Identification of genetic variants controlling RNA editing and their effect on RNA structure stabilization

Abstract

Post-transcriptional modification of RNA (RNA editing, RNAe) results in differences between the RNA transcript and the genomic DNA sequence (RDD). Enzymatic modification of adenosine to inosine (A2I) by ADAR is the most studied type of RNAe. However, few genetic association studies with A2I RNAe events have been conducted. Some studies have analyzed the inter-population RNAe-QTL diversity in humans, but the sample size of these studies was limited. Other types of RNA and DNA differences have been reported but are largely understudied. Here, we report a comprehensive analysis of all types of RDD, based on two independent datasets. We found that A2I was by far the most observed type of RDD. Moreover, manual curation suggests that A2I is likely the only enzymatically driven RNAe type observed in blood derived DNA, all other non-A2I RDD could either be attributed to sequencing and processing artifacts, or are a result of somatic DNA rearrangements. We then conducted an in-cis genetic association study and identified 472 genetic associations (RNAe-QTL), that were replicated in both datasets. We confirm the potential effect of the RNAe-QTL on RNA structure by showing that allele specific RNAe occurs in heterozygotes. Although the generally assumed function of RNAe is to destabilize double stranded RNA structure, we found clear evidence for the potential additional involvement of RNAe in maintaining RNA hairpin that has been altered by the RNAe-QTL. Our study confirms, in two independent datasets, the potential role of RNAe in maintaining RNA structure in the presence of genetic variation.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: Schematic view of the study design.
Fig. 2: Characteristics of detected A2I and non-A2I.
Fig. 3: Effect of the RNAe-QTL on the RNA secondary structure. Three other cases are provided in Fig S4–S6.
Fig. 4: Allele specific RNA editing (ASE).

Data availability

Complete summary statistics for genetic association with RNAe level in both datasets, Gauvadis and QMDiab, are available at https://figshare.com/projects/RNAe/77310.

References

  1. 1.

    Nishikura K. Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem. 2010;79:321–49.

    CAS  Article  Google Scholar 

  2. 2.

    Liddicoat BJ, Piskol R, Chalk AM, Ramaswami G, Higuchi M, Hartner JC, et al. RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself. Science. 2015;349:1115–20.

    CAS  Article  Google Scholar 

  3. 3.

    Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, et al. Dynamic landscape and regulation of RNA editing in mammals. Nature. 2017;550:249–54.

    Article  Google Scholar 

  4. 4.

    Jacobs MM, Fogg RL, Emeson RB, Stanwood GD. ADAR1 and ADAR2 expression and editing activity during forebrain development. Dev Neurosci. 2009;31:223–37.

    CAS  Article  Google Scholar 

  5. 5.

    Ramaswami G, Li JB. RADAR: a rigorously annotated database of A-to-I RNA editing. Nucleic Acids Res. 2014;42 Database issue:D109-113.

  6. 6.

    Kiran AM, O’Mahony JJ, Sanjeev K, Baranov PV. Darned in 2013: inclusion of model organisms and linking with Wikipedia. Nucleic Acids Res. 2013;41 Database issue:D258-261.

  7. 7.

    Stellos K, Gatsiou A, Stamatelopoulos K, Perisic Matic L, John D, Lunella FF, et al. Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation. Nat Med. 2016;22:1140–50.

    CAS  Article  Google Scholar 

  8. 8.

    Prasanth KV, Prasanth SG, Xuan Z, Hearn S, Freier SM, Bennett CF, et al. Regulating gene expression through RNA nuclear retention. Cell. 2005;123:249–63.

    CAS  Article  Google Scholar 

  9. 9.

    Rueter SM, Dawson TR, Emeson RB. Regulation of alternative splicing by RNA editing. Nature. 1999;399:75–80.

    CAS  Article  Google Scholar 

  10. 10.

    Brümmer A, Yang Y, Chan TW, Xiao X. Structure-mediated modulation of mRNA abundance by A-to-I editing. Nat Commun. 2017;8:1255.

