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Linking circular intronic RNA degradation and function in transcription by RNase H1

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Abstract

Circular intronic RNAs (ciRNAs) escaping from DBR1 debranching of intron lariats are co-transcriptionally produced from pre-mRNA splicing, but their turnover and mechanism of action have remained elusive. We report that RNase H1 degrades a subgroup of ciRNAs in human cells. Many ciRNAs contain high GC% and tend to form DNA:RNA hybrids (R-loops) for RNase H1 cleavage, a process that appears to promote Pol II transcriptional elongation at ciRNA-producing loci. One ciRNA, ciankrd52, shows a stronger ability of R-loop formation than that of its cognate pre-mRNA by maintaining a locally open RNA structure in vitro. This allows the release of pre-mRNA from R-loops by ci-ankrd52 replacement and subsequent ciRNA removal via RNase H1 for efficient transcriptional elongation. We propose that such an R-loop dependent ciRNA degradation likely represents a mechanism that on one hand limits ciRNA accumulation by recruiting RNase H1 and on the other hand resolves R-loops for transcriptional elongation at some GC-rich ciRNA-producing loci.

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References

  • Ariel, F., Lucero, L., Christ, A., Mammarella, M.F., Jegu, T., Veluchamy, A., Mariappan, K., Latrasse, D., Blein, T., Liu, C., et al. (2020). R-loop mediated trans action of the APOLO long noncoding RNA. Mol Cell 77, 1055–1065.e4.

    Article  CAS  PubMed  Google Scholar 

  • Armakola, M., Higgins, M.J., Figley, M.D., Barmada, S.J., Scarborough, E. A., Diaz, Z., Fang, X., Shorter, J., Krogan, N.J., Finkbeiner, S., et al. (2012). Inhibition of RNA lariat debranching enzyme suppresses TDP-43 toxicity in ALS disease models. Nat Genet 44, 1302–1309.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bolger, A.M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bonnet, A., Grosso, A.R., Elkaoutari, A., Coleno, E., Presle, A., Sridhara, S.C., Janbon, G., Géli, V., de Almeida, S.F., and Palancade, B. (2017). Introns protect eukaryotic genomes from transcription-associated genetic instability. Mol Cell 67, 608–621.e6.

    Article  CAS  PubMed  Google Scholar 

  • Busan, S., and Weeks, K.M. (2018). Accurate detection of chemical modifications in RNA by mutational profiling (MaP) with ShapeMapper 2. RNA 24, 143–148.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cerritelli, S.M., and Crouch, R.J. (2009). Ribonuclease H: the enzymes in eukaryotes. FEBS J 276, 1494–1505.

    Article  CAS  PubMed  Google Scholar 

  • Chan, Y.A., Aristizabal, M.J., Lu, P.Y.T., Luo, Z., Hamza, A., Kobor, M.S., Stirling, P.C., and Hieter, P. (2014). Genome-wide profiling of yeast DNA:RNA hybrid prone sites with DRIP-chip. PLoS Genet 10, e1004288.

    Article  PubMed  PubMed Central  Google Scholar 

  • Chen, L., Chen, J.Y., Zhang, X., Gu, Y., Xiao, R., Shao, C., Tang, P., Qian, H., Luo, D., Li, H., et al. (2017). R-ChIP using inactive RNase H reveals dynamic coupling of R-loops with transcriptional pausing at gene promoters. Mol Cell 68, 745–757.e5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen, L.L. (2020). The expanding regulatory mechanisms and cellular functions of circular RNAs. Nat Rev Mol Cell Biol 21, 475–490.

    Article  CAS  PubMed  Google Scholar 

  • Chen, P.B., Chen, H.V., Acharya, D., Rando, O.J., and Fazzio, T.G. (2015). R loops regulate promoter-proximal chromatin architecture and cellular differentiation. Nat Struct Mol Biol 22, 999–1007.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Conn, V.M., Hugouvieux, V., Nayak, A., Conos, S.A., Capovilla, G., Cildir, G., Jourdain, A., Tergaonkar, V., Schmid, M., Zubieta, C., et al. (2017). A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. Nat Plants 3, 17053.

    Article  CAS  PubMed  Google Scholar 

  • Cristini, A., Groh, M., Kristiansen, M.S., and Gromak, N. (2018). RNA/DNA hybrid interactome identifies DXH9 as a molecular player in transcriptional termination and R-loop-associated DNA damage. Cell Rep 23, 1891–1905.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • García-Muse, T., and Aguilera, A. (2019). R loops: from physiological to pathological roles. Cell 179, 604–618.

    Article  PubMed  CAS  Google Scholar 

  • Gardner, E.J., Nizami, Z.F., Talbot, C.C., and Gall, J.G. (2012). Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis. Genes Dev 26, 2550–2559.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ginno, P.A., Lott, P.L., Christensen, H.C., Korf, I., and Chédin, F. (2012). R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell 45, 814–825.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grunseich, C., Wang, I.X., Watts, J.A., Burdick, J.T., Guber, R.D., Zhu, Z., Bruzel, A., Lanman, T., Chen, K., Schindler, A.B., et al. (2018). Senataxin mutation reveals how R-loops promote transcription by blocking DNA methylation at gene promoters. Mol Cell 69, 426–437.e7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hesselberth, J.R. (2013). Lives that introns lead after splicing. WIREs RNA 4, 677–691.

