Genome-wide identification of Aedes albopictus long noncoding RNAs and their association with dengue and Zika virus infection.
Journal
PLoS neglected tropical diseases
ISSN: 1935-2735
Titre abrégé: PLoS Negl Trop Dis
Pays: United States
ID NLM: 101291488
Informations de publication
Date de publication:
01 2021
01 2021
Historique:
received:
04
05
2020
accepted:
20
11
2020
revised:
09
02
2021
pubmed:
23
1
2021
medline:
18
5
2021
entrez:
22
1
2021
Statut:
epublish
Résumé
The Asian tiger mosquito, Aedes albopictus (Ae. albopictus), is an important vector that transmits arboviruses such as dengue (DENV), Zika (ZIKV) and Chikungunya virus (CHIKV). Long noncoding RNAs (lncRNAs) are known to regulate various biological processes. Knowledge on Ae. albopictus lncRNAs and their functional role in virus-host interactions are still limited. Here, we identified and characterized the lncRNAs in the genome of an arbovirus vector, Ae. albopictus, and evaluated their potential involvement in DENV and ZIKV infection. We used 148 public datasets, and identified a total of 10, 867 novel lncRNA transcripts, of which 5,809, 4,139, and 919 were intergenic, intronic and antisense respectively. The Ae. albopictus lncRNAs shared many characteristics with other species such as short length, low GC content, and low sequence conservation. RNA-sequencing of Ae. albopictus cells infected with DENV and ZIKV showed that the expression of lncRNAs was altered upon virus infection. Target prediction analysis revealed that Ae. albopictus lncRNAs may regulate the expression of genes involved in immunity and other metabolic and cellular processes. To verify the role of lncRNAs in virus infection, we generated mutations in lncRNA loci using CRISPR-Cas9, and discovered that two lncRNA loci mutations, namely XLOC_029733 (novel lncRNA transcript id: lncRNA_27639.2) and LOC115270134 (known lncRNA transcript id: XR_003899061.1) resulted in enhancement of DENV and ZIKV replication. The results presented here provide an important foundation for future studies of lncRNAs and their relationship with virus infection in Ae. albopictus.
Identifiants
pubmed: 33481791
doi: 10.1371/journal.pntd.0008351
pii: PNTD-D-20-00757
pmc: PMC7872224
doi:
Substances chimiques
RNA, Long Noncoding
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0008351Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
mSphere. 2017 Nov 22;2(6):
pubmed: 29202041
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Genome Res. 2012 Dec;22(12):2529-40
pubmed: 22707570
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Cell Calcium. 2009 Jul;46(1):1-17
pubmed: 19535138
Mol Biol Cell. 2002 Nov;13(11):4060-73
pubmed: 12429846
PLoS One. 2017 Feb 2;12(2):e0171345
pubmed: 28152011
PLoS Genet. 2013 Mar;9(3):e1003368
pubmed: 23555285
PeerJ. 2016 Mar 10;4:e1784
pubmed: 26989622
Trends Genet. 2017 Oct;33(10):665-676
pubmed: 28870653
BMC Plant Biol. 2018 May 4;18(1):75
pubmed: 29728060
Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):E5907-15
pubmed: 26483478
PLoS Comput Biol. 2008 Apr 18;4(4):e1000057
pubmed: 18421372
Front Genet. 2019 Oct 14;10:975
pubmed: 31681418
PLoS One. 2010 May 18;5(5):e10678
pubmed: 20502529
Genes Dev. 2011 Sep 15;25(18):1915-27
pubmed: 21890647
Parassitologia. 1995 Dec;37(2-3):91-7
pubmed: 8778670
Bioinformatics. 2014 Apr 1;30(7):923-30
pubmed: 24227677
J Exp Biol. 2013 Nov 1;216(Pt 21):4082-90
pubmed: 23913949
PLoS One. 2016 Jan 15;11(1):e0147147
pubmed: 26771876
Mem Inst Oswaldo Cruz. 2017 Dec;112(12):829-837
pubmed: 29211244
Science. 2007 Jun 8;316(5830):1484-8
pubmed: 17510325
PLoS One. 2011;6(7):e22553
pubmed: 21799894
PLoS One. 2018 Mar 19;13(3):e0194664
pubmed: 29554153
BMC Bioinformatics. 2014 Sep 19;15:311
pubmed: 25239089
Sci Rep. 2017 Mar 16;7:43618
pubmed: 28300076
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W193-200
pubmed: 17478515
Genomics. 2020 Mar;112(2):1273-1281
pubmed: 31381967
Microbes Infect. 2009 Dec;11(14-15):1177-85
pubmed: 19450706
Sci Rep. 2016 Dec 19;6:39384
pubmed: 27991555
Genome Res. 2016 Sep;26(9):1233-44
pubmed: 27516619
G3 (Bethesda). 2019 Apr 9;9(4):1263-1276
pubmed: 30787031
PLoS One. 2012;7(11):e50512
pubmed: 23209765
Genome Res. 2012 Mar;22(3):577-91
pubmed: 22110045
BMC Genomics. 2019 Jul 8;20(1):559
pubmed: 31286854
EMBO J. 1998 Aug 17;17(16):4585-93
pubmed: 9707418
Genome Res. 2012 Sep;22(9):1775-89
pubmed: 22955988
Sci Rep. 2018 Mar 21;8(1):4960
pubmed: 29563515
J Gen Virol. 2008 Feb;89(Pt 2):474-484
pubmed: 18198378
Biol Open. 2014 Jan 15;3(1):42-9
pubmed: 24326186
Sci Rep. 2015 Sep 28;5:14642
pubmed: 26411386
Trends Genet. 2014 Aug;30(8):348-55
pubmed: 24974018
PLoS One. 2011;6(10):e25229
pubmed: 21991304
Viruses. 2019 Jun 04;11(6):
pubmed: 31167461
Sci Rep. 2017 Nov 20;7(1):15870
pubmed: 29158595
Trends Parasitol. 2013 Sep;29(9):460-8
pubmed: 23916878
Infect Genet Evol. 2019 Apr;69:22-29
pubmed: 30658214
Proc Natl Acad Sci U S A. 2011 Nov 29;108(48):19234-9
pubmed: 22084111
PLoS Negl Trop Dis. 2016 Oct 19;10(10):e0005069
pubmed: 27760142
Nat Biotechnol. 2015 Mar;33(3):290-5
pubmed: 25690850
Sci Rep. 2016 Mar 21;6:23330
pubmed: 26996731
Gigascience. 2018 Mar 1;7(3):1-13
pubmed: 29329394
Bioinformatics. 2015 May 15;31(10):1544-52
pubmed: 25653249
Annu Rev Entomol. 1991;36:459-84
pubmed: 2006869
Front Microbiol. 2017 Oct 23;8:2050
pubmed: 29109710
Sci Rep. 2017 Feb 24;7:43166
pubmed: 28233874
J Virol. 2010 Sep;84(17):8721-31
pubmed: 20538858
Vet Parasitol. 2003 Dec 30;118(3-4):195-202
pubmed: 14729167
Annu Rev Biochem. 2012;81:145-66
pubmed: 22663078
Virology. 2016 May;492:242-50
pubmed: 27003248
Cell Rep. 2015 May 19;11(7):1110-22
pubmed: 25959816
Front Microbiol. 2020 Mar 06;11:242
pubmed: 32210929
Methods. 2001 Dec;25(4):402-8
pubmed: 11846609
Cell. 2018 Jan 25;172(3):393-407
pubmed: 29373828
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
Mol Cell. 2010 Sep 24;39(6):925-38
pubmed: 20797886
Emerg Infect Dis. 2009 Apr;15(4):591-3
pubmed: 19331740
mSphere. 2017 May 3;2(3):
pubmed: 28497119
PLoS Pathog. 2013 Feb;9(2):e1003172
pubmed: 23436995
Genome Biol. 2020 Aug 26;21(1):215
pubmed: 32847630
Development. 2019 Mar 28;146(6):
pubmed: 30923056
J Cell Biol. 2003 Jan 20;160(2):213-22
pubmed: 12538641
Nucleic Acids Res. 2017 Jul 3;45(W1):W12-W16
pubmed: 28521017
PLoS Negl Trop Dis. 2015 Apr 21;9(4):e0003724
pubmed: 25897664
G3 (Bethesda). 2020 Mar 5;10(3):1051-1062
pubmed: 31964684
Nat Protoc. 2013 Aug;8(8):1494-512
pubmed: 23845962
Nucleic Acids Res. 2019 Jul 2;47(W1):W171-W174
pubmed: 31106371
Nucleic Acids Res. 2013 Apr 1;41(6):e74
pubmed: 23335781
Sci Rep. 2019 Aug 21;9(1):12147
pubmed: 31434910
Clin Infect Dis. 2012 Sep;55(6):e45-53
pubmed: 22670036
Pathog Glob Health. 2015 Jul;109(5):207-20
pubmed: 26369436
PLoS Pathog. 2011 Sep;7(9):e1002189
pubmed: 21909258