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Xu C, Gao L, Li J, Shen L, Liang H, Luan K, Wu X. Prediction of RNA secondary structure based on stem region replacement using the RSRNA algorithm. Comput Methods Biomech Biomed Engin 2020; 24:101-114. [PMID: 32901523 DOI: 10.1080/10255842.2020.1813280] [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] [Indexed: 12/14/2022]
Abstract
RNA functions, including the regulation of various cellular activities, seem to be closely related to its structure. However, accurately predicting RNA secondary structures can be difficult. Structural prediction can be achieved by selecting stem areas that are suitable and compatible from stem pools. Here, we propose a method for predicting the secondary structure of non-coding RNA based on stem region substitution, which we named RSRNA. This method is compatible with nested RNA secondary structures, while reducing any randomness. Our algorithm had higher performance and prediction accuracy than other algorithms, which deems it more effective for future RNA structure studies.
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Affiliation(s)
- Chengzhen Xu
- School of Computer Science and Technology, Huaibei Normal University, Huaibei, China.,College of Life Sciences, Huaibei Normal University, Huaibei, China
| | - Longjian Gao
- School of Computer Science and Technology, Huaibei Normal University, Huaibei, China
| | - Jin Li
- College of Automation, Harbin Engineering University, Harbin, China
| | - Longfeng Shen
- School of Computer Science and Technology, Huaibei Normal University, Huaibei, China
| | - Hong Liang
- College of Automation, Harbin Engineering University, Harbin, China
| | - Kuan Luan
- College of Automation, Harbin Engineering University, Harbin, China
| | - Xiaomin Wu
- College of Life Sciences, Huaibei Normal University, Huaibei, China
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2
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Hicks JA, Trakooljul N, Liu HC. Alterations in cellular and viral microRNA and cellular gene expression in Marek's disease virus-transformed T-cell lines treated with sodium butyrate. Poult Sci 2019; 98:642-652. [PMID: 30184155 DOI: 10.3382/ps/pey412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/09/2018] [Indexed: 11/20/2022] Open
Abstract
A shared feature of herpesviruses is their ability to enter a latent state following an initially lytic infection. Marek's disease virus serotype 1 (MDV-1) is an oncogenic avian herpesvirus. Small RNA profiling studies have suggested that microRNAs (miRNAs) are involved in viral latency. Sodium butyrate treatment is known to induce herpesvirus reactivation. The present study was undertaken to determine transcriptome and miRNome changes induced by sodium butyrate in 2 MDV-transformed cell lines, RP2 and CU115. In the first 24 h post-treatment, microarray analysis of transcriptional changes in cell lines RP2 and CU115 identified 137 and 114 differentially expressed genes, respectively. Small RNA deep-sequencing analysis identified 17 cellular miRNAs that were differentially expressed. The expression of MDV-encoded miRNAs was also altered upon treatment. Many of the genes and miRNAs that are differentially expressed are involved in regulation of the cell cycle, mitosis, DNA metabolism, and lymphocyte differentiation.
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Affiliation(s)
- Julie A Hicks
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Nares Trakooljul
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Hsiao-Ching Liu
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, USA
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Islam W, Noman A, Qasim M, Wang L. Plant Responses to Pathogen Attack: Small RNAs in Focus. Int J Mol Sci 2018; 19:E515. [PMID: 29419801 PMCID: PMC5855737 DOI: 10.3390/ijms19020515] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/04/2018] [Accepted: 02/05/2018] [Indexed: 12/25/2022] Open
Abstract
Small RNAs (sRNA) are a significant group of gene expression regulators for multiple biological processes in eukaryotes. In plants, many sRNA silencing pathways produce extensive array of sRNAs with specialized roles. The evidence on record advocates for the functions of sRNAs during plant microbe interactions. Host sRNAs are reckoned as mandatory elements of plant defense. sRNAs involved in plant defense processes via different pathways include both short interfering RNA (siRNA) and microRNA (miRNA) that actively regulate immunity in response to pathogenic attack via tackling pathogen-associated molecular patterns (PAMPs) and other effectors. In response to pathogen attack, plants protect themselves with the help of sRNA-dependent immune systems. That sRNA-mediated plant defense responses play a role during infections is an established fact. However, the regulations of several sRNAs still need extensive research. In this review, we discussed the topical advancements and findings relevant to pathogen attack and plant defense mediated by sRNAs. We attempted to point out diverse sRNAs as key defenders in plant systems. It is hoped that sRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases.
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Affiliation(s)
- Waqar Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad 38040, Pakistan.
