Identification of novel lncRNA by reanalysis of RNA-seq data in Zika Virus Infected hiNPCs
Tóm tắt
The Zika Virus (ZIKV) infection is a serious, public health concern with no vaccines or antiviral treatments. This study aims to identify the differentially expressed long non-coding RNAs (lncRNAs) in ZIKV infected human-induced neuroprogenitor cells (hiNPCs). Though lncRNA is well-known for its role in gene regulation, its role in ZIKV infection remains unclear. Thus, taking advantage of publicly available transcriptome data, BioProject PRJNA551246 was analysed. Performed the gene ontology and pathway analysis of differentially expressed lncRNAs were functionally interpreted based on the neighbouring protein-coding genes (100 kb upstream and downstream of each lncRNAs). The study revealed 19 novels and 237 differentially expressed lncRNAs in ZIKV infected hiNPCs. They are found to be significantly enriched in type I interferon signalling pathway, negative regulation of viral genome replication, defense response to the virus, pathways involved in Influenza A and Herpes simplex infection, tumor necrosis factor signalling pathway, and apoptosis. In ZIKV, associated microcephaly type I interferon act as potential modulating factors. Type-I interferon inhibits ZIKV replication in many human cell types. The results support future studies on understanding the structure and function of the novel lncRNAs and experimental approaches to determine the role of the lncRNAs in ZIKV induced infection.
Tài liệu tham khảo
citation_journal_title=Front Microbiol; citation_title=Aedes aegypti molecular responses to zika virus: Modulation of infection by the toll and Jak/Stat immune pathways and virus host factors; citation_author=YI Angleró-Rodríguez, HJ MacLeod, S Kang, JS Carlson, N Jupatanakul, G Dimopoulos; citation_publication_date=2017; citation_doi=10.3389/fmicb.2017.02050; citation_id=CR1
citation_journal_title=Cell; citation_title=Long noncoding RNAs: cellular address codes in development and disease; citation_author=PJ Batista, HY Chang; citation_volume=152; citation_issue=6; citation_publication_date=2013; citation_pages=1298-1307; citation_doi=10.1016/j.cell.2013.02.012; citation_id=CR2
citation_journal_title=Cell Death Differ; citation_title=Zika Virus E protein alters the properties of human fetal neural stem cells by modulating microRNA circuitry; citation_author=R Bhagat, B Prajapati, S Narwal; citation_volume=25; citation_issue=10; citation_publication_date=2018; citation_pages=1837-1854; citation_doi=10.1038/s41418-018-0163-y; citation_id=CR3
citation_journal_title=J Virol; citation_title=Suppression of Zika Virus Infection and replication in endothelial cells and astrocytes by PKA inhibitor PKI 14–22; citation_author=F Cheng, S Ramos da Silva, I-C Huang, JU Jung, S-J Gao; citation_volume=92; citation_issue=4; citation_publication_date=2018; citation_pages=e02019-e2117; citation_doi=10.1128/JVI.02019-17; citation_id=CR5
citation_journal_title=Non-Coding RNA; citation_title=Functional interplay between RNA viruses and non-coding RNA in mammals; citation_author=ND Damas, N Fossat, TKH Scheel; citation_volume=5; citation_issue=1; citation_publication_date=2019; citation_pages=7; citation_doi=10.3390/ncrna5010007; citation_id=CR6
citation_journal_title=Rev Soc Bras Med Trop; citation_title=One year after the Zika Virus outbreak in Brazil: from hypotheses to evidence; citation_author=CAA Brito, MT Cordeiro; citation_volume=49; citation_issue=5; citation_publication_date=2016; citation_pages=537-543; citation_doi=10.1590/0037-8682-0328-2016; citation_id=CR4
citation_journal_title=Transact R Soc Trop Med Hyg; citation_title=Zika Virus (I). Isolations and serological specificity; citation_author=GWA Dick, SF Kitchen, AJ Haddow; citation_volume=46; citation_issue=5; citation_publication_date=1952; citation_pages=509-520; citation_doi=10.1016/0035-9203(52)90042-4; citation_id=CR7
