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Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo

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Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo

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Yang, M.; Woolfenden, HC.; Zhang, Y.; Fang, X.; Liu, Q.; Vigh, ML.; Cheema, J.... (2020). Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo. Nucleic Acids Research. 48(15):8767-8781. https://doi.org/10.1093/nar/gkaa577

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Title: Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo
Author: Yang, Minglei Woolfenden, Hugh C. Zhang, Yueying Fang, Xiaofeng Liu, Qi Vigh, Maria L. Cheema, Jitender Yang, Xiaofei Norris, Matthew Yu, Sha CARBONELL, ALBERTO Brodersen, Peter Wang, Jiawei Ding, Yiliang
UPV Unit: Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes
Issued date:
[EN] MicroRNA (miRNA)-mediated cleavage is involved in numerous essential cellular pathways. miRNAs recognize target RNAs via sequence complementarity. In addition to complementarity, in vitro and in silico studies have ...[+]
Copyrigths: Reconocimiento (by)
Nucleic Acids Research. (issn: 0305-1048 )
DOI: 10.1093/nar/gkaa577
Oxford University Press
Publisher version: https://doi.org/10.1093/nar/gkaa577
Project ID:
info:eu-repo/grantAgreement/EC/H2020/680324/EU/Investigating the role of in vivo RNA structure in RNA degradation/
info:eu-repo/grantAgreement/UKRI//BB%2FL025000%2F1/GB/The role of RNA structures in plant response to temperature/
Biotechnology and Biological Sciences Research Council [BB/L025000/1]; the NorwichResearch Park Science Links Seed Fund; and European Commission Horizon 2020 European Research Council, Starting Grant [680324]. Funding for ...[+]
Type: Artículo


Fang, W., & Bartel, D. P. (2015). The Menu of Features that Define Primary MicroRNAs and Enable De Novo Design of MicroRNA Genes. Molecular Cell, 60(1), 131-145. doi:10.1016/j.molcel.2015.08.015

Yu, Y., Jia, T., & Chen, X. (2017). The ‘how’ and ‘where’ of plant micro RNA s. New Phytologist, 216(4), 1002-1017. doi:10.1111/nph.14834

Zhang, C., Ng, D. W. ‐K., Lu, J., & Chen, Z. J. (2011). Roles of target site location and sequence complementarityin trans‐acting siRNA formation in Arabidopsis. The Plant Journal, 69(2), 217-226. doi:10.1111/j.1365-313x.2011.04783.x [+]
Fang, W., & Bartel, D. P. (2015). The Menu of Features that Define Primary MicroRNAs and Enable De Novo Design of MicroRNA Genes. Molecular Cell, 60(1), 131-145. doi:10.1016/j.molcel.2015.08.015

Yu, Y., Jia, T., & Chen, X. (2017). The ‘how’ and ‘where’ of plant micro RNA s. New Phytologist, 216(4), 1002-1017. doi:10.1111/nph.14834

Zhang, C., Ng, D. W. ‐K., Lu, J., & Chen, Z. J. (2011). Roles of target site location and sequence complementarityin trans‐acting siRNA formation in Arabidopsis. The Plant Journal, 69(2), 217-226. doi:10.1111/j.1365-313x.2011.04783.x

Liu, Q., Wang, F., & Axtell, M. J. (2014). Analysis of Complementarity Requirements for Plant MicroRNA Targeting Using a Nicotiana benthamiana Quantitative Transient Assay  . The Plant Cell, 26(2), 741-753. doi:10.1105/tpc.113.120972

Ameres, S. L., Martinez, J., & Schroeder, R. (2007). Molecular Basis for Target RNA Recognition and Cleavage by Human RISC. Cell, 130(1), 101-112. doi:10.1016/j.cell.2007.04.037

Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U., & Segal, E. (2007). The role of site accessibility in microRNA target recognition. Nature Genetics, 39(10), 1278-1284. doi:10.1038/ng2135

Long, D., Lee, R., Williams, P., Chan, C. Y., Ambros, V., & Ding, Y. (2007). Potent effect of target structure on microRNA function. Nature Structural & Molecular Biology, 14(4), 287-294. doi:10.1038/nsmb1226

Ding, Y., Tang, Y., Kwok, C. K., Zhang, Y., Bevilacqua, P. C., & Assmann, S. M. (2013). In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature, 505(7485), 696-700. doi:10.1038/nature12756

