In vivo single-molecule analysis reveals COOLAIR RNA structural diversity.

Tytuł:: In vivo single-molecule analysis reveals COOLAIR RNA structural diversity.
Autorzy:: Yang M; John Innes Centre, Norwich Research Park, Norwich, UK.
Zhu P; John Innes Centre, Norwich Research Park, Norwich, UK.
Cheema J; John Innes Centre, Norwich Research Park, Norwich, UK.
Bloomer R; John Innes Centre, Norwich Research Park, Norwich, UK.
Mikulski P; John Innes Centre, Norwich Research Park, Norwich, UK.
Liu Q; John Innes Centre, Norwich Research Park, Norwich, UK.
Zhang Y; John Innes Centre, Norwich Research Park, Norwich, UK.
Dean C; John Innes Centre, Norwich Research Park, Norwich, UK. .
Ding Y; John Innes Centre, Norwich Research Park, Norwich, UK. .
Źródło:: Nature [Nature] 2022 Sep; Vol. 609 (7926), pp. 394-399. Date of Electronic Publication: 2022 Aug 17.
Typ publikacji:: Journal Article
Język:: English
Imprint Name(s):: Publication: Basingstoke : Nature Publishing Group
Original Publication: London, Macmillan Journals ltd.
MeSH Terms:: Arabidopsis*/genetics
Nucleic Acid Conformation*
RNA, Antisense*/chemistry
RNA, Antisense*/genetics
RNA, Plant*/chemistry
RNA, Plant*/genetics
RNA, Untranslated*/chemistry
RNA, Untranslated*/genetics
Single Molecule Imaging*
Arabidopsis Proteins/genetics ; Flowers/genetics ; Flowers/growth & development ; Gene Expression Regulation, Plant ; MADS Domain Proteins/genetics ; Transcription Initiation Site ; Transcription, Genetic
References:: Swiezewski, S., Liu, F., Magusin, A. & Dean, C. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462, 799–802 (2009). (PMID: 2001068810.1038/nature08618)
Xu, C. et al. R-loop resolution promotes co-transcriptional chromatin silencing. Nat. Commun. 12, 1790 (2021). (PMID: 3374198410.1038/s41467-021-22083-67979926)
Zhao, Y. et al. Natural temperature fluctuations promote COOLAIR regulation of FLC. Genes Dev. 35, 888–898 (2021). (PMID: 3398597210.1101/gad.348362.1218168555)
Csorba, T., Questa, J. I., Sun, Q. & Dean, C. Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization. Proc. Natl Acad. Sci. USA 111, 16160–16165 (2014). (PMID: 2534942110.1073/pnas.14190301114234544)
Hawkes, E. J. et al. COOLAIR antisense RNAs form evolutionarily conserved elaborate secondary structures. Cell Rep. 16, 3087–3096 (2016). (PMID: 2765367510.1016/j.celrep.2016.08.0456827332)
Zhu, P., Lister, C. & Dean, C. Cold-induced Arabidopsis FRIGIDA nuclear condensates for FLC repression. Nature 599, 657–661 (2021). (PMID: 3473289110.1038/s41586-021-04062-58612926)
Li, P., Tao, Z. & Dean, C. Phenotypic evolution through variation in splicing of the noncoding RNA COOLAIR. Genes Dev. 29, 696–701 (2015). (PMID: 2580584810.1101/gad.258814.1154387712)
Yang, X., Yang, M., Deng, H. & Ding, Y. New era of studying RNA secondary structure and its influence on gene regulation in plants. Front. Plant Sci. 9, 671 (2018). (PMID: 2987244510.3389/fpls.2018.006715972288)
Aw, J. G. A. et al. Determination of isoform-specific RNA structure with nanopore long reads. Nat. Biotechnol. 39, 336–346 (2021). (PMID: 3310668510.1038/s41587-020-0712-z)
Morandi, E. et al. Genome-scale deconvolution of RNA structure ensembles. Nat. Methods 18, 249–252 (2021). (PMID: 3361939210.1038/s41592-021-01075-w)
Tomezsko, P. J. et al. Determination of RNA structural diversity and its role in HIV-1 RNA splicing. Nature 582, 438–442 (2020). (PMID: 3255546910.1038/s41586-020-2253-57310298)
Yang, H., Howard, M. & Dean, C. Antagonistic roles for H3K36me3 and H3K27me3 in the cold-induced epigenetic switch at Arabidopsis FLC. Curr. Biol. 24, 1793–1797 (2014). (PMID: 2506575010.1016/j.cub.2014.06.0474123163)
Spitale, R. C. et al. RNA SHAPE analysis in living cells. Nat. Chem. Biol. 9, 18–20 (2013). (PMID: 2317893410.1038/nchembio.1131)
Wenger, A. M. et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat. Biotechnol. 37, 1155–1162 (2019). (PMID: 3140632710.1038/s41587-019-0217-96776680)
Cannone, J. J. et al. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinform. 3, 2 (2002). (PMID: 10.1186/1471-2105-3-2)
Mathews, D. H., Moss, W. N. & Turner, D. H. Folding and finding RNA secondary structure. Cold Spring Harb. Perspect. Biol. 2, a003665 (2010). (PMID: 2068584510.1101/cshperspect.a0036652982177)
Rouskin, S., Zubradt, M., Washietl, S., Kellis, M. & Weissman, J. S. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505, 701–705 (2014). (PMID: 2433621410.1038/nature12894)
Legiewicz, M. et al. Resistance to RevM10 inhibition reflects a conformational switch in the HIV-1 Rev response element. Proc. Natl Acad. Sci. USA 105, 14365–14370 (2008). (PMID: 1877604710.1073/pnas.08044611052567145)
Sun, Q., Csorba, T., Skourti-Stathaki, K., Proudfoot, N. J. & Dean, C. R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus. Science 340, 619–621 (2013). (PMID: 2364111510.1126/science.12348485144995)
Zhao, Z., Sentürk, N., Song, C. & Grummt, I. lncRNA PAPAS tethered to the rDNA enhancer recruits hypophosphorylated CHD4/NuRD to repress rRNA synthesis at elevated temperatures. Genes Dev. 32, 836–848 (2018). (PMID: 2990765110.1101/gad.311688.1186049515)