citation_journal_title=N Engl J Med; citation_title=Zika Virus outbreak on yap island, federated states of micronesia; citation_author=MR Duffy, T-H Chen, WT Hancock; citation_volume=360; citation_issue=24; citation_publication_date=2009; citation_pages=2536-2543; citation_doi=10.1056/NEJMoa0805715; citation_id=CR8
citation_journal_title=Nat Protoc; citation_title=Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt; citation_author=S Durinck, PT Spellman, E Birney, W Huber; citation_volume=4; citation_issue=8; citation_publication_date=2009; citation_pages=1184-1191; citation_doi=10.1038/nprot.2009.97; citation_id=CR9
citation_journal_title=Intervirology; citation_title=Zika Virus-Induced Microcephaly and Its Possible Molecular Mechanism; citation_author=MI Faizan, M Abdullah, S Ali, IH Naqvi, A Ahmed, S Parveen; citation_volume=59; citation_issue=3; citation_publication_date=2016; citation_pages=152-158; citation_doi=10.1159/000452950; citation_id=CR10
citation_journal_title=Microorganisms; citation_title=In vitro Zika Virus infection of human neural progenitor cells: Meta-analysis of RNA-seq assays; citation_author=R Gratton, PM Tricarico, A Agrelli; citation_volume=8; citation_issue=2; citation_publication_date=2020; citation_pages=1-13; citation_doi=10.3390/microorganisms8020270; citation_id=CR11
citation_journal_title=Nature; citation_title=Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals; citation_author=M Guttman, I Amit, M Garber; citation_volume=458; citation_issue=7235; citation_publication_date=2009; citation_pages=223-227; citation_doi=10.1038/nature07672; citation_id=CR12
citation_journal_title=Nature; citation_title=Modular regulatory principles of large non-coding RNAs; citation_author=M Guttman, JL Rinn; citation_volume=482; citation_issue=7385; citation_publication_date=2012; citation_pages=339-346; citation_doi=10.1038/nature10887; citation_id=CR13
citation_journal_title=Trends Immunol; citation_title=Long non-coding RNAs in the regulation of the immune response; citation_author=JA Heward, MA Lindsay; citation_volume=35; citation_issue=9; citation_publication_date=2014; citation_pages=408-419; citation_doi=10.1016/j.it.2014.07.005; citation_id=CR14
citation_journal_title=Cell; citation_title=Self-Recognition of an Inducible Host lncRNA by RIG-I Feedback Restricts Innate Immune Response; citation_author=M Jiang, S Zhang, Z Yang; citation_volume=173; citation_issue=4; citation_publication_date=2018; citation_pages=906-919.e13; citation_doi=10.1016/j.cell.2018.03.064; citation_id=CR15
citation_journal_title=Nucleic Acids Res; citation_title=CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features; citation_author=Y-J Kang, D-C Yang, L Kong; citation_volume=45; citation_issue=W1; citation_publication_date=2017; citation_pages=W12-W16; citation_doi=10.1093/nar/gkx428; citation_id=CR16
citation_journal_title=Biochim Biophys Acta; citation_title=Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome; citation_author=K Kashi, L Henderson, A Bonetti, P Carninci; citation_volume=1859; citation_issue=1; citation_publication_date=2016; citation_pages=3-15; citation_doi=10.1016/j.bbagrm.2015.10.010; citation_id=CR17
citation_journal_title=Elife; citation_title=p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-κB complexes; citation_author=M Krawczyk, BM Emerson; citation_volume=3; citation_publication_date=2014; citation_doi=10.7554/eLife.01776; citation_id=CR18
citation_journal_title=Cells; citation_title=Zika Virus induces tumor necrosis factor-related apoptosis-inducing ligand (trail)-mediated apoptosis in human neural progenitor cells; citation_author=JK Lee, J-A Kim, S-J Oh, E-W Lee, OS Shin; citation_volume=9; citation_issue=11; citation_publication_date=2020; citation_pages=2487; citation_doi=10.3390/cells9112487; citation_id=CR19
citation_journal_title=Proc Natl Acad Sci U S A; citation_title=The long noncoding RNA THRIL regulates TNFα expression through its interaction with hnRNPL; citation_author=Z Li, T-C Chao, K-Y Chang; citation_volume=111; citation_issue=3; citation_publication_date=2014; citation_pages=1002-1007; citation_doi=10.1073/pnas.1313768111; citation_id=CR20