Rouskin, S., Zubradt, M., Washietl, S., Kellis, M., & Weissman, J. S. (2013). Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature, 505(7485), 701-705. doi:10.1038/nature12894

Spitale, R. C., Flynn, R. A., Zhang, Q. C., Crisalli, P., Lee, B., Jung, J.-W., … Chang, H. Y. (2015). Structural imprints in vivo decode RNA regulatory mechanisms. Nature, 519(7544), 486-490. doi:10.1038/nature14263

Wells, S. E., Hughes, J. M. ., Haller Igel, A., & Ares, M. (2000). [32] Use of dimethyl sulfate to probe RNA structure in vivo. RNA-Ligand Interactions Part B, 479-493. doi:10.1016/s0076-6879(00)18071-1

Merino, E. J., Wilkinson, K. A., Coughlan, J. L., & Weeks, K. M. (2005). RNA Structure Analysis at Single Nucleotide Resolution by Selective 2‘-Hydroxyl Acylation and Primer Extension (SHAPE). Journal of the American Chemical Society, 127(12), 4223-4231. doi:10.1021/ja043822v

Flynn, R. A., Zhang, Q. C., Spitale, R. C., Lee, B., Mumbach, M. R., & Chang, H. Y. (2016). Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nature Protocols, 11(2), 273-290. doi:10.1038/nprot.2016.011

Talkish, J., May, G., Lin, Y., Woolford, J. L., & McManus, C. J. (2014). Mod-seq: high-throughput sequencing for chemical probing of RNA structure. RNA, 20(5), 713-720. doi:10.1261/rna.042218.113

Zubradt, M., Gupta, P., Persad, S., Lambowitz, A. M., Weissman, J. S., & Rouskin, S. (2016). DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Nature Methods, 14(1), 75-82. doi:10.1038/nmeth.4057

Siegfried, N. A., Busan, S., Rice, G. M., Nelson, J. A. E., & Weeks, K. M. (2014). RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). Nature Methods, 11(9), 959-965. doi:10.1038/nmeth.3029

Souret, F. F., Kastenmayer, J. P., & Green, P. J. (2004). AtXRN4 Degrades mRNA in Arabidopsis and Its Substrates Include Selected miRNA Targets. Molecular Cell, 15(2), 173-183. doi:10.1016/j.molcel.2004.06.006

German, M. A., Pillay, M., Jeong, D.-H., Hetawal, A., Luo, S., Janardhanan, P., … Green, P. J. (2008). Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends. Nature Biotechnology, 26(8), 941-946. doi:10.1038/nbt1417

Spitale, R. C., Crisalli, P., Flynn, R. A., Torre, E. A., Kool, E. T., & Chang, H. Y. (2012). RNA SHAPE analysis in living cells. Nature Chemical Biology, 9(1), 18-20. doi:10.1038/nchembio.1131

Pelechano, V., Wei, W., & Steinmetz, L. M. (2016). Genome-wide quantification of 5′-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics. Nature Protocols, 11(2), 359-376. doi:10.1038/nprot.2016.026

Deigan, K. E., Li, T. W., Mathews, D. H., & Weeks, K. M. (2008). Accurate SHAPE-directed RNA structure determination. Proceedings of the National Academy of Sciences, 106(1), 97-102. doi:10.1073/pnas.0806929106

Addo-Quaye, C., Eshoo, T. W., Bartel, D. P., & Axtell, M. J. (2008). Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome. Current Biology, 18(10), 758-762. doi:10.1016/j.cub.2008.04.042

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10(3), R25. doi:10.1186/gb-2009-10-3-r25

Fahlgren, N., Howell, M. D., Kasschau, K. D., Chapman, E. J., Sullivan, C. M., Cumbie, J. S., … Carrington, J. C. (2007). High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes. PLoS ONE, 2(2), e219. doi:10.1371/journal.pone.0000219

Srivastava, P. K., Moturu, T. R., Pandey, P., Baldwin, I. T., & Pandey, S. P. (2014). A comparison of performance of plant miRNA target prediction tools and the characterization of features for genome-wide target prediction. BMC Genomics, 15(1). doi:10.1186/1471-2164-15-348

Dimitrov, R. (2014). microRNA Gene Finding and Target Prediction - Basic Principles and Challenges. MOJ Proteomics & Bioinformatics, 1(4). doi:10.15406/mojpb.2014.01.00024

Wang, Y., Juranek, S., Li, H., Sheng, G., Tuschl, T., & Patel, D. J. (2008). Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature, 456(7224), 921-926. doi:10.1038/nature07666

Sheng, G., Zhao, H., Wang, J., Rao, Y., Tian, W., Swarts, D. C., … Wang, Y. (2013). Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proceedings of the National Academy of Sciences, 111(2), 652-657. doi:10.1073/pnas.1321032111

Schirle, N. T., & MacRae, I. J. (2012). The Crystal Structure of Human Argonaute2. Science, 336(6084), 1037-1040. doi:10.1126/science.1221551

Nakanishi, K., Weinberg, D. E., Bartel, D. P., & Patel, D. J. (2012). Structure of yeast Argonaute with guide RNA. Nature, 486(7403), 368-374. doi:10.1038/nature11211

Rosta, E., Nowotny, M., Yang, W., & Hummer, G. (2011). Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations. Journal of the American Chemical Society, 133(23), 8934-8941. doi:10.1021/ja200173a

Wu, F.-H., Shen, S.-C., Lee, L.-Y., Lee, S.-H., Chan, M.-T., & Lin, C.-S. (2009). Tape-Arabidopsis Sandwich - a simpler Arabidopsis protoplast isolation method. Plant Methods, 5(1). doi:10.1186/1746-4811-5-16

Kwok, C. K., Ding, Y., Tang, Y., Assmann, S. M., & Bevilacqua, P. C. (2013). Determination of in vivo RNA structure in low-abundance transcripts. Nature Communications, 4(1). doi:10.1038/ncomms3971

McGraw, R. A. (1984). Dideoxy DNA sequencing with end-labeled oligonucleotide primers. Analytical Biochemistry, 143(2), 298-303. doi:10.1016/0003-2697(84)90666-3

Karabiber, F., McGinnis, J. L., Favorov, O. V., & Weeks, K. M. (2012). QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis. RNA, 19(1), 63-73. doi:10.1261/rna.036327.112

Varkonyi-Gasic, E., Wu, R., Wood, M., Walton, E. F., & Hellens, R. P. (2007). Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods, 3(1), 12. doi:10.1186/1746-4811-3-12

Ding, Y., Kwok, C. K., Tang, Y., Bevilacqua, P. C., & Assmann, S. M. (2015). Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq. Nature Protocols, 10(7), 1050-1066. doi:10.1038/nprot.2015.064

Studer, S. M., & Joseph, S. (2006). Unfolding of mRNA Secondary Structure by the Bacterial Translation Initiation Complex. Molecular Cell, 22(1), 105-115. doi:10.1016/j.molcel.2006.02.014

Burkhardt, D. H., Rouskin, S., Zhang, Y., Li, G.-W., Weissman, J. S., & Gross, C. A. (2017). Operon mRNAs are organized into ORF-centric structures that predict translation efficiency. eLife, 6. doi:10.7554/elife.22037

Wan, Y., Qu, K., Zhang, Q. C., Flynn, R. A., Manor, O., Ouyang, Z., … Chang, H. Y. (2014). Landscape and variation of RNA secondary structure across the human transcriptome. Nature, 505(7485), 706-709. doi:10.1038/nature12946

Smola, M. J., & Weeks, K. M. (2018). In-cell RNA structure probing with SHAPE-MaP. Nature Protocols, 13(6), 1181-1195. doi:10.1038/nprot.2018.010

Jackowiak, P., Nowacka, M., Strozycki, P. M., & Figlerowicz, M. (2011). RNA degradome--its biogenesis and functions. Nucleic Acids Research, 39(17), 7361-7370. doi:10.1093/nar/gkr450

Aukerman, M. J., & Sakai, H. (2003). Regulation of Flowering Time and Floral Organ Identity by a MicroRNA and Its APETALA2-Like Target Genes. The Plant Cell, 15(11), 2730-2741. doi:10.1105/tpc.016238

Li, S., Liu, L., Zhuang, X., Yu, Y., Liu, X., Cui, X., … Chen, X. (2013). MicroRNAs Inhibit the Translation of Target mRNAs on the Endoplasmic Reticulum in Arabidopsis. Cell, 153(3), 562-574. doi:10.1016/j.cell.2013.04.005

Chen, X. (2004). A MicroRNA as a Translational Repressor of APETALA2 in Arabidopsis Flower Development. Science, 303(5666), 2022-2025. doi:10.1126/science.1088060

