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Hoshizaki J, Adjalley SH, Thathy V, Judge K, Berriman M, Reid AJ, Lee MCS. A manually curated annotation characterises genomic features of P. falciparum lncRNAs. BMC Genomics 2022; 23:780. [PMID: 36451097 PMCID: PMC9710153 DOI: 10.1186/s12864-022-09017-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Important regulation occurs at the level of transcription in Plasmodium falciparum and growing evidence suggests that these apicomplexan parasites have complex regulatory networks. Recent studies implicate long noncoding RNAs (lncRNAs) as transcriptional regulators in P. falciparum. However, due to limited research and the lack of necessary experimental tools, our understanding of their role in the malaria-causing parasite remains largely unelucidated. In this work, we address one of these limitations, the lack of an updated and improved lncRNA annotation in P. falciparum. RESULTS We generated long-read RNA sequencing data and integrated information extracted and curated from multiple sources to manually annotate lncRNAs. We identified 1119 novel lncRNAs and validated and refined 1250 existing annotations. Utilising the collated datasets, we generated evidence-based ranking scores for each annotation and characterised the distinct genomic contexts and features of P. falciparum lncRNAs. Certain features indicated subsets with potential biological significance such as 25 lncRNAs containing multiple introns, 335 lncRNAs lacking mutations in piggyBac mutagenic studies and lncRNAs associated with specific biologic processes including two new types of lncRNAs found proximal to var genes. CONCLUSIONS The insights and the annotation presented in this study will serve as valuable tools for researchers seeking to understand the role of lncRNAs in parasite biology through both bioinformatics and experimental approaches.
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Affiliation(s)
- Johanna Hoshizaki
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Sophie H. Adjalley
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK ,Micrographia Bio, London, W12 0BZ UK
| | - Vandana Thathy
- grid.4991.50000 0004 1936 8948MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS UK ,grid.239585.00000 0001 2285 2675Present address: Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY10032 USA
| | - Kim Judge
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Matthew Berriman
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK ,grid.8756.c0000 0001 2193 314XWellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, G12 8TA UK
| | - Adam J. Reid
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK ,grid.5335.00000000121885934Present address: Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN UK
| | - Marcus C. S. Lee
- grid.52788.300000 0004 0427 7672Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
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Hong L, Hu Q, Zang X, Xie Y, Zhou C, Zou X, Li Y, Deng M, Guo Y, Liu G, Liu D. Analysis and Screening of Reproductive Long Non-coding RNAs Through Genome-Wide Analyses of Goat Endometrium During the Pre-attachment Phase. Front Genet 2020; 11:568017. [PMID: 33193661 PMCID: PMC7649795 DOI: 10.3389/fgene.2020.568017] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/05/2020] [Indexed: 11/30/2022] Open
Abstract
Reproduction in goat is highly impeded by implantation failure. Of concern, the underlying mechanism leading to embryo implantation remains unclear. In this study, deep sequencing was employed through strand-specific Ribo-Zero RNA-Seq to characterize transcriptome changes in the endometrium during the maternal recognition of pregnancy. A total of 996 differential transcripts (115 lncRNAs and 881 mRNAs) existing between the pregnant and non-pregnant endometrium were revealed through bioinformatics analysis. The screening was performed on lncRNAs (XR_001918173.1, LNC_002760, and LNC_000599) and LNC_009053, to determine their potential role in regulating the synthesis of retinol and endometrium remolding through the proteasome pathway, respectively. The hypothesis of whether certain lncRNAs, namely, LNC_007223, LNC_005256, and LNC_010092 could play important roles in embryo implantation was tested. These novel findings are of paramount relevance to further elucidate the molecular mechanisms of embryo implantation and uncover new targets to improve goat reproduction.
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Affiliation(s)
- Linjun Hong
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Qun Hu
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Xupeng Zang
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Yanshe Xie
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Chen Zhou
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Xian Zou
- College of Animal Science, South China Agricultural University, Guangzhou, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Ming Deng
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Yongqing Guo
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
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Abla M, Sun H, Li Z, Wei C, Gao F, Zhou Y, Feng J. Identification of miRNAs and Their Response to Cold Stress in Astragalus Membranaceus. Biomolecules 2019; 9:biom9050182. [PMID: 31083391 PMCID: PMC6572118 DOI: 10.3390/biom9050182] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 04/29/2019] [Accepted: 05/09/2019] [Indexed: 12/17/2022] Open
Abstract
Astragalus membranaceus is an important medicinal plant widely cultivated in East Asia. MicroRNAs (miRNAs) are endogenous regulatory molecules that play essential roles in plant growth, development, and the response to environmental stresses. Cold is one of the key environmental factors affecting the yield and quality of A. membranaceus, and miRNAs may mediate the gene regulation network under cold stress in A. membranaceus. To identify miRNAs and reveal their functions in cold stress response in A. membranaceus, small RNA sequencing was conducted followed by bioinformatics analysis, and quantitative real time PCR (qRT-PCR) analysis was performed to profile the expression of miRNAs under cold stress. A total of 168 conserved miRNAs belonging to 34 families and 14 putative non-conserved miRNAs were identified. Many miRNA targets were predicted and these targets were involved in diversified regulatory and metabolic pathways. By using qRT-PCR, 27 miRNAs were found to be responsive to cold stress, including 4 cold stress-induced and 17 cold-repressed conserved miRNAs, and 6 cold-induced non-conserved miRNAs. These cold-responsive miRNAs probably mediate the response to cold stress by regulating development, hormone signaling, defense, redox homeostasis, and secondary metabolism in A. membranaceus. These cold-corresponsive miRNAs may be used as the candidate genes in further molecular breeding for improving cold tolerance of A. membranaceus.
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Affiliation(s)
- Merhaba Abla
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Huigai Sun
- School of Pharmacology, Hebei University of Chinese Medicine, Shijiazhuang 050200, China.
| | - Zhuyun Li
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Chunxiang Wei
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Fei Gao
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Yijun Zhou
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Jinchao Feng
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
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