    Article  Google Scholar 

  11. 11.

    Miyamura Y, Suzuki T, Kono M, Inagaki K, Ito S, Suzuki N, et al. Mutations of the RNA-specific adenosine deaminase gene (DSRAD) are involved in dyschromatosis symmetrica hereditaria. Am J Hum Genet. 2003;73:693–9.

    CAS  Article  Google Scholar 

  12. 12.

    Rice GI, Kasher PR, Forte GMA, Mannion NM, Greenwood SM, Szynkiewicz M, et al. Mutations in ADAR1 cause Aicardi-Goutières syndrome associated with a type I interferon signature. Nat Genet. 2012;44:1243–8.

    CAS  Article  Google Scholar 

  13. 13.

    Gaisler-Salomon I, Kravitz E, Feiler Y, Safran M, Biegon A, Amariglio N, et al. Hippocampus-specific deficiency in RNA editing of GluA2 in Alzheimer’s disease. Neurobiol Aging. 2014;35:1785–91.

    CAS  Article  Google Scholar 

  14. 14.

    Galeano F, Rossetti C, Tomaselli S, Cifaldi L, Lezzerini M, Pezzullo M, et al. ADAR2-editing activity inhibits glioblastoma growth through the modulation of the CDC14B/Skp2/p21/p27 axis. Oncogene. 2013;32:998–1009.

    CAS  Article  Google Scholar 

  15. 15.

    Chen L, Li Y, Lin CH, Chan THM, Chow RKK, Song Y, et al. Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma. Nat Med. 2013;19:209–16.

    Article  Google Scholar 

  16. 16.

    Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, Burleigh A, et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009;461:809–13.

    CAS  Article  Google Scholar 

  17. 17.

    Zipeto MA, Court AC, Sadarangani A, Delos Santos NP, Balaian L, Chun H-J, et al. ADAR1 Activation Drives Leukemia Stem Cell Self-Renewal by Impairing Let-7 Biogenesis. Cell Stem Cell. 2016;19:177–91.

    CAS  Article  Google Scholar 

  18. 18.

    Park E, Guo J, Shen S, Demirdjian L, Wu YN, Lin L, et al. Population and allelic variation of A-to-I RNA editing in human transcriptomes. Genome Biol. 2017;18:143.

    Article  Google Scholar 

  19. 19.

    Ramaswami G, Deng P, Zhang R, Anna Carbone M, Mackay TFC, Li JB. Genetic mapping uncovers cis-regulatory landscape of RNA editing. Nat Commun. 2015;6:8194.

    Article  Google Scholar 

  20. 20.

    Kurmangaliyev YZ, Ali S, Nuzhdin SV. Genetic determinants of RNA editing levels of ADAR targets in drosophila melanogaster. G3. 2015;6:391–6.

    Article  Google Scholar 

  21. 21.

    Franzén O, Ermel R, Sukhavasi K, Jain R, Jain A, Betsholtz C, et al. Global analysis of A-to-I RNA editing reveals association with common disease variants. PeerJ. 2018;6:e4466.

    Article  Google Scholar 

  22. 22.

    Ouyang Z, Ren C, Liu F, An G, Bo X, Shu W. The landscape of the A-to-I RNA editome from 462 human genomes. Sci Rep. 2018;8:12069.

    Article  Google Scholar 

  23. 23.

    Mook-Kanamori DO, MME-D Selim, Takiddin AH, Al-Homsi H, KAS Al-Mahmoud, Al-Obaidli A, et al. 1,5-Anhydroglucitol in saliva is a noninvasive marker of short-term glycemic control. J Clin Endocrinol Metab. 2014;99:E479–483.

    CAS  Article  Google Scholar 

  24. 24.

    Lappalainen T, Sammeth M, Friedländer MR, t Hoen PAC, Monlong J, Rivas MA, et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature. 2013;501:506–11.

    CAS  Article  Google Scholar 

  25. 25.

    Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinforma Oxf Engl. 2013;29:15–21.

    CAS  Article  Google Scholar 

  26. 26.

    McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303.

    CAS  Article  Google Scholar 

  27. 27.

    Yang H, Wang K. Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nat Protoc. 2015;10:1556–66.

    CAS  Article  Google Scholar 

  28. 28.

    R: a language and environment for statistical computing. https://www.gbif.org/tool/81287/r-a-language-and-environment-for-statistical-computing. Accessed 8 Nov 2018.

  29. 29.

    Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience. 2015;4:7.

    Article  Google Scholar 

  30. 30.

    Delaneau O, Zagury J-F, Marchini J. Improved whole-chromosome phasing for disease and population genetic studies. Nat Methods. 2013;10:5–6.

    CAS  Article  Google Scholar 

  31. 31.

    Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 2009;5:e1000529.

    Article  Google Scholar 

  32. 32.

    Walkley CR, Li JB. Rewriting the transcriptome: adenosine-to-inosine RNA editing by ADARs. Genome Biol 2017;18:205.

    Article  Google Scholar 

  33. 33.

    Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:4673–80.

    CAS  Article  Google Scholar 

  34. 34.

    Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, et al. ViennaRNA Package 2.0. Algorithms Mol Biol Amb. 2011;6:26.

    Article  Google Scholar 

  35. 35.

    Roth SH, Levanon EY, Eisenberg E. Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity. Nat Methods. 2019;16:1131–8.

    CAS  Article  Google Scholar 

  36. 36.

    Robinson JT, Thorvaldsdóttir H, Wenger AM, Zehir A, Mesirov JP. Variant review with the integrative genomics viewer. Cancer Res 2017;77:e31–4.

    CAS  Article  Google Scholar 

  37. 37.

    Kleinberger Y, Eisenberg E. Large-scale analysis of structural, sequence and thermodynamic characteristics of A-to-I RNA editing sites in human Alu repeats. BMC Genomics. 2010;11:453.

    Article  Google Scholar 

  38. 38.

    Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, et al. Widespread RNA and DNA sequence differences in the human transcriptome. Science. 2011;333:53–8.

    CAS  Article  Google Scholar 

  39. 39.

    Kleinman CL, Majewski J. Comment on “Widespread RNA and DNA sequence differences in the human transcriptome.”. Science. 2012;335:1302. author reply 1302.

    CAS  Article  Google Scholar 

  40. 40.

    Harjanto D, Papamarkou T, Oates CJ, Rayon-Estrada V, Papavasiliou FN, Papavasiliou A. RNA editing generates cellular subsets with diverse sequence within populations. Nat Commun. 2016;7:12145.

    CAS  Article  Google Scholar 

  41. 41.

    Wu Y, Shi B, Ding X, Liu T, Hu X, Yip KY, et al. Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data. Nucleic Acids Res. 2015;43:7247–59.

    CAS  Article  Google Scholar 

  42. 42.

    Zhou Z-Y, Hu Y, Li A, Li Y-J, Zhao H, Wang S-Q, et al. Genome wide analyses uncover allele-specific RNA editing in human and mouse. Nucleic Acids Res. 2018;46:8888–97.

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank the staff of the HMC dermatology department and of WCM-Q for their contribution to QMDiab. We thank Laurent Abel from the human genetics of infectious diseases lab for the scientific discussions. Finally, we are grateful to all study participants of QMDiab for their invaluable contributions to this study.

Funding

This work was supported by the Biomedical Research Program at Weill Cornell Medicine in Qatar, a program funded by the Qatar Foundation. The statements made herein are solely the responsibility of the authors.

Author information

Affiliations

Authors

Corresponding authors

Correspondence to Aziz Belkadi or Karsten Suhre.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Belkadi, A., Thareja, G., Halama, A. et al. Identification of genetic variants controlling RNA editing and their effect on RNA structure stabilization. Eur J Hum Genet 28, 1753–1762 (2020). https://doi.org/10.1038/s41431-020-0688-7

Download citation

Search