Schwab, R., Palatnik, J. F., Riester, M., Schommer, C., Schmid, M., & Weigel, D. (2005). Specific Effects of MicroRNAs on the Plant Transcriptome. Developmental Cell, 8(4), 517-527. doi:10.1016/j.devcel.2005.01.018

Yoshikawa, M. (2005). A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes & Development, 19(18), 2164-2175. doi:10.1101/gad.1352605

McGinnis, J. L., Dunkle, J. A., Cate, J. H. D., & Weeks, K. M. (2012). The Mechanisms of RNA SHAPE Chemistry. Journal of the American Chemical Society, 134(15), 6617-6624. doi:10.1021/ja2104075

Bisaria, N., Jarmoskaite, I., & Herschlag, D. (2017). Lessons from Enzyme Kinetics Reveal Specificity Principles for RNA-Guided Nucleases in RNA Interference and CRISPR-Based Genome Editing. Cell Systems, 4(1), 21-29. doi:10.1016/j.cels.2016.12.010

Carbonell, A., Fahlgren, N., Garcia-Ruiz, H., Gilbert, K. B., Montgomery, T. A., Nguyen, T., … Carrington, J. C. (2012). Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer-Defective Mutants  . The Plant Cell, 24(9), 3613-3629. doi:10.1105/tpc.112.099945

Lorenz, R., Hofacker, I. L., & Stadler, P. F. (2016). RNA folding with hard and soft constraints. Algorithms for Molecular Biology, 11(1). doi:10.1186/s13015-016-0070-z

Li, F., Zheng, Q., Vandivier, L. E., Willmann, M. R., Chen, Y., & Gregory, B. D. (2012). Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome. The Plant Cell, 24(11), 4346-4359. doi:10.1105/tpc.112.104232

Dolata, J., Taube, M., Bajczyk, M., Jarmolowski, A., Szweykowska-Kulinska, Z., & Bielewicz, D. (2018). Regulation of Plant Microprocessor Function in Shaping microRNA Landscape. Frontiers in Plant Science, 9. doi:10.3389/fpls.2018.00753

Ji, L., & Chen, X. (2012). Regulation of small RNA stability: methylation and beyond. Cell Research, 22(4), 624-636. doi:10.1038/cr.2012.36

Muqbil, I., Bao, B., Abou-Samra, A., Mohammad, R., & Azmi, A. (2013). Nuclear Export Mediated Regulation of MicroRNAs: Potential Target for Drug Intervention. Current Drug Targets, 14(10), 1094-1100. doi:10.2174/1389450111314100002

Li, S., Le, B., Ma, X., Li, S., You, C., Yu, Y., … Chen, X. (2016). Biogenesis of phased siRNAs on membrane-bound polysomes in Arabidopsis. eLife, 5. doi:10.7554/elife.22750

Bartel, D. P. (2009). MicroRNAs: Target Recognition and Regulatory Functions. Cell, 136(2), 215-233. doi:10.1016/j.cell.2009.01.002

Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C., & Doudna, J. A. (2014). DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature, 507(7490), 62-67. doi:10.1038/nature13011

O’Connell, M. R., Oakes, B. L., Sternberg, S. H., East-Seletsky, A., Kaplan, M., & Doudna, J. A. (2014). Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature, 516(7530), 263-266. doi:10.1038/nature13769

Tambe, A., East-Seletsky, A., Knott, G. J., Doudna, J. A., & O’Connell, M. R. (2018). RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a. Cell Reports, 24(4), 1025-1036. doi:10.1016/j.celrep.2018.06.105

Dagdas, Y. S., Chen, J. S., Sternberg, S. H., Doudna, J. A., & Yildiz, A. (2017). A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9. Science Advances, 3(8). doi:10.1126/sciadv.aao0027

Chen, J. S., & Doudna, J. A. (2017). The chemistry of Cas9 and its CRISPR colleagues. Nature Reviews Chemistry, 1(10). doi:10.1038/s41570-017-0078

Meister, G. (2013). Argonaute proteins: functional insights and emerging roles. Nature Reviews Genetics, 14(7), 447-459. doi:10.1038/nrg3462

Hentze, M. W., Castello, A., Schwarzl, T., & Preiss, T. (2018). A brave new world of RNA-binding proteins. Nature Reviews Molecular Cell Biology, 19(5), 327-341. doi:10.1038/nrm.2017.130

Zuber, J., Cabral, B. J., McFadyen, I., Mauger, D. M., & Mathews, D. H. (2018). Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction. RNA, 24(11), 1568-1582. doi:10.1261/rna.065102.117




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