References
Beverly, M., Hagen, C., and Slack, O. (2018). Poly A tail length analysis of in vitro transcribed mRNA by LC-MS. Anal Bioanal Chem 410, 1667–1677.
Chang, H., Lim, J., Ha, M., and Kim, V.N. (2014). TAIL-seq: genome-wide determination of poly(A) tail length and 3′ end modifications. Mol Cell 53, 1044–1052.
Colgan, D.F., and Manley, J.L. (1997). Mechanism and regulation of mRNA polyadenylation. Genes Dev 11, 2755–2766.
Gu, W., Crawford, E.D., O’Donovan, B.D., Wilson, M.R., Chow, E.D., Retallack, H., and DeRisi, J.L. (2016). Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biol 17, 41.
Hu, S.B., Xiang, J.F., Li, X., Xu, Y., Xue, W., Huang, M., Wong, C.C., Sagum, C.A., Bedford, M.T., Yang, L., et al. (2015). Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus. Genes Dev 29, 630–645.
Legnini, I., Alles, J., Karaiskos, N., Ayoub, S., and Rajewsky, N. (2019). FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control. Nat Methods 16, 879–886.
Lim, J., Ha, M., Chang, H., Kwon, S.C., Simanshu, D.K., Patel, D.J., and Kim, V.N. (2014). Uridylation by TUT4 and TUT7 marks mRNA for degradation. Cell 159, 1365–1376.
Lim, J., Kim, D., Lee, Y.S., Ha, M., Lee, M., Yeo, J., Chang, H., Song, J., Ahn, K., and Kim, V.N. (2018). Mixed tailing by TENT4A and TENT4B shields mRNA from rapid deadenylation. Science 361, 701–704.
Liu, Y., Nie, H., Liu, H., and Lu, F. (2019). Poly(A) inclusive RNA isoform sequencing (PAIso-seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails. Nat Commun 10, 5292.
Liu, Y., Zhang, Y., Wang, J., and Lu, F. (2022). Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq. Nat Protoc,, doi: https://doi.org/10.1038/s41596-022-00704-8.
Long, Y., Jia, J., Mo, W., Jin, X., and Zhai, J. (2021). FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing. Nat Protoc 16, 4355–4381.
Saw, P.E., Xu, X., Chen, J., and Song, E.W. (2021). Non-coding RNAs: the new central dogma of cancer biology. Sci China Life Sci 64, 22–50.
Subtelny, A.O., Eichhorn, S.W., Chen, G.R., Sive, H., and Bartel, D.P. (2014). Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 508, 66–71.
Trepotec, Z., Geiger, J., Plank, C., Aneja, M.K., and Rudolph, C. (2019). Segmented poly(A) tails significantly reduce recombination of plasmid DNA without affecting mRNA translation efficiency or half-life. RNA 25, 507–518.
Yu, S., and Kim, V.N. (2020). A tale of non-canonical tails: gene regulation by post-transcriptional RNA tailing. Nat Rev Mol Cell Biol 21, 542–556.
Acknowledgements
This work was supported by the National Key Research and Development Program of China (2018YFA0107001, 2020YFA0804000), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA24020203), the CAS Project for Young Scientists in Basic Research (YSBR-012), the National Natural Science Foundation of China (31970588, 32170606), the Natural Science Foundation of Heilongjiang province (YQ2020C003), the China Postdoctoral Science Foundation (2020M670516, 2020T130687), and the State Key Laboratory of Molecular Developmental Biology. We thank Ying Liu for her technical assistance in cell culturing.
Author information
Authors and Affiliations
Corresponding authors
Additional information
Compliance and ethics
The author(s) declare that they have no conflict of interest.
Supplementary Information
Rights and permissions
About this article
Cite this article
Liu, Y., Nie, H., Zhang, Y. et al. Comprehensive analysis of mRNA poly(A) tails by PAIso-seq2. Sci. China Life Sci. 66, 187–190 (2023). https://doi.org/10.1007/s11427-022-2186-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11427-022-2186-8