Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Poly(A)-specific ribonuclease (PARN) mediates 3′-end maturation of the telomerase RNA component

Abstract

Mutations in the PARN gene (encoding poly(A)-specific ribonuclease) cause telomere diseases including familial idiopathic pulmonary fibrosis (IPF) and dyskeratosis congenita1,2, but how PARN deficiency impairs telomere maintenance is unclear. Here, using somatic cells and induced pluripotent stem cells (iPSCs) from patients with dyskeratosis congenita with PARN mutations, we show that PARN is required for the 3′-end maturation of the telomerase RNA component (TERC). Patient-derived cells as well as immortalized cells in which PARN is disrupted show decreased levels of TERC. Deep sequencing of TERC RNA 3′ termini shows that PARN is required for removal of post-transcriptionally acquired oligo(A) tails that target nuclear RNAs for degradation. Diminished TERC levels and the increased proportion of oligo(A) forms of TERC are normalized by restoring PARN, which is limiting for TERC maturation in cells. Our results demonstrate a new role for PARN in the biogenesis of TERC and provide a mechanism linking PARN mutations to telomere diseases.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: PARN mutations in two families with dyskeratosis congenita.
Figure 2: PARN deficiency results in decreased TERC levels, telomerase activity and telomere length.
Figure 3: PARN deficiency results in abnormal TERC 3′ ends.
Figure 4: Decreased proportion of mature TERC and increased proportion of 3′-extended TERC species in PARN-deficient patient-derived cells.
Figure 5: Decreased stability of TERC in PARN-deficient cells.
Figure 6: Ectopic expression of PARN rescues TERC maturation in PARN-deficient cells and shows that PARN is limiting for TERC biogenesis.

Accession codes

Primary accessions

Gene Expression Omnibus

Referenced accessions

NCBI Reference Sequence

References

  1. 1

    Stuart, B.D. et al. Exome sequencing links mutations in PARN and RTEL1 with familial pulmonary fibrosis and telomere shortening. Nat. Genet. 47, 512–517 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. 2

    Tummala, H. et al. Poly(A)-specific ribonuclease deficiency impacts telomere biology and causes dyskeratosis congenita. J. Clin. Invest. 125, 2151–2160 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  3. 3

    Dehlin, E., Wormington, M., Korner, C.G. & Wahle, E. Cap-dependent deadenylation of mRNA. EMBO J. 19, 1079–1086 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. 4

    Körner, C.G. & Wahle, E. Poly(A) tail shortening by a mammalian poly(A)-specific 3′-exoribonuclease. J. Biol. Chem. 272, 10448–10456 (1997).

    Article  PubMed  PubMed Central  Google Scholar 

  5. 5

    Körner, C.G. et al. The deadenylating nuclease (DAN) is involved in poly(A) tail removal during the meiotic maturation of Xenopus oocytes. EMBO J. 17, 5427–5437 (1998).

    Article  PubMed  PubMed Central  Google Scholar 

  6. 6

    Virtanen, A., Henriksson, N., Nilsson, P. & Nissbeck, M. Poly(A)-specific ribonuclease (PARN): an allosterically regulated, processive and mRNA cap–interacting deadenylase. Crit. Rev. Biochem. Mol. Biol. 48, 192–209 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. 7

    Yoda, M. et al. Poly(A)-specific ribonuclease mediates 3′-end trimming of Argonaute2-cleaved precursor microRNAs. Cell Rep. 5, 715–726 (2013).

    Article  CAS  Google Scholar 

  8. 8

    Berndt, H. et al. Maturation of mammalian H/ACA box snoRNAs: PAPD5-dependent adenylation and PARN-dependent trimming. RNA 18, 958–972 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. 9

    Mason, P.J. & Bessler, M. mRNA deadenylation and telomere disease. J. Clin. Invest. 125, 1796–1798 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  10. 10

    Egan, E.D. & Collins, K. An enhanced H/ACA RNP assembly mechanism for human telomerase RNA. Mol. Cell. Biol. 32, 2428–2439 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. 11

    Feng, J. et al. The RNA component of human telomerase. Science 269, 1236–1241 (1995).

    Article  CAS  Google Scholar 

  12. 12

    Venteicher, A.S. et al. A human telomerase holoenzyme protein required for Cajal body localization and telomere synthesis. Science 323, 644–648 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. 13

    Greider, C.W. Telomerase RNA levels limit the telomere length equilibrium. Cold Spring Harb. Symp. Quant. Biol. 71, 225–229 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. 14

    Cristofari, G. & Lingner, J. Telomere length homeostasis requires that telomerase levels are limiting. EMBO J. 25, 565–574 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. 15

    Cao, Y., Bryan, T.M. & Reddel, R.R. Increased copy number of the TERT and TERC telomerase subunit genes in cancer cells. Cancer Sci. 99, 1092–1099 (2008).

    Article  CAS  Google Scholar 

  16. 16

    Soder, A.I. et al. Amplification, increased dosage and in situ expression of the telomerase RNA gene in human cancer. Oncogene 14, 1013–1021 (1997).

    Article  CAS  Google Scholar 

  17. 17

    Heiss, N.S. et al. X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions. Nat. Genet. 19, 32–38 (1998).

    Article  CAS  Google Scholar 

  18. 18

    Mitchell, J.R., Wood, E. & Collins, K. A telomerase component is defective in the human disease dyskeratosis congenita. Nature 402, 551–555 (1999).

    Article  CAS  Google Scholar 

  19. 19

    Vulliamy, T. et al. Mutations in the telomerase component NHP2 cause the premature ageing syndrome dyskeratosis congenita. Proc. Natl. Acad. Sci. USA 105, 8073–8078 (2008).

    Article  Google Scholar 

  20. 20

    Vulliamy, T. et al. The RNA component of telomerase is mutated in autosomal dominant dyskeratosis congenita. Nature 413, 432–435 (2001).

    Article  CAS  Google Scholar 

  21. 21

    Walne, A.J. et al. Genetic heterogeneity in autosomal recessive dyskeratosis congenita with one subtype due to mutations in the telomerase-associated protein NOP10. Hum. Mol. Genet. 16, 1619–1629 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. 22

    Mitchell, J.R., Cheng, J. & Collins, K. A box H/ACA small nucleolar RNA–like domain at the human telomerase RNA 3′ end. Mol. Cell. Biol. 19, 567–576 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. 23

    Houseley, J. & Tollervey, D. The many pathways of RNA degradation. Cell 136, 763–776 (2009).

    Article  CAS  Google Scholar 

  24. 24

    Schmidt, K. & Butler, J.S. Nuclear RNA surveillance: role of TRAMP in controlling exosome specificity. Wiley Interdiscip. Rev. RNA 4, 217–231 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. 25

    Kiss, T., Fayet-Lebaron, E. & Jady, B.E. Box H/ACA small ribonucleoproteins. Mol. Cell 37, 597–606 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  26. 26

    Rammelt, C., Bilen, B., Zavolan, M. & Keller, W. PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif. RNA 17, 1737–1746 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. 27

    LaCava, J. et al. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121, 713–724 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. 28

    Fu, D. & Collins, K. Distinct biogenesis pathways for human telomerase RNA and H/ACA small nucleolar RNAs. Mol. Cell 11, 1361–1372 (2003).

    Article  CAS  Google Scholar 

  29. 29

    Zaug, A.J., Linger, J. & Cech, T.R. Method for determining RNA 3′ ends and application to human telomerase RNA. Nucleic Acids Res. 24, 532–533 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. 30

    Goldfarb, K.C. & Cech, T.R. 3′ terminal diversity of MRP RNA and other human noncoding RNAs revealed by deep sequencing. BMC Mol. Biol. 14, 23 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. 31

    Jongmans, M.C. et al. Revertant somatic mosaicism by mitotic recombination in dyskeratosis congenita. Am. J. Hum. Genet. 90, 426–433 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. 32

    Kirwan, M. et al. Exogenous TERC alone can enhance proliferative potential, telomerase activity and telomere length in lymphocytes from dyskeratosis congenita patients. Br. J. Haematol. 144, 771–781 (2009).

    Article  CAS  Google Scholar 

  33. 33

    Westin, E.R. et al. Telomere restoration and extension of proliferative lifespan in dyskeratosis congenita fibroblasts. Aging Cell 6, 383–394 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. 34

    Wong, J.M. & Collins, K. Telomerase RNA level limits telomere maintenance in X-linked dyskeratosis congenita. Genes Dev. 20, 2848–2858 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. 35

    Hao, L.Y. et al. Short telomeres, even in the presence of telomerase, limit tissue renewal capacity. Cell 123, 1121–1131 (2005).

