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Circular RNA–MicroRNA–MRNA interaction predictions in SARS-CoV-2 infection

Yılmaz Mehmet Demirci, Müşerref Duygu Saçar Demirci
2021 Journal of Integrative Bioinformatics  
In this work, a machine learning based miRNA analysis workflow was developed to predict differential expression patterns of human miRNAs during SARS-CoV-2 infection.  ...  Since miRNAs seem to be involved in host–pathogen interactions, many studies attempted to identify whether human miRNAs could target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNAs as  ...  In addition, a comprehensive circRNA-miRNA-mRNA targeting network analysis is performed to identify biologically significant processes in SARS-CoV-2 infection.  ... 
doi:10.1515/jib-2020-0047 pmid:33725751 fatcat:li7ckr5f2veqvfktmmp7dio5zq

SARS-CoV-2 and miRNA-like inhibition power [article]

Jacques Demongeot, Hervé Seligmann
2020 arXiv   pre-print
immune response as described by clinicians; (2) Methods: We compare RNA subsequences of SARS-CoV-2 protein S and RNA-dependent RNA polymerase genes to mRNA sequences of beta-globin and type I interferons  ...  ; (3) Results: RNA subsequences longer than eight nucleotides from SARS-CoV-2 genome could hybridize subsequences of the mRNA of beta-globin and of type I interferons; (4) Conclusions: Beyond viral protein  ...  We can also notice the resemblance of a SARS-CoV-2 sub-sequence with hsa-miR-let-7b, the microRNA the most upregulated in Kawasaki disease [43] described as potentially linked to SARS-CoV-2 infection  ... 
arXiv:2008.00126v1 fatcat:jffhnkwbmffvzptjdyvlcdugru

The miRNA: a small but powerful RNA for COVID-19

Song Zhang, Kuerbannisha Amahong, Xiuna Sun, Xichen Lian, Jin Liu, Huaicheng Sun, Yan Lou, Feng Zhu, Yunqing Qiu
2021 Briefings in Bioinformatics  
A few scattered studies used bioinformatics methods to explore the role of microRNA (miRNA) in COVID-19 infection.  ...  In detail, SARS-CoV-2 can be regarded as a sponge to adsorb host immune-related miRNA, which forces host fall into dysfunction status of immune system.  ...  2 (SARS-CoV-2), a single-stranded RNA virus with high similarity in its genome and symptoms with SARS-CoV epidemic in 2002-04 [2] .  ... 
doi:10.1093/bib/bbab062 pmid:33675361 pmcid:PMC7989616 fatcat:zumfh7yhhbaujpt27j6ycu5nri

Co-Regulation of Protein Coding Genes by Transcription Factor and Long Non-Coding RNA in SARS-CoV-2 Infected Cells: An In Silico Analysis

Chinmay Saha, Sayantan Laha, Raghunath Chatterjee, Nitai P. Bhattacharyya
2021 Non-Coding RNA  
Many targets of deregulated lncRNA could also interact with SARS-CoV-2 coded proteins, modulated by IFN treatment and identified in CRISPR screening to modulate SARS-CoV-2 infection.  ...  Altered expression of protein coding gene (PCG) and long non-coding RNA (lncRNA) have been identified in SARS-CoV-2 infected cells and tissues from COVID-19 patients.  ...  Deregulation of microRNA and Circular RNAs in SARS-CoV-2 Infected Cells Altered expression of microRNA, the negative regulator of PCG, has been observed in different viral infections including SARS-CoV  ... 
doi:10.3390/ncrna7040074 pmid:34940755 pmcid:PMC8708613 fatcat:7wrzkofkyfcdlje4m6h4funavy

MicroRNAs and Long Non-Coding RNAs as Potential Candidates to Target Specific Motifs of SARS-CoV-2

Lucia Natarelli, Luca Parca, Tommaso Mazza, Christian Weber, Fabio Virgili, Deborah Fratantonio
2021 Non-Coding RNA  
Notably, some of the non-coding RNAs identified in our study as candidates for inhibiting SARS-CoV-2 gene expression have already been proposed against diverse viral infections, pulmonary arterial hypertension  ...  Here, we report a computational study demonstrating the existence of target motifs in the SARS-CoV-2 genome suitable for specific binding with endogenous human micro and long non-coding RNAs (miRNAs and  ...  oligosequences, in example circular RNAs.  ... 
doi:10.3390/ncrna7010014 pmid:33670580 fatcat:ihddh32oujcljflyyysqodbu2u

Perversely expressed long noncoding RNAs can alter host response and viral proliferation in SARS-CoV-2 infection [article]

Rafeed Rahman Turjya, Md. Abdullah-Al-Kamran Khan, Abul B.M.M.K. Islam
2020 bioRxiv   pre-print
To elucidate possible functions of lncRNAs in the COVID-19 pathobiology, we have utilized RNA-seq dataset of SARS-CoV-2 infected lung epithelial cells.  ...  , HECTD1, LARP4B, LARP7, MIPOL1, UPF1, MOV10 and PRKAR2A, host genes that interact with SARS-CoV-2 proteins.  ...  with SARS-CoV--7f can target 20 of the upregulated genes in SARS-CoV-2 infection, including 188 SOCS3.  ... 
doi:10.1101/2020.06.29.177204 fatcat:gywqn6tuyvfujhivilwrdwkusq

Viral Circular RNAs and Their Possible Roles in Virus-Host Interaction

Xing Zhang, Zi Liang, Chonglong Wang, Zeen Shen, Sufei Sun, Chengliang Gong, Xiaolong Hu
2022 Frontiers in Immunology  
Circular RNAs (circRNAs) as novel regulatory molecules have been recognized in diverse species, including viruses.  ...  This review will elaborate on new insights gained on viruses encoded circRNAs during virus infection.  ...  MERS-CoV, SARS-CoV-1, SARS-CoV-2, GCRV-873, and BmCPV are RNA viruses. HPV16, HBV, MDV, EBV, KSHV, and MCPyV are DNA viruses.  ... 
doi:10.3389/fimmu.2022.939768 pmid:35784275 pmcid:PMC9247149 fatcat:5hpu53prpbb3veihbqdsbkoncm

Noncoding RNAs implication in cardiovascular diseases in the COVID-19 era

S. Greco, A. Madè, C. Gaetano, Y. Devaux, C. Emanueli, F. Martelli
2020 Journal of Translational Medicine  
COronaVIrus Disease 19 (COVID-19) is caused by the infection of the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2).  ...  Understanding both direct and indirect damage caused to the heart and the vascular system by SARS-CoV-2 infection is necessary to identify optimal clinical care strategies.  ...  The most studied small ncRNAs are microRNAs (miRNAs) and long ncR-NAs, which include also circular RNAs (circRNAs) [11, 13] .  ... 
doi:10.1186/s12967-020-02582-8 pmid:33129318 fatcat:nwxtwz26iraadmjygkln33cgtq

Implications of SARS-CoV-2 Mutations for Genomic RNA Structure and Host microRNA Targeting

Ali Hosseini Rad Sm, Alexander D McLellan
2020 International Journal of Molecular Sciences  
We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary  ...  Filtering to targets matching miRNAs expressed in SARS-CoV-2-permissive host cells, we identified ten separate target sequences in the SARS-CoV-2 genome; three of these targets have been lost through conserved  ...  Potential Interaction of SARS-CoV-2 Transcripts and Human miRNAs Using databases and published data, we filtered our considered miRNA to those with documented expression in SARS-CoV-2 target cells, and  ... 
doi:10.3390/ijms21134807 pmid:32645951 pmcid:PMC7370282 fatcat:o5n53g3frfe4tck4e2f3uf5pdu

Viral MicroRNAs Encoded by Nucleocapsid Gene of SARS-CoV-2 Are Detected during Infection, and Targeting Metabolic Pathways in Host Cells

Fei Meng, Gilman Kit-Hang Siu, Bobo Wing-Yee Mok, Jiahong Sun, Kitty S. C. Fung, Jimmy Yiu-Wing Lam, Nonthaphat Kent Wong, Lealem Gedefaw, Shumeng Luo, Thomas M. H. Lee, Shea Ping Yip, Chien-Ling Huang
2021 Cells  
In this study, SARS-CoV-2 v-miRNAs were identified by deep sequencing in infected Calu-3 and Vero E6 cell lines.  ...  Among the ~0.1% small RNA sequences mapped to the SARS-CoV-2 genome, the top ten SARS-CoV-2 v-miRNAs (including three encoded by the N gene; v-miRNA-N) were selected.  ...  For SARS-CoV-2-infected cells, total RNA was isolated by precipitation method in the BSL-3 laboratory.  ... 
doi:10.3390/cells10071762 fatcat:jsni76viafd43caw7ib42hr7dm

