A highly sensitive biotin-based probe for small RNA northern blot and its application in dissecting miRNA function in pepper.
Capsicum annuum
NLR
Phytophthora capsici
biotin probe
disease resistance
miR6027
miRNA
northern blot
Journal
The Plant journal : for cell and molecular biology
ISSN: 1365-313X
Titre abrégé: Plant J
Pays: England
ID NLM: 9207397
Informations de publication
Date de publication:
11 Dec 2023
11 Dec 2023
Historique:
revised:
26
11
2023
received:
16
10
2023
accepted:
01
12
2023
medline:
11
12
2023
pubmed:
11
12
2023
entrez:
11
12
2023
Statut:
aheadofprint
Résumé
Small RNAs play important roles in regulation of plant development and response to various stresses. Northern blot is an important technique in small RNA research. Isotope- and biotin- (or digoxigenin) labeled probes are frequently used in small RNA northern blot. However, isotope-based probe is limited by strict environmental regulation and availability in many places in the world while biotin-based probe is usually suffered from low sensitivity. In this study, we developed a T4 DNA polymerase-based method for incorporation of a cluster of 33 biotin-labeled C in small RNA probe (T4BC33 probe). T4BC33 probe reaches similar sensitivity as
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : National Natural Science Foundation of China
ID : 31972420
Organisme : National Natural Science Foundation of China
ID : 32272491
Organisme : National Key Research and Development Program of China
ID : 2018YFD1000800
Informations de copyright
© 2023 Society for Experimental Biology and John Wiley & Sons Ltd.
Références
Ambros, V. (2011) MicroRNAs and developmental timing. Current Opinion in Genetics & Development, 21, 511-517.
Axtell, M.J. (2013) Classification and comparison of small RNAs from plants. Annual Review of Plant Biology, 64, 137-159.
Bologna, N.G. & Voinnet, O. (2014) The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Annual Review of Plant Biology, 65, 473-503.
Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D.H., Johnson, D. et al. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnology, 18, 630-634.
Canto-Pastor, A., Santos, B.A.M.C., Valli, A.A., Summers, W., Schornack, S. & Baulcombe, D.C. (2019) Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato. Proceedings of the National Academy of Sciences of the United States of America, 116, 2755-2760.
Chen, H.M., Chen, L.T., Patel, K., Li, Y.H., Baulcombe, D.C. & Wu, S.H. (2010) 22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proceedings of the National Academy of Sciences of the United States of America, 107, 15269-15274.
Cuperus, J.T., Carbonell, A., Fahlgren, N., Garcia-Ruiz, H., Burke, R.T., Takeda, A. et al. (2010) Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nature Structural & Molecular Biology, 17, 997-1003.
Deng, Y., Wang, J., Tung, J., Liu, D., Zhou, Y., He, S. et al. (2018) A role for small RNA in regulating innate immunity during plant growth. PLoS Pathogens, 14, e1006756.
Felsenstein, J. (1985) Confidence-limits on phylogenies - an approach using the bootstrap. Evolution, 39, 783-791.
Flickinger, J.L., Gebeyehu, G., Buchman, G., Haces, A. & Rashtchian, A. (1992) Differential incorporation of biotinylated nucleotides by terminal deoxynucleotidyl transferase. Nucleic Acids Research, 20, 2382.
Freitag, S., Le Trong, I., Chilkoti, A., Klumb, L.A., Stayton, P.S. & Stenkamp, R.E. (1998) Structural studies of binding site tryptophan mutants in the high-affinity streptavidin-biotin complex. Journal of Molecular Biology, 279, 211-221.
Hamilton, A.J. & Baulcombe, D.C. (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science, 286, 950-952.
Hong, Y., Meng, J., He, X., Zhang, Y., Liu, Y., Zhang, C. et al. (2021) Editing miR482b and miR482c simultaneously by CRISPR/Cas9 enhanced tomato resistance to Phytophthora infestans. Phytopathology, 111, 1008-1016.
Jiang, N., Meng, J., Cui, J., Sun, G. & Luan, Y. (2018) Function identification of miR482b, a negative regulator during tomato resistance to Phytophthora infestans. Horticulture Research, 5, 9.
Kim, S.W., Li, Z., Moore, P.S., Monaghan, A.P., Chang, Y., Nichols, M. et al. (2010) A sensitive non-radioactive northern blot method to detect small RNAs. Nucleic Acids Research, 38, e98.
Kumar, P., Johnston, B.H. & Kazakov, S.A. (2011) miR-ID: a novel, circularization-based platform for detection of microRNAs. RNA, 17, 365-380.
Kumar, S., Stecher, G. & Tamura, K. (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870-1874.
Lagos-Quintana, M., Rauhut, R., Lendeckel, W. & Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs. Science, 294, 853-858.
Lau, N.C., Lim, L.P., Weinstein, E.G. & Bartel, D.P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294, 858-862.
Lee, R.C. & Ambros, V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science, 294, 862-864.
Lee, R.C., Feinbaum, R.L. & Ambros, V. (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75, 843-854.
Li, F., Orban, R. & Baker, B. (2012) SoMART: a web server for plant miRNA, tasiRNA and target gene analysis. The Plant Journal, 70, 891-901.
Li, F., Pignatta, D., Bendix, C., Brunkard, J.O., Cohn, M.M., Tung, J. et al. (2012) MicroRNA regulation of plant innate immune receptors. Proceedings of the National Academy of Sciences of the United States of America, 109, 1790-1795.
Li, S., Castillo-Gonzalez, C., Yu, B. & Zhang, X. (2017) The functions of plant small RNAs in development and in stress responses. The Plant Journal, 90, 654-670.
Lister, R., O'Malley, R.C., Tonti-Filippini, J., Gregory, B.D., Berry, C.C., Millar, A.H. et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell, 133, 523-536.
Liu, F., Zhao, J.T., Sun, H.H., Xiong, C., Sun, X.P., Wang, X. et al. (2023) Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation. Nature Communications, 14, 5487.
Lopez-Gomollon, S. & Baulcombe, D.C. (2022) Roles of RNA silencing in viral and non-viral plant immunity and in the crosstalk between disease resistance systems. Nature Reviews. Molecular Cell Biology, 23, 645-662.
Lu, C., Tej, S.S., Luo, S., Haudenschild, C.D., Meyers, B.C. & Green, P.J. (2005) Elucidation of the small RNA component of the transcriptome. Science, 309, 1567-1569.
Mahalingam, G. & Meyers, B.C. (2010) Computational methods for comparative analysis of plant small RNAs. Methods in Molecular Biology, 592, 163-181.
Mateos, J.L., Bologna, N.G., Chorostecki, U. & Palatnik, J.F. (2010) Identification of microRNA processing determinants by random mutagenesis of Arabidopsis MIR172a precursor. Current Biology, 20, 49-54.
Miller, B.R., Wei, T., Fields, C.J., Sheng, P. & Xie, M. (2018) Near-infrared fluorescent northern blot. RNA, 24, 1871-1877.
Nei, M. & Kumar, S. (2000) Molecular evolution and phylogenetics. New York: Oxford University Press.
Nobuta, K., Lu, C., Shrivastava, R., Pillay, M., De Paoli, E., Accerbi, M. et al. (2008) Distinct size distribution of endogeneous siRNAs in maize: evidence from deep sequencing in the mop1-1 mutant. Proceedings of the National Academy of Sciences of the United States of America, 105, 14958-14963.
Pall, G.S. & Hamilton, A.J. (2008) Improved northern blot method for enhanced detection of small RNA. Nature Protocols, 3, 1077-1084.
Potato Genome Sequencing Consortium, Xu, X., Pan, S., Cheng, S., Zhang, B., Mu, D. et al. (2011) Genome sequence and analysis of the tuber crop potato. Nature, 475, 189-195.
Qin, C., Yu, C., Shen, Y., Fang, X., Chen, L., Min, J. et al. (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proceedings of the National Academy of Sciences of the United States of America, 111, 5135-5140.
Rogers, K. & Chen, X. (2013) Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell, 25, 2383-2399.
Saitou, N. & Nei, M. (1987) The neighbor-joining method - a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T. et al. (2012) Fiji: an open-source platform for biological-image analysis. Nature Methods, 9, 676-682.
Sha, A., Zhao, J., Yin, K., Tang, Y., Wang, Y., Wei, X. et al. (2014) Virus-based microRNA silencing in plants. Plant Physiology, 164, 36-47.
Shi, R. & Chiang, V.L. (2005) Facile means for quantifying microRNA expression by real-time PCR. BioTechniques, 39, 519-525.
Sierro, N., Battey, J.N., Ouadi, S., Bakaher, N., Bovet, L., Willig, A. et al. (2014) The tobacco genome sequence and its comparison with those of tomato and potato. Nature Communications, 5, 3833.
Song, L., Axtell, M.J. & Fedoroff, N.V. (2010) RNA secondary structural determinants of miRNA precursor processing in Arabidopsis. Current Biology, 20, 37-41.
Tomato Genome Consortium. (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485, 635-641.
Valoczi, A., Hornyik, C., Varga, N., Burgyan, J., Kauppinen, S. & Havelda, Z. (2004) Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Research, 32, e175.
Werner, S., Wollmann, H., Schneeberger, K. & Weigel, D. (2010) Structure determinants for accurate processing of miR172a in Arabidopsis thaliana. Current Biology, 20, 42-48.
Zhang, X., Zhang, Q., Cheng, L., Liu, D., Wang, H., Zhou, Y. et al. (2022) A new biotin labeling and high-molecular-weight RNA northern method and its application in viral RNA detection. Viruses, 14, 2664.
Zhou, Y., Deng, Y., Liu, D., Wang, H., Zhang, X., Liu, T. et al. (2021) Promoting virus-induced gene silencing of pepper genes by a heterologous viral silencing suppressor. Plant Biotechnology Journal, 19, 2398-2400.
Zhu, H., Zhou, Y., Castillo-Gonzalez, C., Lu, A., Ge, C., Zhao, Y.-T. et al. (2013) Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1. Nature Structural & Molecular Biology, 20, 1106-1115.