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Muhammad Qasim
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Liande Wang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Mengardi C, Limousin T, Ricci EP, Soto-Rifo R, Decimo D, Ohlmann T. microRNAs stimulate translation initiation mediated by HCV-like IRESes. Nucleic Acids Res 2017; 45:4810-4824. [PMID: 28077561 PMCID: PMC5416841 DOI: 10.1093/nar/gkw1345] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 12/22/2016] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression by recognizing and hybridizing to a specific sequence generally located in the 3΄ untranslated region (UTR) of targeted mRNAs. miRNA-induced inhibition of translation occurs during the initiation step, most probably at the level of ribosome scanning. In this process, the RNA-induced silencing complex interacts both with PABP and the 43S pre-initiation complex to disrupt scanning of the 40S ribosome. However, in some specific cases, miRNAs can stimulate translation. Although the mechanism of miRNA-mediated upregulation is unknown, it appears that the poly(A) tail and the lack of availability of the TNRC6 proteins are amongst major determinants. The genomic RNA of the Hepatitis C Virus is uncapped, non-polyadenylated and harbors a peculiar internal ribosome entry site (IRES) that binds the ribosome directly to the AUG codon. Thus, we have exploited the unique properties of the HCV IRES and other related IRESes (HCV-like) to study how translation initiation can be modulated by miRNAs on these elements. Here, we report that miRNA binding to the 3΄ UTR can stimulate translation of a reporter gene given that its expression is driven by an HCV-like IRES and that it lacks a poly(A) tail at its 3΄ extremity.
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Affiliation(s)
- Chloé Mengardi
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Taran Limousin
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Emiliano P Ricci
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Ricardo Soto-Rifo
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Didier Decimo
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
| | - Théophile Ohlmann
- CIRI, International Center for Infectiology Research, Université de Lyon, 69364 Lyon, France.,INSERM, U1111, Lyon, France.,Ecole Normale Supérieure de Lyon, Lyon, France.,Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France.,CNRS, UMR5308, Lyon, France
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Li Y, Zheng G, Zhang Y, Yang X, Liu H, Chang H, Wang X, Zhao J, Wang C, Chen L. MicroRNA analysis in mouse neuro-2a cells after pseudorabies virus infection. J Neurovirol 2017; 23:430-440. [PMID: 28130759 DOI: 10.1007/s13365-016-0511-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/23/2016] [Accepted: 12/29/2016] [Indexed: 11/30/2022]
Abstract
Pseudorabies virus (PRV), an alpha herpesvirus can enter the mammalian nervous system, causing Aujezsky's disease. Previous studies have reported an alteration of microRNA (miRNA) expression levels during PRV infections. However, knowledge regarding miRNA response in nervous cells to PRV infection is still unknown. To address this issue, small RNA libraries from infected and uninfected mouse neuroblastoma cells were assessed after Illumina deep sequencing. A total of eight viral miRNA were identified, and ten host miRNAs showed significantly different expression upon PRV infection. Among these, five were analyzed by stem-loop RT-qPCR, which confirmed the above data. Interestingly, these viral miRNAs were mainly found in the large latency transcript region of PRV, and predicted to target a variety of genes, forming a complicated regulatory network. Moreover, ten cellular miRNAs were expressed differently upon PRV infection, including nine upregulated and one downregulated miRNAs. Host targets of these miRNAs obtained by bioinformatics analysis belonged to large signaling networks, mainly encompassing calcium signaling pathway, cAMP signaling pathway, MAPK signaling pathway, and other nervous-associated pathways. These findings further highlighted miRNA features in nervous cells after PRV infection and contributed to unveil the underlying mechanisms of neurotropism as well as the neuropathogenesis of PRV.
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Affiliation(s)
- Yongtao Li
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guanmin Zheng
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yujuan Zhang
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xia Yang
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongying Liu
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongtao Chang
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xinwei Wang
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jun Zhao
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chuanqing Wang
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lu Chen
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China.
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Promoter Targeting RNAs: Unexpected Contributors to the Control of HIV-1 Transcription. MOLECULAR THERAPY-NUCLEIC ACIDS 2015; 4:e222. [PMID: 25625613 PMCID: PMC4345301 DOI: 10.1038/mtna.2014.67] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 11/01/2014] [Indexed: 11/22/2022]
Abstract
In spite of prolonged and intensive treatment with combined antiretroviral therapy (cART), which efficiently suppresses plasma viremia, the integrated provirus of HIV-1 persists in resting memory CD4+ T cells as latent infection. Treatment with cART does not substantially reduce the burden of latent infection. Once cART is ceased, HIV-1 replication recrudesces from these reservoirs in the overwhelming majority of patients. There is increasing evidence supporting a role for noncoding RNAs (ncRNA), including microRNAs (miRNAs), antisense (as)RNAs, and short interfering (si)RNA in the regulation of HIV-1 transcription. This appears to be mediated by interaction with the HIV-1 promoter region. Viral miRNAs have the potential to act as positive or negative regulators of HIV transcription. Moreover, inhibition of virally encoded long-asRNA can induce positive transcriptional regulation, while antisense strands of siRNA targeting the NF-κB region suppress viral transcription. An in-depth understanding of the interaction between ncRNAs and the HIV-1 U3 promoter region may lead to new approaches for the control of HIV reservoirs. This review focuses on promoter associated ncRNAs, with particular emphasis on their role in determining whether HIV-1 establishes active or latent infection.
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