Maldonado, R., Filarsky, M., Grummt, I. & Längst, G. Purine- and pyrimidine-triple-helix-forming oligonucleotides recognize qualitatively different target sites at the ribosomal DNA locus. RNA 24, 371–380 (2018). (PMID: 2922211810.1261/rna.063800.1175824356)
Li, Z., Jiang, D. & He, Y. FRIGIDA establishes a local chromosomal environment for FLOWERING LOCUS C mRNA production. Nat. Plants 4, 836–846 (2018). (PMID: 3022466210.1038/s41477-018-0250-6)
Hepworth, J. et al. Natural variation in autumn expression is the major adaptive determinant distinguishing Arabidopsis FLC haplotypes. eLife 9, e57671 (2020). (PMID: 3290238010.7554/eLife.576717518893)
Chung, B. Y. W. et al. An RNA thermoswitch regulates daytime growth in Arabidopsis. Nat. Plants 6, 522–532 (2020). (PMID: 3228454410.1038/s41477-020-0633-37231574)
Li, W. et al. EIN2-directed translational regulation of ethylene signaling in Arabidopsis. Cell 163, 670–683 (2015). (PMID: 2649660710.1016/j.cell.2015.09.037)
Jones, J. D. G. et al. Effective vectors for transformation, expression of heterologous genes, and assaying transposon excision in transgenic plants. Transgenic Res. 1, 285–297 (1992). (PMID: 133869610.1007/BF02525170)
Chaisson, M. J. & Tesler, G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinform. 13, 238 (2012). (PMID: 10.1186/1471-2105-13-238)
Spitale, R. C. et al. Structural imprints in vivo decode RNA regulatory mechanisms. Nature 519, 486–490 (2015). (PMID: 2579999310.1038/nature142634376618)
Do, C. B., Woods, D. A. & Batzoglou, S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 22, e90–e98 (2006). (PMID: 1687352710.1093/bioinformatics/btl246)
Hamada, M., Kiryu, H., Sato, K., Mituyama, T. & Asai, K. Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics 25, 465–473 (2009). (PMID: 1909570010.1093/bioinformatics/btn601)
Thiel, B. C., Beckmann, I. K., Kerpedjiev, P. & Hofacker, I. L. 3D based on 2D: calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. F1000Res. 8, 287 (2019). (PMID: 10.12688/f1000research.18458.2)
Pedregosa, F. et al. Scikit-Learn: machine learning in Python. J. Mach. Learn. Res. 12, 2825–2830 (2011).
Zhang, Y. et al. A stress response that monitors and regulates mRNA structure is central to cold shock adaptation. Mol. Cell 70, 274–286 (2018). (PMID: 2962830710.1016/j.molcel.2018.02.0355910227)
Smola, M. J., Rice, G. M., Busan, S., Siegfried, N. A. & Weeks, K. M. Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis. Nat. Protoc. 10, 1643–1669 (2015). (PMID: 2642649910.1038/nprot.2015.1034900152)
Lorenz, R. et al. ViennaRNA package 2.0. Algorithms Mol. Biol. 6, 26 (2011). (PMID: 2211518910.1186/1748-7188-6-263319429)
Box, M. S., Coustham, V., Dean, C. & Mylne, J. S. Protocol: a simple phenol-based method for 96-well extraction of high quality RNA from Arabidopsis. Plant Methods 7, 7 (2011). (PMID: 2139612510.1186/1746-4811-7-73069952)
Wu, Z. et al. Quantitative regulation of FLC via coordinated transcriptional initiation and elongation. Proc. Natl Acad. Sci. USA 113, 218–223 (2015). (PMID: 2669951310.1073/pnas.15183691124711845)
Wu, Z. et al. RNA binding proteins RZ-1B and RZ-1C play critical roles in regulating pre-mRNA splicing and gene expression during development in Arabidopsis. Plant Cell 28, 55–73 (2016). (PMID: 2672186310.1105/tpc.15.00949)
Zhu, P. et al. Arabidopsis small nucleolar RNA monitors the efficient pre-rRNA processing during ribosome biogenesis. Proc. Natl Acad. Sci. USA 113, 11967–11972 (2016). (PMID: 2770816110.1073/pnas.16148521135081647)
Chu, C., Quinn, J. & Chang, H. Y. Chromatin isolation by RNA purification (ChIRP). J. Vis. Exp. https://doi.org/10.3791/3912 (2012).
Yang, M. et al. Intact RNA structurome reveals mRNA structure-mediated regulation of miRNA cleavage in vivo. Nucleic Acids Res. 48, 8767–8781 (2020). (PMID: 3265204110.1093/nar/gkaa5777470952)
Dowell, R. D. & Eddy, S. R. Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinform. 5, 71 (2004). (PMID: 10.1186/1471-2105-5-71)
Jiang, T., Wang, L. & Zhang, K. Alignment of trees—an alternative to tree edit. Theor. Comput. Sci. 143, 137–148 (1995). (PMID: 10.1016/0304-3975(95)80029-9)
Deigan, K. E., Li, T. W., Mathews, D. H. & Weeks, K. M. Accurate SHAPE-directed RNA structure determination. Proc. Natl Acad. Sci. USA 106, 97–102 (2009). (PMID: 1910944110.1073/pnas.0806929106)
Buske, F. A., Bauer, D. C., Mattick, J. S. & Bailey, T. L. Triplexator: detecting nucleic acid triple helices in genomic and transcriptomic data. Genome Res. 22, 1372–1381 (2012). (PMID: 2255001210.1101/gr.130237.1113396377)
Grant Information:: BBS/E/J/000PR9788 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; BBS/E/J/000PR9773 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; 680324 International ERC_ European Research Council; 210654 United Kingdom WT_ Wellcome Trust; 210654/Z/18/Z United Kingdom WT_ Wellcome Trust
Substance Nomenclature:: 0 (Arabidopsis Proteins)
0 (FLF protein, Arabidopsis)
0 (MADS Domain Proteins)
0 (RNA, Antisense)
0 (RNA, Plant)
0 (RNA, Untranslated)
Entry Date(s):: Date Created: 20220817 Date Completed: 20220909 Latest Revision: 20240214
Update Code:: 20240214
PubMed Central ID:: PMC9452300
DOI:: 10.1038/s41586-022-05135-9
PMID:: 35978193
: Czasopismo naukowe

