Feeding exogenous dsRNA interferes with endogenous sRNA accumulation in Paramecium.

Paramecium / genetics RNA Interference RNA, Double-Stranded / metabolism RNA, Messenger / metabolism RNA, Small Interfering / metabolism Ribonuclease III / genetics
dsRNA feeding environmental RNAi off-target siRNA

Journal

DNA research : an international journal for rapid publication of reports on genes and genomes
ISSN: 1756-1663
Titre abrégé: DNA Res
Pays: England
ID NLM: 9423827

Informations de publication

Date de publication:
01 Feb 2020
Historique:
received: 30 08 2019
accepted: 21 04 2020
pubmed: 28 4 2020
medline: 12 3 2021
entrez: 28 4 2020
Statut: ppublish

Résumé

Supply of exogenous dsRNA (exo-dsRNA), either by injection or by feeding, is a fast and powerful alternative to classical knockout studies. The biotechnical potential of feeding techniques is evident from the numerous studies focusing on oral administration of dsRNA to control pests and viral infection in crops/animal farming. We aimed to dissect the direct and indirect effects of exo-dsRNA feeding on the endogenous short interfering RNA (endo-siRNA) populations of the free-living ciliate Paramecium. We introduced dsRNA fragments against Dicer1 (DCR1), involved in RNA interference (RNAi) against exo- and few endo-siRNAs, and an RNAi unrelated gene, ND169. Any feeding, even the control dsRNA, diminishes genome wide the accumulation of endo-siRNAs and mRNAs. This cannot be explained by direct off-target effects and suggests mechanistic overlaps of the exo- and endo-RNAi mechanisms. Nevertheless, we observe a stronger down-regulation of mRNAs in DCR1 feeding compared with ND169 knockdown. This is likely due to the direct involvement of DCR1 in endo-siRNA accumulation. We further observed a cis-regulatory effect on mRNAs that overlap with phased endo-siRNAs. This interference of exo-dsRNA with endo-siRNAs warrants further investigations into secondary effects in target species/consumers, risk assessment of dsRNA feeding applications, and environmental pollution with dsRNA.

Identifiants

DOI: 10.1093/dnares/dsaa005 PMID: 32339224 PMC: PMC7315353
pubmed: 32339224
pii: 5825730
doi: 10.1093/dnares/dsaa005
pmc: PMC7315353
pii:
doi:

Substances chimiques

RNA, Double-Stranded 0
RNA, Messenger 0
RNA, Small Interfering 0
Ribonuclease III EC 3.1.26.3

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

© The Author(s) 2020. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Références

Life Sci Alliance. 2019 Feb 26;2(1):
pubmed: 30808654
Nucleic Acids Res. 2015 Feb 18;43(3):1818-33
pubmed: 25593325
Gene Expr. 2006;13(3):167-78
pubmed: 17193923
Trends Genet. 2002 Jan;18(1):11-2
pubmed: 11750689
BMC Genomics. 2017 Jun 26;18(1):483
pubmed: 28651633
Science. 2015 May 15;348(6236):817-21
pubmed: 25977554
PeerJ. 2019 Apr 10;7:e6710
pubmed: 30993044
Cell. 2006 Jan 27;124(2):343-54
pubmed: 16439208
Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10565-70
pubmed: 17563372
Bioinformatics. 2015 Jan 15;31(2):166-9
pubmed: 25260700
J Insect Physiol. 2010 Mar;56(3):227-35
pubmed: 19837076
Genome Biol. 2014;15(12):550
pubmed: 25516281
Mar Biotechnol (NY). 2008 May-Jun;10(3):242-9
pubmed: 18202890
Genes (Basel). 2012 Oct 19;3(4):
pubmed: 23483754
Trends Parasitol. 2011 Nov;27(11):505-13
pubmed: 21885343
Plant Physiol. 2020 Jan;182(1):38-50
pubmed: 31285292
Nucleic Acids Res. 2009 Feb;37(3):903-15
pubmed: 19103667
Science. 2002 Mar 29;295(5564):2456-9
pubmed: 11834782
Genes (Basel). 2018 Feb 21;9(2):
pubmed: 29466322
Nucleic Acids Res. 2016 Jul 8;44(12):5908-23
pubmed: 27085807
Nucleic Acids Res. 2019 Sep 5;47(15):8036-8049
pubmed: 31251800
Cell. 2005 Apr 22;121(2):207-21
pubmed: 15851028
Nucleic Acids Res. 2010 Jul;38(12):4092-107
pubmed: 20200046
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Dev Dyn. 2013 Jun;242(6):718-30
pubmed: 23441014
Bioinformatics. 2008 Jul 15;24(14):1650-1
pubmed: 18511468
Trends Genet. 2008 Jun;24(6):297-305
pubmed: 18450316
Bioinformatics. 2017 Sep 15;33(18):2938-2940
pubmed: 28645171
Nucleic Acids Res. 2019 May 7;47(8):3957-3969
pubmed: 30838421
DNA Res. 2015 Aug;22(4):293-305
pubmed: 26231545
Nucleic Acids Res. 2014 Jun;42(11):7268-80
pubmed: 24860163
Nat Methods. 2017 Apr;14(4):417-419
pubmed: 28263959
Mol Cell. 2014 Dec 4;56(5):708-16
pubmed: 25453759
Mar Biotechnol (NY). 2008 Mar-Apr;10(2):198-206
pubmed: 17965920

Auteurs

Sivarajan Karunanithi (S)

Cluster of Excellence for Multimodal Computing and Interaction, and Department for Computational Biology & Applied Algorithms, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.
Graduate School of Computer Science, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany.
Institute for Cardiovascular Regeneration, Goethe University Hospital, Frankfurt am Main, Germany.

Vidya Oruganti (V)

Cluster of Excellence for Multimodal Computing and Interaction, and Department for Computational Biology & Applied Algorithms, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.

Raphael de Wijn (R)

Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany.

Franziska Drews (F)

Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany.

Miriam Cheaib (M)

Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany.

Karl Nordström (K)

Genetics/Epigenetics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany.

Martin Simon (M)

Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken, Germany.
Molecular Cell Biology and Microbiology, Wuppertal University, Wuppertal, Germany.

Marcel H Schulz (MH)

Cluster of Excellence for Multimodal Computing and Interaction, and Department for Computational Biology & Applied Algorithms, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.
Institute for Cardiovascular Regeneration, Goethe University Hospital, Frankfurt am Main, Germany.

Articles similaires

Human DCP1 is crucial for mRNA decapping and possesses paralog-specific gene regulating functions.

Ting-Wen Chen, Hsiao-Wei Liao, Michelle Noble et al.
1.00
Humans Endoribonucleases RNA, Messenger RNA Caps Gene Expression Regulation

A cytoplasmic osmosensing mechanism mediated by molecular crowding-sensitive DCP5.

Zhenyu Wang, Qiuhua Yang, Dan Zhang et al.
1.00
Arabidopsis Arabidopsis Proteins Osmotic Pressure Cytoplasm RNA, Messenger

The SARS-CoV-2 ORF6 protein inhibits nuclear export of mRNA and spliceosomal U snRNA.

Ichiro Taniguchi
1.00
Animals Active Transport, Cell Nucleus RNA, Messenger Humans SARS-CoV-2

The mRNA and protein datasets after cold stress of red tilapia.

Lanmei Wang, Haoran Yang, Herbert Brightmore Munyaradzia et al.
1.00
Animals Tilapia Cold-Shock Response RNA, Messenger Transcriptome

Classifications MeSH

questionsmedicales.fr › Eucaryotes › Alveolata › Ciliophora › Oligohymenophorea › Hymenostomatida › Peniculina › Paramecium › Feeding exogenous dsRNA interferes with...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Épigenèse génétique › Extinction de l'expression des gènes › Interférence par ARN › Feeding exogenous dsRNA interferes with...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › ARN double brin › Feeding exogenous dsRNA interferes with...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN messager › Feeding exogenous dsRNA interferes with...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › Petit ARN non traduit › Petit ARN interférent › Feeding exogenous dsRNA interferes with...
questionsmedicales.fr › Enzymes et coenzymes › Enzymes › Hydrolases › Esterases › Ribonucléases › Endoribonucleases › Ribonuclease III › Feeding exogenous dsRNA interferes with...