Conclusion: miR-150-5p exhibited an opposite regulation and function pattern between HSCs and hepatocytes during liver fibrosis.
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Affiliation(s)
- Wei Chen
- Experimental & Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, PR China.,Beijing Key Laboratory of Tolerance Induction & Organ Protection in Transplantation, Beijing Friendship Hospital, Capital Medical University, Beijing, PR China
| | - Xuzhen Yan
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, PR China
| | - Aiting Yang
- Experimental & Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, PR China.,Beijing Key Laboratory of Tolerance Induction & Organ Protection in Transplantation, Beijing Friendship Hospital, Capital Medical University, Beijing, PR China
| | - Anjian Xu
- Experimental & Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, PR China.,Beijing Key Laboratory of Tolerance Induction & Organ Protection in Transplantation, Beijing Friendship Hospital, Capital Medical University, Beijing, PR China
| | - Tao Huang
- Experimental & Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, PR China.,Beijing Key Laboratory of Tolerance Induction & Organ Protection in Transplantation, Beijing Friendship Hospital, Capital Medical University, Beijing, PR China
| | - Hong You
- Experimental & Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, PR China.,Beijing Key Laboratory of Tolerance Induction & Organ Protection in Transplantation, Beijing Friendship Hospital, Capital Medical University, Beijing, PR China.,Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, PR China
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Islam R, Lai C. A Brief Overview of lncRNAs in Endothelial Dysfunction-Associated Diseases: From Discovery to Characterization. EPIGENOMES 2019; 3:epigenomes3030020. [PMID: 34968230 PMCID: PMC8594677 DOI: 10.3390/epigenomes3030020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 11/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a novel class of regulatory RNA molecules and they are involved in many biological processes and disease developments. Several unique features of lncRNAs have been identified, such as tissue-and/or cell-specific expression pattern, which suggest that they could be potential candidates for therapeutic and diagnostic applications. More recently, the scope of lncRNA studies has been extended to endothelial biology research. Many of lncRNAs were found to be critically involved in the regulation of endothelial function and its associated disease progression. An improved understanding of endothelial biology can thus facilitate the discovery of novel biomarkers and therapeutic targets for endothelial dysfunction-associated diseases, such as abnormal angiogenesis, hypertension, diabetes, and atherosclerosis. Nevertheless, the underlying mechanism of lncRNA remains undefined in previous published studies. Therefore, in this review, we aimed to discuss the current methodologies for discovering and investigating the functions of lncRNAs and, in particular, to address the functions of selected lncRNAs in endothelial dysfunction-associated diseases.
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Affiliation(s)
- Rashidul Islam
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong, China;
| | - Christopher Lai
- Health and Social Sciences Cluster, Singapore Institute of Technology, Singapore 138683, Singapore
- Correspondence: ; Tel.: +65-6592-1045
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Zhang X, Sun L, Chen W, Wu S, Li Y, Li X, Zhang B, Yao J, Wang H, Xu A. ARHGEF4-mediates the actin cytoskeleton reorganization of hepatic stellate cells in 3-dimensional collagen matrices. Cell Adh Migr 2019; 13:169-181. [PMID: 30871422 PMCID: PMC6527375 DOI: 10.1080/19336918.2019.1594497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The actin cytoskeleton of hepatic stellate cells (HSCs) is reorganized when they are cultured in 3D collagen matrices. Here, we investigated the molecular mechanism of actin cytoskeleton reorganization in HSCs cultured in 3D floating collagen matrices (FCM) compared to those on 2D polystyrene surfaces (PS). First, we found that the generation of dendritic cellular processes was controlled by Rac1. Next, we examined the differential gene expression of HSCs cultured on 2D PS and in 3D FCM by RNA-Seq and focused on the changes of actin cytoskeleton reorganization-related molecular components and guanine nucleotide exchange factors (GEFs). The results showed that the expression of genes associated with actin cytoskeleton reorganization-related cellular components, filopodia and lamellipodia, were significantly decreased, but podosome-related genes was significantly increased in 3D FCM. Furthermore, we found that a Rac1-specific GEF, ARHGEF4, played roles in morphological changes, migration and podosome-related gene expression in HSCs cultured in 3D FCM. Abbreviations: 2D PS: 2-dimensional polystyrene surface; 3D FCM: 3-dimensional floating collagen matrices; ARHGEF4: Rho guanine nucleotide exchange factor 4; ARHGEF6: Rho guanine nucleotide exchange factor 6; GEF: guanine nucleotide exchange factor; HSC: hepatic stellate cell
