Expanding the Repertoire of Deadenylases

Overview

Journal RNA Biol

Specialty Molecular Biology

Date 2017 Mar 8

PMID 28267419

Citations 3

Authors

Ilias Skeparnias

Dimitrios Anastasakis

Athanasios-Nasir Shaukat

Katerina Grafanaki

Constantinos Stathopoulos

Affiliations

Soon will be listed here.

Abstract

Deadenylases belong to an expanding family of exoribonucleases involved mainly in mRNA stability and turnover, with the exception of PARN which has additional roles in the biogenesis of several important non-coding RNAs, including miRNAs and piRNAs. Recently, PARN in C. elegans and its homolog PNLDC1 in B. mori were reported as the elusive trimmers mediating piRNA biogenesis. In addition, characterization of mammalian PNLDC1 in comparison to PARN, showed that is specifically expressed in embryonic stem and germ cells, as well as during early embryo development. Moreover, its expression is correlated with epigenetic events mediated by the de novo DNMT3b methyltransferase and knockdown in stem cells upregulates important genes that regulate multipotency. The recent data suggest that at least some new deadenylases may have expanded roles in cell metabolism as regulators of gene expression, through mRNA deadenylation, ncRNAs biogenesis and ncRNA-mediated mRNA targeting, linking essential mechanisms that regulate epigenetic control and transition events during differentiation. The possible roles of mammalian PNLDC1 along those dynamic networks are discussed in the light of new extremely important findings.

Citing Articles

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References

Ku H, Lin H . PIWI proteins and their interactors in piRNA biogenesis, germline development and gene expression. Natl Sci Rev. 2014; 1(2):205-218. PMC: 4265212. DOI: 10.1093/nsr/nwu014. View

Balatsos N, Maragozidis P, Anastasakis D, Stathopoulos C . Modulation of poly(A)-specific ribonuclease (PARN): current knowledge and perspectives. Curr Med Chem. 2012; 19(28):4838-49. DOI: 10.2174/092986712803341539. View

Liu Y, Lu X, Shi J, Yu X, Zhang X, Zhu K . BTG4 is a key regulator for maternal mRNA clearance during mouse early embryogenesis. J Mol Cell Biol. 2016; 8(4):366-8. DOI: 10.1093/jmcb/mjw023. View

Chen C, Jin J, James D, Adams-Cioaba M, Park J, Guo Y . Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi. Proc Natl Acad Sci U S A. 2009; 106(48):20336-41. PMC: 2787181. DOI: 10.1073/pnas.0911640106. View

Aravin A, Sachidanandam R, Bourchis D, Schaefer C, Pezic D, Fejes Toth K . A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell. 2008; 31(6):785-99. PMC: 2730041. DOI: 10.1016/j.molcel.2008.09.003. View

Ye J, Blelloch R . Regulation of pluripotency by RNA binding proteins. Cell Stem Cell. 2014; 15(3):271-280. PMC: 4372238. DOI: 10.1016/j.stem.2014.08.010. View

Iwasaki Y, Siomi M, Siomi H . PIWI-Interacting RNA: Its Biogenesis and Functions. Annu Rev Biochem. 2015; 84:405-33. DOI: 10.1146/annurev-biochem-060614-034258. View

Gu W, Shirayama M, Conte Jr D, Vasale J, Batista P, Claycomb J . Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol Cell. 2009; 36(2):231-44. PMC: 2776052. DOI: 10.1016/j.molcel.2009.09.020. View

Park J, Yi H, Kim Y, Chang H, Kim V . Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle. Mol Cell. 2016; 62(3):462-471. DOI: 10.1016/j.molcel.2016.04.007. View

10.

Izumi N, Shoji K, Sakaguchi Y, Honda S, Kirino Y, Suzuki T . Identification and Functional Analysis of the Pre-piRNA 3' Trimmer in Silkworms. Cell. 2016; 164(5):962-73. PMC: 4856147. DOI: 10.1016/j.cell.2016.01.008. View

11.

Yoda M, Cifuentes D, Izumi N, Sakaguchi Y, Suzuki T, Giraldez A . Poly(A)-specific ribonuclease mediates 3'-end trimming of Argonaute2-cleaved precursor microRNAs. Cell Rep. 2013; 5(3):715-26. PMC: 3856240. DOI: 10.1016/j.celrep.2013.09.029. View

12.

Weick E, Miska E . piRNAs: from biogenesis to function. Development. 2014; 141(18):3458-71. DOI: 10.1242/dev.094037. View

13.

Zhang X, Devany E, Murphy M, Glazman G, Persaud M, Kleiman F . PARN deadenylase is involved in miRNA-dependent degradation of TP53 mRNA in mammalian cells. Nucleic Acids Res. 2015; 43(22):10925-38. PMC: 4678859. DOI: 10.1093/nar/gkv959. View

14.

Wang H, Morita M, Yang X, Suzuki T, Yang W, Wang J . Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity. EMBO J. 2010; 29(15):2566-76. PMC: 2928688. DOI: 10.1038/emboj.2010.152. View

15.

Okano M, BELL D, Haber D, Li E . DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell. 1999; 99(3):247-57. DOI: 10.1016/s0092-8674(00)81656-6. View

16.

Balatsos N, Vlachakis D, Maragozidis P, Manta S, Anastasakis D, Kyritsis A . Competitive inhibition of human poly(A)-specific ribonuclease (PARN) by synthetic fluoro-pyranosyl nucleosides. Biochemistry. 2009; 48(26):6044-51. DOI: 10.1021/bi900236k. View

17.

Liu N, Abe M, Sabin L, Hendriks G, Naqvi A, Yu Z . The exoribonuclease Nibbler controls 3' end processing of microRNAs in Drosophila. Curr Biol. 2011; 21(22):1888-93. PMC: 3255556. DOI: 10.1016/j.cub.2011.10.006. View

18.

Tessema M, Willink R, Do K, Yu Y, Yu W, Machida E . Promoter methylation of genes in and around the candidate lung cancer susceptibility locus 6q23-25. Cancer Res. 2008; 68(6):1707-14. DOI: 10.1158/0008-5472.CAN-07-6325. View

19.

Stuart B, Choi J, Zaidi S, Xing C, Holohan B, Chen R . Exome sequencing links mutations in PARN and RTEL1 with familial pulmonary fibrosis and telomere shortening. Nat Genet. 2015; 47(5):512-7. PMC: 4414891. DOI: 10.1038/ng.3278. View

20.

Tummala H, Walne A, Collopy L, Cardoso S, de la Fuente J, Lawson S . Poly(A)-specific ribonuclease deficiency impacts telomere biology and causes dyskeratosis congenita. J Clin Invest. 2015; 125(5):2151-60. PMC: 4463202. DOI: 10.1172/JCI78963. View