Novel SARS-CoV-2 encoded small RNAs in the passage to humans

Gabriela A Merino, Jonathan Raad, Leandro A Bugnon, Cristian Yones, Laura Kamenetzky, Juan Claus, Federico Ariel, Diego H Milone, Georgina Stegmayer, Peter Robinson
2020 Bioinformatics  
Among the precursors, the expression of eight mature miRNAs-like sequences was confirmed in small RNA-seq data from SARS-CoV-2 infected human cells.  ...  Remarkably, 28 of those genes potentially targeted by SARS-CoV-2 miRNAs are down-regulated in infected human cells.  ...  D) Predicted hairpin structures of the two SARS-CoV-2 pre-miRNAs shown in C). Figure 2 : 2 Predicted viral miRNA targets in the human genome and differentially expressed genes upon infection.  ... 
doi:10.1093/bioinformatics/btaa1002 pmid:33244583 fatcat:y5o7roijmvcpzeg23hpfsx4o5m

Unravelling host-pathogen interactions: ceRNA network in SARS-CoV-2 infection (COVID-19)

Shweta Arora, Prithvi Singh, Ravins Dohare, Rishabh Jha, Mansoor Ali Syed
2020 Gene  
We have predicted a ceRNA network involving one miRNA (miR-124-3p), one mRNA (Ddx58), one lncRNA (Gm26917) and two circRNAs (Ppp1r10, C330019G07RiK) in SARS-CoV infected cells.  ...  COVID-19 is a lurking calamitous disease caused by an unusual virus, SARS-CoV-2, causing massive deaths worldwide.  ...  Since these genes are also found to be deregulated in studies associated with SARS-CoV-2 infection (Blanco-Melo et al., 2020) , it is assumed to have similar effects in SARS-CoV-2 infection.  ... 
doi:10.1016/j.gene.2020.145057 pmid:32805314 pmcid:PMC7428439 fatcat:bkssl7baovcxjcdx6yhvsoea5u

Implications of SARS-CoV-2 mutations for genomic RNA structure and host microRNA targeting [article]

Ali Hosseini Rad, Alexander Donald McLellan
2020 bioRxiv   pre-print
We have analysed subsets of genomes from SARS-CoV-2 isolates from around the globe and show that several mutations introduce changes in Watson-Crick pairing, with resultant changes in predicted secondary  ...  Filtering to targets matching miRNAs expressed in SARS-CoV-2 permissive host cells, we identified twelve separate target sequences in the SARS-CoV-2 genome; eight of these targets have been lost through  ...  Therefore, our study has additionally identified and mapped mutations to predicted mRNA splice sites within the SARS-CoV-2 genome.  ... 
doi:10.1101/2020.05.15.098947 fatcat:33meoirqcjbhhmriml6p6yff6y

SARS-CoV-2, Cardiovascular Diseases and Noncoding RNAs: A Connected Triad

Lucia Natarelli, Fabio Virgili, Christian Weber
2021 International Journal of Molecular Sciences  
In this review, we introduce known associations and interactions between COVID-19 and CVD, discussing the role of ncRNAs within SARS-CoV-2 infection from the perspective of the development of efficient  ...  Coronavirus Disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is characterized by important respiratory impairments frequently associated with severe  ...  In addition, a computational analysis on lncRNA interaction against the SARS-CoV-2 genome reveal that H19 can interact with the SARS-CoV-2 genome and the Spike transcript [56] .  ... 
doi:10.3390/ijms222212243 pmid:34830125 pmcid:PMC8620514 fatcat:lxrozzlapravdbecabxp32q3dq

miRNAs, from Evolutionary Junk to Possible Prognostic Markers and Therapeutic Targets in COVID-19

Brandon Bautista-Becerril, Guillermo Pérez-Dimas, Paola C. Sommerhalder-Nava, Alejandro Hanono, Julio A. Martínez-Cisneros, Bárbara Zarate-Maldonado, Evangelina Muñoz-Soria, Arnoldo Aquino-Gálvez, Manuel Castillejos-López, Armida Juárez-Cisneros, Jose S. Lopez-Gonzalez, Angel Camarena
2021 Viruses  
Here, we review the interaction of host and viral microRNAs with molecular and cellular elements that could potentiate the main pulmonary, cardiac, renal, circulatory, and neuronal complications in COVID  ...  In addition, increased expression of miR-15b, -199a, and -491 are related to the prognosis of the disease, and miR-192 and miR-323a were identified as clinical predictors of mortality in patients admitted  ...  kidney injury in SARS-CoV-2 infection.  ... 
doi:10.3390/v14010041 pmid:35062245 pmcid:PMC8781105 fatcat:3gim4pakara6rpsgi7qwbxotcy
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