    Article  CAS  PubMed  Google Scholar 

  • Kim, D., and Salzberg, S.L. (2011). TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol 12, R72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim, G.J., Sock, E., Buchberger, A., Just, W., Denzer, F., Hoepffner, W., German, J., Cole, T., Mann, J., Seguin, J.H., et al. (2015). Copy number variation of two separate regulatory regions upstream of SOX9 causes isolated 46,XY or 46,XX disorder of sex development. J Med Genet 52, 240–247.

    Article  CAS  PubMed  Google Scholar 

  • Langmead, B., Trapnell, C., Pop, M., and Salzberg, S.L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079.

    PubMed  PubMed Central  Google Scholar 

  • Li, X., and Manley, J.L. (2005). Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell 122, 365–378.

    Article  CAS  PubMed  Google Scholar 

  • Li, X., Yang, L., and Chen, L.L. (2018). The biogenesis, functions, and challenges of circular RNAs. Mol Cell 71, 428–442.

    Article  CAS  PubMed  Google Scholar 

  • Liao, Y., Smyth, G.K., and Shi, W. (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930.

    Article  CAS  PubMed  Google Scholar 

  • Liu, C.X., Li, X., Nan, F., Jiang, S., Gao, X., Guo, S.K., Xue, W., Cui, Y., Dong, K., Ding, H., et al. (2019). Structure and degradation of circular RNAs regulate PKR activation in innate immunity. Cell 177, 865–880.e21.

    Article  CAS  PubMed  Google Scholar 

  • Liu, Y., and Schmidt, B. (2012). Long read alignment based on maximal exact match seeds. Bioinformatics 28, i318–i324.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lorenz, R., Bernhart, S.H., Höner Zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P.F., and Hofacker, I.L. (2011). ViennaRNA Package 2.0. Algorithms Mol Biol 6, 26.

    Article  PubMed  PubMed Central  Google Scholar 

  • Ma, X.K., Wang, M.R., Liu, C.X., Dong, R., Carmichael, G.G., Chen, L.L., and Yang, L. (2019). CIRCexplorer3: a CLEAR pipeline for direct comparison of circular and linear RNA expression. Genom Proteom Bioinf 17, 511–521.

    Article  Google Scholar 

  • Mersaoui, S.Y., Yu, Z., Coulombe, Y., Karam, M., Busatto, F.F., Masson, J. Y., and Richard, S. (2019). Arginine methylation of the DDX 5 helicase RGG/RG motif by PRMT 5 regulates resolution of RNA:DNA hybrids. EMBO J 38, e100986.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mohanta, A., and Chakrabarti, K. (2020). Dbr1 functions in mRNA processing, intron turnover and human diseases. Biochimie 180, 134–142.

    Article  PubMed  CAS  Google Scholar 

  • Morgan, J.T., Fink, G.R., and Bartel, D.P. (2019). Excised linear introns regulate growth in yeast. Nature 565, 606–611.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., and Wold, B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5, 621–628.

    Article  CAS  PubMed  Google Scholar 

  • Niehrs, C., and Luke, B. (2020). Regulatory R-loops as facilitators of gene expression and genome stability. Nat Rev Mol Cell Biol 21, 167–178.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parenteau, J., Maignon, L., Berthoumieux, M., Catala, M., Gagnon, V., and Abou Elela, S. (2019). Introns are mediators of cell response to starvation. Nature 565, 612–617.

    Article  CAS  PubMed  Google Scholar 

  • Pek, J.W., Osman, I., Tay, M.L.I., and Zheng, R.T. (2015). Stable intronic sequence RNAs have possible regulatory roles in Drosophila melanogaster. J Cell Biol 211, 243–251.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Postepska-Igielska, A., Giwojna, A., Gasri-Plotnitsky, L., Schmitt, N., Dold, A., Ginsberg, D., and Grummt, I. (2015). LncRNA Khps1 regulates expression of the proto-oncogene SPHK1 via triplex-mediated changes in chromatin structure. Mol Cell 60, 626–636.

    Article  CAS  PubMed  Google Scholar 

  • Quinlan, A.R., and Hall, I.M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ribeiro de Almeida, C., Dhir, S., Dhir, A., Moghaddam, A.E., Sattentau, Q., Meinhart, A., and Proudfoot, N.J. (2018). RNA helicase DDX1 converts RNA G-quadruplex structures into R-loops to promote IgH class switch recombination. Mol Cell 70, 650–662.e8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sanz, L.A., and Chédin, F. (2019). High-resolution, strand-specific R-loop mapping via S9.6-based DNA-RNA immunoprecipitation and high-throughput sequencing. Nat Protoc 14, 1734–1755.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shivji, M.K.K., Renaudin, X., Williams, Ç. H., and Venkitaraman, A.R. (2018). BRCA2 regulates transcription elongation by RNA polymerase II to prevent R-loop accumulation. Cell Rep 22, 1031–1039.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song, C., Hotz-Wagenblatt, A., Voit, R., and Grummt, I. (2017). SIRT7 and the DEAD-box helicase DDX21 cooperate to resolve genomic R loops and safeguard genome stability. Genes Dev 31, 1370–1381.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tadokoro, T., and Kanaya, S. (2009). Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes. FEBS J 276, 1482–1493.