citation_journal_title=BMC Bioinform; citation_title=PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme; citation_author=A Li, J Zhang, Z Zhou; citation_volume=15; citation_issue=1; citation_publication_date=2014; citation_pages=311; citation_doi=10.1186/1471-2105-15-311; citation_id=CR21
citation_journal_title=Bioinformatics; citation_title=featureCounts: an efficient general purpose program for assigning sequence reads to genomic features; citation_author=Y Liao, GK Smyth, W Shi; citation_volume=30; citation_issue=7; citation_publication_date=2014; citation_pages=923-930; citation_doi=10.1093/bioinformatics/btt656; citation_id=CR22
citation_journal_title=Front Immunol; citation_title=The transcriptional and protein profile from human infected neuroprogenitor cells is strongly correlated to Zika Virus microcephaly cytokines phenotype evidencing a persistent inflammation in the CNS; citation_author=MC Lima, LR Mendonça, AM Rezende; citation_volume=10; citation_publication_date=2019; citation_pages=1928; citation_doi=10.3389/fimmu.2019.01928; citation_id=CR23
citation_journal_title=Nucleic Acids Res; citation_title=NONCODE: an integrated knowledge database of non-coding RNAs; citation_author=C Liu; citation_volume=33; citation_issue=Database issue; citation_publication_date=2004; citation_pages=D112-D115; citation_doi=10.1093/nar/gki041; citation_id=CR24
citation_journal_title=Front Cell Infect Microbiol; citation_title=Roles of LncRNAs in Viral Infections; citation_author=W Liu, C Ding; citation_volume=7; citation_publication_date=2017; citation_pages=205; citation_doi=10.3389/fcimb.2017.00205; citation_id=CR25
citation_journal_title=Rev Med Virol; citation_title=Long noncoding RNAs: Novel regulators of virus-host interactions; citation_author=S Liu, X Liu, J Li; citation_volume=29; citation_issue=4; citation_publication_date=2019; citation_doi=10.1002/rmv.2046; citation_id=CR26
citation_journal_title=Nucleic Acids Res; citation_title=Moderated estimation of fold change and dispersion for RNA seqdata with DESeq2; citation_author=MI Love, W Huber, S Anders; citation_volume=15; citation_publication_date=2014; citation_pages=1-21; citation_doi=10.1186/s13059-014-0550-8; citation_id=CR27
citation_journal_title=Int J Mol Sci; citation_title=Involvement of host non-coding rnas in the pathogenesis of the influenza virus; citation_author=Y Ma, J Ouyang, J Wei, M Maarouf, JL Chen; citation_volume=18; citation_issue=1; citation_publication_date=2016; citation_pages=39; citation_doi=10.3390/ijms18010039; citation_id=CR28
citation_journal_title=Stem Cell Reports; citation_title=Differential responses of human fetal brain neural stem cells to Zika Virus infection; citation_author=EL McGrath, SL Rossi, J Gao; citation_volume=8; citation_issue=3; citation_publication_date=2017; citation_pages=715-727; citation_doi=10.1016/j.stemcr.2017.01.008; citation_id=CR29
citation_journal_title=Biochem Biophys Res Commun; citation_title=Antagonism of type I interferon by flaviviruses; citation_author=L Miorin, AM Maestre, A Fernandez-Sesma, A García-Sastre; citation_volume=492; citation_issue=4; citation_publication_date=2017; citation_pages=587-596; citation_doi=10.1016/j.bbrc.2017.05.146; citation_id=CR30
citation_journal_title=RNA Biol; citation_title=Long non-coding RNA PSMB8-AS1 regulates influenza virus replication; citation_author=S More, Z Zhu, K Lin; citation_volume=16; citation_issue=3; citation_publication_date=2019; citation_pages=340-353; citation_doi=10.1080/15476286.2019.1572448; citation_id=CR31
citation_title=The innate immune response during Zika Virus infection; citation_inbook_title=Zika Virus biology, transmission, and pathology; citation_publication_date=2021; citation_pages=19-29; citation_id=CR32; citation_author=MSL Nascimento; citation_author=W Victor; citation_author=A Santos; citation_author=CA Salmeron; citation_author=JM Galvão; citation_author=J Araújo; citation_author=V Fernandes; citation_author=PMM Guedes; citation_publisher=Elsevier