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Affiliation(s)
- Xiaowei Zhang
- b State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , China
| | - Lan Sun
- c Department of Pathology, Beijing Friendship Hospital , Capital Medical University , Beijing , China
| | - Wei Chen
- a Experimental Center, Beijing Friendship Hospital , Capital Medical University , Beijing , China
| | - Shanna Wu
- d Clinical Laboratory Center, Beijing Friendship Hospital , Capital Medical University , Beijing , China
| | - Yanmeng Li
- a Experimental Center, Beijing Friendship Hospital , Capital Medical University , Beijing , China
| | - Xiaojin Li
- a Experimental Center, Beijing Friendship Hospital , Capital Medical University , Beijing , China
| | - Bei Zhang
- a Experimental Center, Beijing Friendship Hospital , Capital Medical University , Beijing , China
| | - Jingyi Yao
- a Experimental Center, Beijing Friendship Hospital , Capital Medical University , Beijing , China
| | - Huan Wang
- a Experimental Center, Beijing Friendship Hospital , Capital Medical University , Beijing , China
| | - Anjian Xu
- a Experimental Center, Beijing Friendship Hospital , Capital Medical University , Beijing , China
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Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly. BMC Bioinformatics 2017; 18:382. [PMID: 28984182 PMCID: PMC5629565 DOI: 10.1186/s12859-017-1801-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background It is generally thought that most canonical or non-canonical splicing events involving U2- and U12 spliceosomes occur within nuclear pre-mRNAs. However, the question of whether at least some U12-type splicing occurs in the cytoplasm is still unclear. In recent years next-generation sequencing technologies have revolutionized the field. The “Read-Split-Walk” (RSW) and “Read-Split-Run” (RSR) methods were developed to identify genome-wide non-canonical spliced regions including special events occurring in cytoplasm. As the significant amount of genome/transcriptome data such as, Encyclopedia of DNA Elements (ENCODE) project, have been generated, we have advanced a newer more memory-efficient version of the algorithm, “Read-Split-Fly” (RSF), which can detect non-canonical spliced regions with higher sensitivity and improved speed. The RSF algorithm also outputs the spliced sequences for further downstream biological function analysis. Results We used open access ENCODE project RNA-Seq data to search spliced intron sequences against the U12-type spliced intron sequence database to examine whether some events could occur as potential signatures of U12-type splicing. The check was performed by searching spliced sequences against 5’ss and 3’ss sequences from the well-known orthologous U12-type spliceosomal intron database U12DB. Preliminary results of searching 70 ENCODE samples indicated that the presence of 5’ss with U12-type signature is more frequent than U2-type and prevalent in non-canonical junctions reported by RSF. The selected spliced sequences have also been further studied using miRBase to elucidate their functionality. Preliminary results from 70 samples of ENCODE datasets show that several miRNAs are prevalent in studied ENCODE samples. Two of these are associated with many diseases as suggested in the literature. Specifically, hsa-miR-1273 and hsa-miR-548 are associated with many diseases and cancers. Conclusions Our RSF pipeline is able to detect many possible junctions (especially those with a high RPKM) with very high overall accuracy and relative high accuracy for novel junctions. We have incorporated useful parameter features into the pipeline such as, handling variable-length read data, and searching spliced sequences for splicing signatures and miRNA events. We suggest RSF, a tool for identifying novel splicing events, is applicable to study a range of diseases across biological systems under different experimental conditions. Electronic supplementary material The online version of this article (10.1186/s12859-017-1801-y) contains supplementary material, which is available to authorized users.