    Article  CAS  PubMed  Google Scholar 

  • Talhouarne, G.J.S., and Gall, J.G. (2018). Lariat intronic RNAs in the cytoplasm of vertebrate cells. Proc Natl Acad Sci USA 115, E7970–E7977.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tan-Wong, S.M., Dhir, S., and Proudfoot, N.J. (2019). R-loops promote antisense transcription across the mammalian genome. Mol Cell 76, 600–616.e6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tian, D., Sun, S., and Lee, J.T. (2010). The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 143, 390–403.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J., and Pachter, L. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28, 511–515.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wilusz, J.E. (2018). A 360° view of circular RNAs: from biogenesis to functions. WIREs RNA 9, e1478.

    Article  PubMed  CAS  Google Scholar 

  • Wu, H., Yin, Q.F., Luo, Z., Yao, R.W., Zheng, C.C., Zhang, J., Xiang, J.F., Yang, L., and Chen, L.L. (2016). Unusual processing generates SPA LncRNAs that sequester multiple RNA binding proteins. Mol Cell 64, 534–548.

    Article  CAS  PubMed  Google Scholar 

  • Xing, Y.H., Yao, R.W., Zhang, Y., Guo, C.J., Jiang, S., Xu, G., Dong, R., Yang, L., and Chen, L.L. (2017). SLERT regulates DDX21 rings associated with Pol I transcription. Cell 169, 664–678.e16.

    Article  CAS  PubMed  Google Scholar 

  • Xu, X., Zhang, J., Tian, Y., Gao, Y., Dong, X., Chen, W., Yuan, X., Yin, W., Xu, J., Chen, K., et al. (2020). CircRNA inhibits DNA damage repair by interacting with host gene. Mol Cancer 19, 128.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yin, Q.F., Yang, L., Zhang, Y., Xiang, J.F., Wu, Y.W., Carmichael, G.G., and Chen, L.L. (2012). Long noncoding RNAs with snoRNA ends. Mol Cell 48, 219–230.

    Article  CAS  PubMed  Google Scholar 

  • You, X., Vlatkovic, I., Babic, A., Will, T., Epstein, I., Tushev, G., Akbalik, G., Wang, M., Glock, C., Quedenau, C., et al. (2015). Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity. Nat Neurosci 18, 603–610.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, S.Y., Clark, N.E., Freije, C.A., Pauwels, E., Taggart, A.J., Okada, S., Mandel, H., Garcia, P., Ciancanelli, M.J., Biran, A., et al. (2018). Inborn errors of RNA lariat metabolism in humans with brainstem viral infection. Cell 172, 952–965.e18.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, X.O., Dong, R., Zhang, Y., Zhang, J.L., Luo, Z., Zhang, J., Chen, L. L., and Yang, L. (2016a). Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res 26, 1277–1287.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, X.O., Wang, H.B., Zhang, Y., Lu, X., Chen, L.L., and Yang, L. (2014). Complementary sequence-mediated exon circularization. Cell 159, 134–147.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, Y., Xue, W., Li, X., Zhang, J., Chen, S., Zhang, J.L., Yang, L., and Chen, L.L. (2016b). The biogenesis of nascent circular RNAs. Cell Rep 15, 611–624.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, Y., Zhang, X.O., Chen, T., Xiang, J.F., Yin, Q.F., Xing, Y.H., Zhu, S., Yang, L., and Chen, L.L. (2013). Circular intronic long noncoding RNAs. Mol Cell 51, 792–806.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We would like to thank Chen and Yang laboratories for discussion, and Qianwen Sun for providing helpful comments on DRIP assays. This work was supported by the National Natural Science Foundation of China (NSFC) (91940303, 31725009) and the HHMI International Program (55008728) to L.-L.C., NSFC (31730111, 31925011) to L.Y. and Young Elite Scientists Sponsorship Program (2020QNRC001) to X.L. L.-L. C. acknowledges the support from the XPLORER PRIZE.

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  1. Yang Zhang

    Present address: Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02115, USA

Authors and Affiliations

  1. School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China

    Xiang Li, Jia-Lin Zhang & Ling-Ling Chen

  2. State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China

    Xiang Li, Xiao-Qi Liu, Yang Zhang, Xiang Gao, Jun Zhang & Ling-Ling Chen

  3. CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China

    Jia-Lin Zhang, Yun-Ni Lei, Wei Xue, Fan Nan, Jia Wei & Li Yang

  4. School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China

    Yun-Ni Lei, Xiang Gao, Li Yang & Ling-Ling Chen

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Li, X., Zhang, JL., Lei, YN. et al. Linking circular intronic RNA degradation and function in transcription by RNase H1. Sci. China Life Sci. 64, 1795–1809 (2021). https://doi.org/10.1007/s11427-021-1993-6

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