Full Text Finder

Cellular RNAs are heterogeneous with respect to their alternative processing and secondary structures, but the functional importance of this complexity is still poorly understood. A set of alternatively processed antisense non-coding transcripts, which are collectively called COOLAIR, are generated at the Arabidopsis floral-repressor locus FLOWERING LOCUS C (FLC) 1 . Different isoforms of COOLAIR influence FLC transcriptional output in warm and cold conditions 2-7 . Here, to further investigate the function of COOLAIR, we developed an RNA structure-profiling method to determine the in vivo structure of single RNA molecules rather than the RNA population average. This revealed that individual isoforms of the COOLAIR transcript adopt multiple structures with different conformational dynamics. The major distally polyadenylated COOLAIR isoform in warm conditions adopts three predominant structural conformations, the proportions and conformations of which change after cold exposure. An alternatively spliced, strongly cold-upregulated distal COOLAIR isoform 6 shows high structural diversity, in contrast to proximally polyadenylated COOLAIR. A hyper-variable COOLAIR structural element was identified that was complementary to the FLC transcription start site. Mutations altering the structure of this region changed FLC expression and flowering time, consistent with an important regulatory role of the COOLAIR structure in FLC transcription. Our work demonstrates that isoforms of non-coding RNA transcripts adopt multiple distinct and functionally relevant structural conformations, which change in abundance and shape in response to external conditions.
(© 2022. The Author(s).)

Comment in: Nat Rev Mol Cell Biol. 2022 Oct;23(10):642-643. (PMID: 36045176)
Comment in: Dev Cell. 2022 Oct 10;57(19):2254-2256. (PMID: 36220080)
Comment in: Trends Biochem Sci. 2023 Mar;48(3):211-212. (PMID: 36670017)

Informacja