citation_journal_title=Bioinformatics; citation_title=BEDOPS: high-performance genomic feature operations; citation_author=S Neph, MS Kuehn, AP Reynolds; citation_volume=28; citation_issue=14; citation_publication_date=2012; citation_pages=1919-1920; citation_doi=10.1093/bioinformatics/bts277; citation_id=CR33
citation_journal_title=Front Immunol; citation_title=Zika Virus promotes neuronal cell death in a non-cell autonomous manner by triggering the release of neurotoxic factors; citation_author=IG Olmo, TG Carvalho, VV Costa; citation_volume=8; citation_publication_date=2017; citation_pages=1016; citation_doi=10.3389/fimmu.2017.01016; citation_id=CR34
citation_journal_title=Cell Host Microbe; citation_title=NRAV, a long noncoding RNA, modulates antiviral responses through suppression of interferon-stimulated gene transcription; citation_author=J Ouyang, X Zhu, Y Chen; citation_volume=16; citation_issue=5; citation_publication_date=2014; citation_pages=616-626; citation_doi=10.1016/j.chom.2014.10.001; citation_id=CR35
citation_journal_title=F1000Research; citation_title=GFF Utilities: GffRead and GffCompare; citation_author=G Pertea, M Pertea; citation_volume=9; citation_publication_date=2020; citation_pages=304; citation_doi=10.12688/f1000research.23297.2; citation_id=CR36
citation_journal_title=Nat Biotechnol; citation_title=stringTie enables improved reconstruction of a transcriptome from RNA-seq reads; citation_author=M Pertea, GM Pertea, CM Antonescu, TC Chang, JT Mendell, SL Salzberg; citation_volume=33; citation_issue=3; citation_publication_date=2015; citation_pages=290-295; citation_doi=10.1038/nbt.3122; citation_id=CR37
citation_journal_title=Cell; citation_title=Evolution and functions of long noncoding RNAs; citation_author=CP Ponting, PL Oliver, W Reik; citation_volume=136; citation_issue=4; citation_publication_date=2009; citation_pages=629-641; citation_doi=10.1016/j.cell.2009.02.006; citation_id=CR38
citation_journal_title=Front Microbiol; citation_title=Long Non-coding RNAs: Regulators of Viral Infection and the Interferon Antiviral Response; citation_author=L Qiu, T Wang, Q Tang, G Li, P Wu, K Chen; citation_volume=9; citation_publication_date=2018; citation_pages=1621; citation_doi=10.3389/fmicb.2018.01621; citation_id=CR39
citation_journal_title=Bioinformatics; citation_title=BEDTools: a flexible suite of utilities for comparing genomic features; citation_author=AR Quinlan, IM Hall; citation_volume=26; citation_issue=6; citation_publication_date=2010; citation_pages=841-842; citation_doi=10.1093/bioinformatics/btq033; citation_id=CR40
citation_journal_title=Trends Cell Biol; citation_title=Long noncoding RNAs: an emerging link between gene regulation and nuclear organization; citation_author=S Quinodoz, M Guttman; citation_volume=24; citation_issue=11; citation_publication_date=2014; citation_pages=651-663; citation_doi=10.1016/j.tcb.2014.08.009; citation_id=CR41
citation_journal_title=Biochim Biophys acta Gene Regul Mech; citation_title=The how and why of lncRNA function: An innate immune perspective; citation_author=EK Robinson, S Covarrubias, S Carpenter; citation_volume=1863; citation_issue=4; citation_publication_date=2020; citation_doi=10.1016/j.bbagrm.2019.194419; citation_id=CR42
citation_journal_title=Mol Neurobiol; citation_title=Zika Virus and the metabolism of neuronal cells; citation_author=HA Rothan, S Fang, M Mahesh, SN Byrareddy; citation_volume=56; citation_issue=4; citation_publication_date=2019; citation_pages=2551-2557; citation_doi=10.1007/s12035-018-1263-x; citation_id=CR43
citation_journal_title=MMWR Morb Mortal Wkly Rep; citation_title=Possible association between Zika Virus infection and microcephaly - Brazil, 2015; citation_author=L Schuler-Faccini, EM Ribeiro, IML Feitosa; citation_volume=65; citation_issue=3; citation_publication_date=2016; citation_pages=59-62; citation_doi=10.15585/mmwr.mm6503e2; citation_id=CR44
citation_journal_title=Front Neurol; citation_title=Zika Virus potentiates the development of neurological defects and microcephaly: Challenges and control strategies; citation_author=R Siddique, Y Liu, G Nabi, W Sajjad, M Xue, S Khan; citation_volume=10; citation_publication_date=2019; citation_pages=319; citation_doi=10.3389/fneur.2019.00319; citation_id=CR45