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Ding L, Rath E, Bai Y. Comparison of Alternative Splicing Junction Detection Tools Using RNA-Seq Data. Curr Genomics 2017; 18:268-277. [PMID: 28659722 PMCID: PMC5476949 DOI: 10.2174/1389202918666170215125048] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/28/2016] [Accepted: 12/01/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) is a posttranscriptional process that produces differ-ent transcripts from the same gene and is important to produce diverse protein products in response to environmental stimuli. AS occurs at specific sites on the mRNA sequence, some of which have been de-fined. Multiple bioinformatics tools have been developed to detect AS from experimental data. OBJECTIVES The goal of this review is to help researchers use specific tools to aid their research and to develop new AS detection tools based on these previously established tools. METHOD We selected 15 AS detection tools that were recently published; we classified and delineated them on several aspects. Also, a performance comparison of these tools with the same starting input was conducted. RESULT We reviewed the following categorized features of the tools: Publication information, working principles, generic and distinct workflows, running platform, input data requirement, sequencing depth dependency, reads mapped to multiple locations, isoform annotation basis, precise detected AS types, and performance benchmarks. CONCLUSION Through comparisons of these tools, we provide a panorama of the advantages and short-comings of each tool and their scopes of application.
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Affiliation(s)
| | | | - Yongsheng Bai
- Department of Biology.,The Center for Genomic Advocacy, Indiana State University, Terre Haute, IN, USA
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The impact of the RBM4-initiated splicing cascade on modulating the carcinogenic signature of colorectal cancer cells. Sci Rep 2017; 7:44204. [PMID: 28276498 PMCID: PMC5343574 DOI: 10.1038/srep44204] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/06/2017] [Indexed: 12/31/2022] Open
Abstract
A growing body of studies has demonstrated that dysregulated splicing profiles constitute pivotal mechanisms for carcinogenesis. In this study, we identified discriminative splicing profiles of colorectal cancer (CRC) cells compared to adjacent normal tissues using deep RNA-sequencing (RNA-seq). The RNA-seq results and cohort studies indicated a relatively high ratio of exon 4-excluded neuro-oncological ventral antigen 1 (Nova1−4) and intron 2-retained SRSF6 (SRSF6+intron 2) transcripts in CRC tissues and cell lines. Nova1 variants exhibited differential effects on eliminating SRSF6 expression in CRC cells by inducing SRSF6+intron 2 transcripts which were considered to be the putative target of alternative splicing-coupled nonsense-mediated decay mechanism. Moreover, the splicing profile of vascular endothelial growth factor (VEGF)165/VEGF165b transcripts was relevant to SRSF6 expression, which manipulates the progression of CRC calls. These results highlight the novel and hierarchical role of an alternative splicing cascade that is involved in the development of CRC.
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Huang K, Liu Y, Huang Y, Li L, Cooper L, Ruan J, Zhao Z. Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science. BMC Genomics 2016; 17 Suppl 7:524. [PMID: 27556295 PMCID: PMC5001210 DOI: 10.1186/s12864-016-2893-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We summarize the 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) and the editorial report of the supplement to BMC Genomics. The supplement includes 20 research articles selected from the manuscripts submitted to ICIBM 2015. The conference was held on November 13-15, 2015 at Indianapolis, Indiana, USA. It included eight scientific sessions, three tutorials, four keynote presentations, three highlight talks, and a poster session that covered current research in bioinformatics, systems biology, computational biology, biotechnologies, and computational medicine.
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Affiliation(s)
- Kun Huang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210 USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Yufei Huang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX 78249 USA
| | - Lang Li
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Lee Cooper
- Department of Biomedical Informatics, Emory University, Atlanta, GA 30322 USA
- Department of Biomedical Engineering, Emory University / Georgia Institute of Technology, Atlanta, GA 30322 USA
| | - Jianhua Ruan
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249 USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
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