2,200
Views
3
CrossRef citations to date
0
Altmetric
Review

Small RNA-directed DNA elimination: the molecular mechanism and its potential for genome editing

ORCID Icon & ORCID Icon
Pages 1540-1545 | Received 16 Nov 2020, Accepted 30 Jan 2021, Published online: 08 Feb 2021

References

  • Hamilton EP, Kapusta A, Huvos PE, et al. Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome. Elife. 2016 Nov; 5: DOI:10.7554/eLife.19090
  • Mochizuki K, Fine NA, Fujisawa T, et al. Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena. Cell. 2002 Sep;110(6):689–699.
  • Noto T, Kataoka K, Suhren JH, et al. Small-RNA-mediated genome-wide trans-recognition network in tetrahymena DNA elimination. Mol Cell. 2015;59(2):229–242.
  • Mochizuki K, Noto T. Whats, hows and whys of programmed DNA elimination in Tetrahymena. Open Biol. 2017;7(10):170–172.
  • Yao MC, Yao CH, Monks B. The controlling sequence for site-specific chromosome breakage in tetrahymena. Cell. 1990 Nov;63(4):763–772.
  • Coyne RS, Nikiforov MA, Smothers JF, et al. Parental expression of the chromodomain protein Pdd1p is required for completion of programmed DNA elimination and nuclear differentiation. Mol Cell. 1999 Nov;4(5):865–872.
  • Malone CD, Anderson AM, Motl JA, et al. Germ line transcripts are processed by a Dicer-like protein that is essential for developmentally programmed genome rearrangements of Tetrahymena thermophila. Molecular and Cellular Biology. 2005 Oct;25(20):9151–9164.
  • Mochizuki K, Gorovsky MA. A Dicer-like protein in tetrahymena has distinct functions in genome rearrangement, chromosome segregation, and meiotic prophase. Genes Dev. 2005 Jan;19(1):77–89.
  • Cheng CY, Young JM, Lin CYG, et al. The piggyBac transposon-derived genes TPB1 and TPB6 mediate essential transposon-like excision during the developmental rearrangement of key genes in Tetrahymena thermophila. Genes Dev. 2016 Dec;30(24):2724–2736.
  • Chao J-L, Lin C-YG, Yao M-C, et al. Setting boundaries for genome-wide heterochromatic DNA deletions through flanking inverted repeats in tetrahymena thermophila. Nucleic Acids Res. 2019 Mar;47(10):5181–5192.
  • Bischerour J, Bhullar S, Wilkes CD, et al. Six domesticated piggybac transposases together carry out programmed DNA elimination in paramecium. Elife. 2018 Sep; 7: DOI:10.7554/eLife.37927
  • Cary LC, Goebel M, Corsaro BG, et al. Transposon mutagenesis of baculoviruses: analysis of Trichoplusia ni transposon IFP2 insertions within the FP-locus of nuclear polyhedrosis viruses. Virology. 1989 Sep;172(1):156–169.
  • Cheng C-Y, Vogt A, Mochizuki K, et al. A domesticated piggybac transposase plays key roles in heterochromatin dynamics and DNA cleavage during programmed DNA deletion in tetrahymena thermophila. Mol Biol Cell. 2010 Mar;21(10):1753–1762.
  • Mochizuki K, Gorovsky MA. Conjugation-specific small RNAs in tetrahymena have predicted properties of scan (scn) RNAs involved in genome rearrangement. Genes Dev. 2004 Sep;18(17):2068–2073.
  • Schoeberl UE, Kurth HM, Noto T, et al. Biased transcription and selective degradation of small RNAs shape the pattern of DNA elimination in Tetrahymena. Genes Dev. 2012 Aug;26(15):1729–1742.
  • Liu Y, Taverna SD, Muratore TL, et al. RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena. Genes Dev. 2007 Jun;21(12):1530–1545.
  • Couvillion MT, Lee SR, Hogstad B, et al. Sequence, biogenesis, and function of diverse small RNA classes bound to the piwi family proteins of tetrahymena thermophila. Genes Dev. 2009 Sep;23(17):2016–2032.
  • Noto T, Kurth HM, Kataoka K, et al. The tetrahymena argonaute-binding protein giw1p directs a mature argonaute-siRNA complex to the nucleus. Cell. 2010 Mar;140(5):692–703.
  • Aronica L, Bednenko J, