KARR-seq Reveals Cellular Higher-order RNA Structures and RNA-RNA Interactions

Overview

Journal Nat Biotechnol

Specialty Biotechnology

Date 2024 Jan 18

PMID 38238480

Authors

Tong Wu

Anthony Youzhi Cheng

Yuexiu Zhang

Jiayu Xu

Jinjun Wu

Li Wen

Xiao Li

Bei Liu

Xiaoyang Dou

Pingluan Wang

Linda Zhang

Jingyi Fei

Jianrong Li

Zhengqing Ouyang

Chuan He

Affiliations

Soon will be listed here.

Abstract

RNA fate and function are affected by their structures and interactomes. However, how RNA and RNA-binding proteins (RBPs) assemble into higher-order structures and how RNA molecules may interact with each other to facilitate functions remain largely unknown. Here we present KARR-seq, which uses N-kethoxal labeling and multifunctional chemical crosslinkers to covalently trap and determine RNA-RNA interactions and higher-order RNA structures inside cells, independent of local protein binding to RNA. KARR-seq depicts higher-order RNA structure and detects widespread intermolecular RNA-RNA interactions with high sensitivity and accuracy. Using KARR-seq, we show that translation represses mRNA compaction under native and stress conditions. We determined the higher-order RNA structures of respiratory syncytial virus (RSV) and vesicular stomatitis virus (VSV) and identified RNA-RNA interactions between the viruses and the host RNAs that potentially regulate viral replication.

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References

Somasekharan S, Zhang F, Saxena N, Huang J, Kuo I, Low C . G3BP1-linked mRNA partitioning supports selective protein synthesis in response to oxidative stress. Nucleic Acids Res. 2020; 48(12):6855-6873. PMC: 7337521. DOI: 10.1093/nar/gkaa376. View

Quinodoz S, Jachowicz J, Bhat P, Ollikainen N, Banerjee A, Goronzy I . RNA promotes the formation of spatial compartments in the nucleus. Cell. 2021; 184(23):5775-5790.e30. PMC: 9115877. DOI: 10.1016/j.cell.2021.10.014. View

Ivanov P, Kedersha N, Anderson P . Stress Granules and Processing Bodies in Translational Control. Cold Spring Harb Perspect Biol. 2018; 11(5). PMC: 6496347. DOI: 10.1101/cshperspect.a032813. View

Kedersha N, Panas M, Achorn C, Lyons S, Tisdale S, Hickman T . G3BP-Caprin1-USP10 complexes mediate stress granule condensation and associate with 40S subunits. J Cell Biol. 2016; 212(7):845-60. PMC: 4810302. DOI: 10.1083/jcb.201508028. View

Nicholson B, White K . Functional long-range RNA-RNA interactions in positive-strand RNA viruses. Nat Rev Microbiol. 2014; 12(7):493-504. PMC: 7097572. DOI: 10.1038/nrmicro3288. View

Lu Z, Zhang Q, Lee B, Flynn R, Smith M, Robinson J . RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. Cell. 2016; 165(5):1267-1279. PMC: 5029792. DOI: 10.1016/j.cell.2016.04.028. View

Henras A, Plisson-Chastang C, ODonohue M, Chakraborty A, Gleizes P . An overview of pre-ribosomal RNA processing in eukaryotes. Wiley Interdiscip Rev RNA. 2014; 6(2):225-42. PMC: 4361047. DOI: 10.1002/wrna.1269. View

Van Nostrand E, Freese P, Pratt G, Wang X, Wei X, Xiao R . A large-scale binding and functional map of human RNA-binding proteins. Nature. 2020; 583(7818):711-719. PMC: 7410833. DOI: 10.1038/s41586-020-2077-3. View

Kedersha N, Gupta M, Li W, Miller I, Anderson P . RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF-2 alpha to the assembly of mammalian stress granules. J Cell Biol. 1999; 147(7):1431-42. PMC: 2174242. DOI: 10.1083/jcb.147.7.1431. View

10.

Ouyang Z, Zhou Q, Wong W . ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci U S A. 2009; 106(51):21521-6. PMC: 2789751. DOI: 10.1073/pnas.0904863106. View

11.

Dutca L, Gallagher J, Baserga S . The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing. Nucleic Acids Res. 2011; 39(12):5164-80. PMC: 3130255. DOI: 10.1093/nar/gkr044. View

12.

Yang S, DeFalco L, Anderson D, Zhang Y, Aw J, Lim S . Comprehensive mapping of SARS-CoV-2 interactions in vivo reveals functional virus-host interactions. Nat Commun. 2021; 12(1):5113. PMC: 8387478. DOI: 10.1038/s41467-021-25357-1. View

13.

Metkar M, Ozadam H, Lajoie B, Imakaev M, Mirny L, Dekker J . Higher-Order Organization Principles of Pre-translational mRNPs. Mol Cell. 2018; 72(4):715-726.e3. PMC: 6239896. DOI: 10.1016/j.molcel.2018.09.012. View

14.

Engreitz J, Sirokman K, McDonel P, Shishkin A, Surka C, Russell P . RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites. Cell. 2014; 159(1):188-199. PMC: 4177037. DOI: 10.1016/j.cell.2014.08.018. View

15.

Shah A, Qian Y, Weyn-Vanhentenryck S, Zhang C . CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data. Bioinformatics. 2016; 33(4):566-567. PMC: 6041811. DOI: 10.1093/bioinformatics/btw653. View

16.

Charenton C, Wilkinson M, Nagai K . Mechanism of 5' splice site transfer for human spliceosome activation. Science. 2019; 364(6438):362-367. PMC: 6525098. DOI: 10.1126/science.aax3289. View

17.

Sharma E, Sterne-Weiler T, OHanlon D, Blencowe B . Global Mapping of Human RNA-RNA Interactions. Mol Cell. 2016; 62(4):618-26. DOI: 10.1016/j.molcel.2016.04.030. View

18.

Love M, Huber W, Anders S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15(12):550. PMC: 4302049. DOI: 10.1186/s13059-014-0550-8. View

19.

Lestrade L, Weber M . snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res. 2005; 34(Database issue):D158-62. PMC: 1347365. DOI: 10.1093/nar/gkj002. View

20.

Raj A, Bogaard P, Rifkin S, van Oudenaarden A, Tyagi S . Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods. 2008; 5(10):877-9. PMC: 3126653. DOI: 10.1038/nmeth.1253. View