Skip to main content
Log in

NAD+-capped RNAs are widespread in rice (Oryza sativa) and spatiotemporally modulated during development

  • Letter to the Editor
  • Published:
Science China Life Sciences Aims and scope Submit manuscript

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

References

  • Bird, J.G., Basu, U., Kuster, D., Ramachandran, A., Grudzien-Nogalska E., Towheed, A., Wallace, D.C., Kiledjian, M., Temiakov, D., Patel, S.S., et al. (2018). Highly efficient 5′ capping of mitochondrial RNA with NAD+ and NADH by yeast and human mitochondrial RNA polymerase. elife 7, e42179.

    Article  Google Scholar 

  • Bird, J.G., Zhang, Y., Tian, Y., Panova, N., Barvík, I., Greene, L., Liu, M., Buckley, B., Krásný, L., Lee, J.K., et al. (2016). The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA. Nature 535, 444–447.

    Article  CAS  Google Scholar 

  • Cahová, H., Winz, M.L., Höfer, K., Nübel, G., and Jäschke, A. (2015). NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs. Nature 519, 374–377.

    Article  Google Scholar 

  • Fei, Q., Xia, R., and Meyers, B.C. (2013). Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks. Plant Cell 25, 2400–2415.

    Article  CAS  Google Scholar 

  • Grudzien-Nogalska, E., Bird, J.G., Nickels, B.E., and Kiledjian, M. (2018). “NAD-capQ” detection and quantitation of NAD caps. RNA 24, 1418–1425.

    Article  CAS  Google Scholar 

  • Hu, H., Flynn, N., and Chen, X. (2021). Discovery, processing, and potential role of noncanonical caps in RNA. In: Jurga, S., and Barciszewski, J., eds. Epitranscriptomics. RNA Technologies. Cham: Springer. 435–469.

    Chapter  Google Scholar 

  • Jiao, X., Doamekpor, S.K., Bird, J.G., Nickels, B.E., Tong, L., Hart, R.P., and Kiledjian, M. (2017). 5′ end nicotinamide adenine dinucleotide cap in human cells promotes RNA decay through DXO-mediated deNADding. Cell 168, 1015–1027.e10.

    Article  CAS  Google Scholar 

  • Walters, R.W., Matheny, T., Mizoue, L.S., Rao, B.S., Muhlrad, D., and Parker, R. (2017). Identification of NAD+ capped mRNAs in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 114, 480–485.

    Article  CAS  Google Scholar 

  • Wang, Y., Li, S., Zhao, Y., You, C., Le, B., Gong, Z., Mo, B., Xia, Y., and Chen, X. (2019). NAD+-capped RNAs are widespread in the Arabidopsis transcriptome and can probably be translated. Proc Natl Acad Sci USA 116, 12094–12102.

    Article  CAS  Google Scholar 

  • Yu, X., Willmann, M.R., Vandivier, L.E., Trefely, S., Kramer, M.C., Shapiro, J., Guo, R., Lyons, E., Snyder, N.W., and Gregory, B.D. (2021). Messenger RNA 5′ NAD+ capping is a dynamic regulatory epitranscriptome mark that is required for proper response to abscisic acid in Arabidopsis. Dev Cell 56, 125–140.e6.

    Article  CAS  Google Scholar 

  • Zhang, H., Zhong, H., Zhang, S., Shao, X., Ni, M., Cai, Z., Chen, X., and Xia, Y. (2019). NAD tagSeq reveals that NAD+-capped RNAs are mostly produced from a large number of protein-coding genes in Arabidopsis. Proc Natl Acad Sci USA 116, 12072–12077.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Key Research and Development Program of China (2019YFA0903900), Guangdong Innovation Research Team Fund (2014ZT05S078), the National Natural Science Foundation of China (32000153), and China Postdoctoral Science Foundation (2018M640822, 2019T120753). We thank Drs. Yuan Wang, Hao Hu, Xiaoyu Yang and Hailei Zhang for discussions.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Yu Yu or Xuemei Chen.

Ethics declarations

Compliance and ethics The author(s) declare that they have no conflict of interest.

Electronic supplementary material

NAD+-capped RNAs are widespread in rice (Oryza sativa) and spatiotemporally modulated during development

Table S1. Genes producing NAD+-capped RNAs (NAD-RNAs) in rice shoots

Table S2. Genes producing NAD-RNAs in rice roots

Table S3. GO enrichments for shoot NAD-RNA producing genes

Table S4. GO enrichments for root NAD-RNA producing genes

Supplemental Table 5: GO enrichments of shoot specific NAD-RNAs

Supplemental Table 6: GO enrichments of root specific NAD-RNAs

Table S7. Genes producing NAD-RNAs in spikelets (Stage 3)

Table S8. Genes producing NAD-RNAs in spikelets (Stage 5)

Table S9. Genes producing NAD-RNAs in spikelets (Stage 7)

Table S10. GO enrichments for NAD-RNA producing genes at stage 3 in spikelets

Table S11. GO enrichments for NAD-RNA producing genes at stage 5 in spikelets

Table S12. GO enrichments for NAD-RNA producing genes at stage 7 in spikelets

Table S13. Oligonucleotides used in this study

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Dong, H., Wang, X., Tan, C. et al. NAD+-capped RNAs are widespread in rice (Oryza sativa) and spatiotemporally modulated during development. Sci. China Life Sci. 65, 2121–2124 (2022). https://doi.org/10.1007/s11427-021-2113-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11427-021-2113-7

Navigation