citation_journal_title=J Infect Dis; citation_title=Zika Virus structure, maturation, and receptors; citation_author=D Sirohi, RJ Kuhn; citation_publication_date=2017; citation_doi=10.1093/infdis/jix515; citation_id=CR46
citation_journal_title=Cell Stem Cell; citation_title=Zika Virus infects human cortical neural progenitors and attenuates their growth; citation_author=H Tang, C Hammack, SC Ogden; citation_volume=18; citation_issue=5; citation_publication_date=2016; citation_pages=587-590; citation_doi=10.1016/j.stem.2016.02.016; citation_id=CR47
citation_journal_title=Nucleic Acids Res; citation_title=RNAcentral: a hub of information for non-coding RNA sequences; citation_author=; citation_volume=47; citation_issue=D1; citation_publication_date=2019; citation_pages=D221-D229; citation_doi=10.1093/nar/gky1034; citation_id=CR48
citation_journal_title=Int J Mol Sci; citation_title=Apoptosis during ZIKA Virus Infection: Too soon or too late?; citation_author=J Turpin, D Safadi, G Lebeau, M Krejbich, C Chatelain, P Desprès, W Viranaïcken, P Krejbich-Trotot; citation_volume=23; citation_issue=3; citation_publication_date=2022; citation_pages=1287; citation_doi=10.3390/ijms23031287; citation_id=CR49
citation_journal_title=Trends Genet; citation_title=Transcriptional regulatory functions of nuclear long noncoding RNAs; citation_author=KW Vance, CP Ponting; citation_volume=30; citation_issue=8; citation_publication_date=2014; citation_pages=348-355; citation_doi=10.1016/j.tig.2014.06.001; citation_id=CR50
citation_journal_title=Nucleic Acid Res; citation_title=LNCipedia: a database for annotated human lncRNA transcript sequences and structures; citation_author=PJ Volders, K Helsens, X Wang, B Menten, L Martens, K Gevaert, J Vandesompele, P Mestdagh; citation_volume=41; citation_issue=D1; citation_publication_date=2013; citation_pages=D246-D251; citation_doi=10.1093/nar/gks915; citation_id=CR51
citation_journal_title=Emerg Microbes Infect; citation_title=Roles of lncRNAs in influenza virus infection; citation_author=J Wang, S Cen; citation_volume=9; citation_issue=1; citation_publication_date=2020; citation_pages=1407-1414; citation_doi=10.1080/22221751.2020.1778429; citation_id=CR52
citation_journal_title=Nucleic Acids Res; citation_title=CPAT: Coding-potential assessment tool using an alignment-free logistic regression model; citation_author=L Wang, HJ Park, S Dasari, S Wang, J-P Kocher, W Li; citation_volume=41; citation_issue=6; citation_publication_date=2013; citation_pages=e74-e74; citation_doi=10.1093/nar/gkt006; citation_id=CR53
citation_journal_title=J Med Virol; citation_title=Long noncoding RNA TSPOAP1 antisense RNA 1 negatively modulates type I IFN signaling to facilitate influenza A virus replication; citation_author=Q Wang, D Zhang, W Feng; citation_volume=94; citation_publication_date=2019; citation_pages=557-566; citation_doi=10.1002/jmv.25483; citation_id=CR54
citation_journal_title=Ann Neurol; citation_title=Zika virus: An emergent neuropathological agent; citation_author=MK White, HS Wollebo, J David Beckham, KL Tyler, K Khalili; citation_volume=80; citation_issue=4; citation_publication_date=2016; citation_pages=479-489; citation_doi=10.1002/ana.24748; citation_id=CR55
citation_journal_title=RNA Biol; citation_title=Evidence for a crucial role of a host non-coding RNA in influenza A virus replication; citation_author=C Winterling, M Koch, M Koeppel, F Garcia-Alcalde, A Karlas, TF Meyer; citation_volume=11; citation_issue=1; citation_publication_date=2014; citation_pages=66-75; citation_doi=10.4161/rna.27504; citation_id=CR56
citation_journal_title=Front Biosci; citation_title=Long noncoding RNA and its role in virus infection and pathogenesis; citation_author=T Zhao; citation_volume=24; citation_issue=4; citation_publication_date=2019; citation_pages=777-789; citation_doi=10.2741/4750; citation_id=CR57