Advanced search
Publication Cover
RNA Biology Volume 18, 2021 - Issue sup2
Submit an article Journal homepage
1,690
Views
0
CrossRef citations to date
0
Altmetric
Technical Paper

Reproducible and efficient new method of RNA 3’-end labelling by CutA nucleotidyltransferase-mediated CC-tailing

Rafal Tomeckia Laboratory of Rna Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland;b Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, PolandCorrespondence[email protected]
ORCID Iconhttps://orcid.org/0000-0003-2473-5004View further author information
ORCID Icon,
Kamil Kobyleckia Laboratory of Rna Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, PolandORCID Iconhttps://orcid.org/0000-0003-3019-0274View further author information
ORCID Icon,
Karolina Drazkowskac Centre of New Technologies, University of Warsaw, Warsaw, PolandORCID Iconhttps://orcid.org/0000-0003-2673-7126View further author information
ORCID Icon,
Malwina Hyjek-Skladanowskad Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Warsaw, PolandORCID Iconhttps://orcid.org/0000-0001-8276-4845View further author information
ORCID Icon &
Andrzej Dziembowskib Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland;e Laboratory of Rna Biology, International Institute of Molecular and Cell Biology, Warsaw, PolandORCID Iconhttps://orcid.org/0000-0001-8492-7572View further author information
ORCID Icon
Pages 623-639 | Received 26 Jul 2021, Accepted 24 Oct 2021, Published online: 12 Nov 2021

References

  • Liudkovska V, Dziembowski A. Functions and mechanisms of RNA tailing by metazoan terminal nucleotidyltransferases. Wiley Interdiscip Rev RNA. 2021;12(2):e1622.
  • Yu S, Kim VN. A tale of non-canonical tails: gene regulation by post-transcriptional RNA tailing. Nat Rev Mol Cell Biol. 2020;21(9):542–556.
  • Shukla A, Yan J, Pagano DJ, et al. Poly(UG)-tailed RNAs in genome protection and epigenetic inheritance. Nature. 2020;582(7811):283–288.
  • Preston MA, Porter DF, Chen F, et al. Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase. Nat Methods. 2019;16(5):437–445.
  • Malik D, Kobylecki K, and Krawczyk P, et al. Structure and mechanism of CutA, RNA nucleotidyl transferase with an unusual preferece for cytosine. Nucleic Acids Res. 2020;48(16):9387–9405.
  • Kobylecki K, Kuchta K, Dziembowski A, et al. Biochemical and structural bioinformatics studies of fungal CutA nucleotidyltransferases explain their unusual specificity toward CTP and increased tendency for cytidine incorporation at the 3ʹ-terminal positions of synthesized tails. RNA. 2017;23(12):1902–1926.
  • Tomecki R, Drazkowska K, Krawczyk A, et al. Purification of eukaryotic exoribonucleases following heterologous expression in bacteria and analysis of their biochemical properties by in vitro enzymatic assays. Methods Mol Biol. 2015;1259:417–452.
  • Wang Z, Kiledjian M. The poly(A)-binding protein and an mRNA stability protein jointly regulate an endoribonuclease activity. Mol Cell Biol. 2000;20(17):6334–6341.
  • Schwarz DS, Tomari Y, Zamore PD. The RNA-induced silencing complex is a Mg2+-dependent endonuclease. Curr Biol. 2004;14(9):787–791.
  • Lebreton A, Tomecki R, Dziembowski A, et al. Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature. 2008;456(7224):993–996.
  • Aphasizhev R, Simpson L. Isolation and characterization of a U-specific 3ʹ-5ʹ-exonuclease from mitochondria of Leishmania tarentolae. J Biol Chem. 2001;276(24):21280–21284.
  • Clouet-d’Orval B, Rinaldi D, Quentin Y, et al. Euryarchaeal beta-CASP proteins with homology to bacterial RNase J have 5ʹ- to 3ʹ-exoribonuclease activity. J Biol Chem. 2010;285(23):17574–17583.
  • Klocker N, Weissenboeck FP, Rentmeister A. Covalent labeling of nucleic acids. Chem Soc Rev. 2020;49(23):8749–8773.
  • Rio DC. 5′-End Labeling of RNA with [γ-32P]ATP and T4 polynucleotide kinase. Cold Spring Harb Protoc. 2014;2014(4):441–443.
  • Gaastra W, Josephsen J. Radiolabeling of DNA using polynucleotide kinase. Methods Mol Biol. 1985;2:263–268.
  • Nilsen TW. 3′-End Labeling of RNA with [5′-32P]Cytidine 3′,5′-Bis(Phosphate) and T4 RNA Ligase 1. Cold Spring Harb Protoc. 2014;2014(4):444–446.
  • England TE, Bruce AG, and Uhlenbeck OC. Specific labeling of 3ʹ termini of RNA with T4 RNA ligase. Methods Enzymol. 1980;65(1):65–74.
  • England TE, Uhlenbeck OC. 3ʹ-terminal labelling of RNA with T4 RNA ligase. Nature. 1978;275(5680):560–561.
  • Lingner J, Keller W. 3ʹ-end labeling of RNA with recombinant yeast poly(A) polymerase. Nucleic Acids Res. 1993;21(12):2917–2920.
  • Rio DC. 3ʹ-end labeling of RNA with yeast poly(A) polymerase and 3ʹ-deoxyadenosine 5ʹ-[alpha-32P]triphosphate. Cold Spring Harb Protoc. 2014;2014(6):687–689.
  • Huang Z, Szostak JW. A simple method for 3ʹ-labeling of RNA. Nucleic Acids Res. 1996;24(21):4360–4361.
  • Lorentzen E, Basquin J, Tomecki R, et al. Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family. Mol Cell. 2008;29(6):717–728.
  • Tomecki R, Kristiansen MS, Lykke-Andersen S, et al. The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L. EMBO J. 2010;29(14):2342–2357.
  • Zinder JC, Wasmuth EV, Lima CD. Nuclear RNA exosome at 3.1 Å reveals substrate specificities, RNA paths, and allosteric inhibition of Rrp44/Dis3. Mol Cell. 2016;64(4):734–745.
  • Wu S, Mao G, Kirsebom LA. Inhibition of bacterial RNase P RNA by phenothiazine derivatives. Biomolecules. 2016;6(3):38.
  • Jung E, Lee J, Hong HJ, et al. RNA recognition by a human antibody against brain cytoplasmic 200 RNA. RNA. 2014;20(6):805–814.
  • Nikpour N, Salavati R. The RNA binding activity of the first identified trypanosome protein with Z-DNA-binding domains. Sci Rep. 2019;9(1):5904.
  • Xing L, Niu M, Zhao X, et al. Roles of the linker region of RNA helicase A in HIV-1 RNA metabolism. PLoS One. 2013;8(11):e78596.
  • Sikorski PJ, Warminski M, Kubacka D, et al. The identity and methylation status of the first transcribed nucleotide in eukaryotic mRNA 5ʹ cap modulates protein expression in living cells. Nucleic Acids Res. 2020;48(4):1607–1626.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.