    Article  CAS  Google Scholar 

  36. 36

    Alter, B.P., Giri, N., Savage, S.A. & Rosenberg, P.S. Cancer in dyskeratosis congenita. Blood 113, 6549–6557 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. 37

    Armanios, M.Y. et al. Telomerase mutations in families with idiopathic pulmonary fibrosis. N. Engl. J. Med. 356, 1317–1326 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. 38

    Calado, R.T. et al. Constitutional telomerase mutations are genetic risk factors for cirrhosis. Hepatology 53, 1600–1607 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. 39

    Kirwan, M. et al. Defining the pathogenic role of telomerase mutations in myelodysplastic syndrome and acute myeloid leukemia. Hum. Mutat. 30, 1567–1573 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. 40

    Tsakiri, K.D. et al. Adult-onset pulmonary fibrosis caused by mutations in telomerase. Proc. Natl. Acad. Sci. USA 104, 7552–7557 (2007).

    Article  CAS  Google Scholar 

  41. 41

    Yamaguchi, H. et al. Mutations of the human telomerase RNA gene (TERC) in aplastic anemia and myelodysplastic syndrome. Blood 102, 916–918 (2003).

    Article  CAS  Google Scholar 

  42. 42

    Trapp, S. et al. A virus-encoded telomerase RNA promotes malignant T cell lymphomagenesis. J. Exp. Med. 203, 1307–1317 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. 43

    Codd, V. et al. Common variants near TERC are associated with mean telomere length. Nat. Genet. 42, 197–199 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. 44

    Soerensen, M. et al. Genetic variation in TERT and TERC and human leukocyte telomere length and longevity: a cross-sectional and longitudinal analysis. Aging Cell 11, 223–227 (2012).

    Article  CAS  Google Scholar 

  45. 45

    Lee, J.E. et al. The PARN deadenylase targets a discrete set of mRNAs for decay and regulates cell motility in mouse myoblasts. PLoS Genet. 8, e1002901 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. 46

    Aubert, G., Baerlocher, G.M., Vulto, I., Poon, S.S. & Lansdorp, P.M. Collapse of telomere homeostasis in hematopoietic cells caused by heterozygous mutations in telomerase genes. PLoS Genet. 8, e1002696 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. 47

    Park, I.H. et al. Reprogramming of human somatic cells to pluripotency with defined factors. Nature 451, 141–146 (2008).

    Article  CAS  Google Scholar 

  48. 48

    Park, I.H., Lerou, P.H., Zhao, R., Huo, H. & Daley, G.Q. Generation of human-induced pluripotent stem cells. Nat. Protoc. 3, 1180–1186 (2008).

    Article  CAS  Google Scholar 

  49. 49

    Warlich, E. et al. Lentiviral vector design and imaging approaches to visualize the early stages of cellular reprogramming. Mol. Ther. 19, 782–789 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. 50

    Bolger, A.M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. 51

    Magocč, T. & Salzberg, S.L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).

    Article  CAS  Google Scholar 

  52. 52

    Langmead, B. & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. 53

    Kim, D., Langmead, B. & Salzberg, S.L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. 54

    Patro, R., Duggal, G. & Kingsford, C. Salmon: accurate, versatile and ultrafast quantification from RNA-seq data using lightweight-alignment. bioRxiv 10.1101/021592 (2015).

Download references

Acknowledgements

We thank the patients and their families for participation in the research; B.A. Croker, G.Q. Daley and L.I. Zon for comments on the manuscript; and K.E. Gagne for technical assistance. The work was funded in part by the Translational Research Program and the Stem Cell Program, Boston Children's Hospital (S.A.); the Manton Center for Orphan Disease Research (D.H.M.); and the Scientific and Technological Research Council of Turkey (B.B.).

Author information

Affiliations

Authors

Contributions

S.A. and D.H.M. conceived the study, executed experiments, analyzed data, prepared figures and wrote the manuscript. B.B. and M.S. executed experiments, analyzed data and prepared figures. E.G. provided patient information. I.H. provided registry infrastructure. P.C. wrote custom bioinformatics scripts and analyzed the RNA-seq data. A.K.T. performed next-generation sequencing, wrote custom bioinformatics scripts and analyzed the 3′ RACE deep sequencing data.

Corresponding author

Correspondence to Suneet Agarwal.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–10 and Supplementary Tables 1–7. (PDF 4968 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Moon, D., Segal, M., Boyraz, B. et al. Poly(A)-specific ribonuclease (PARN) mediates 3′-end maturation of the telomerase RNA component. Nat Genet 47, 1482–1488 (2015). https://doi.org/10.1038/ng.3423

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing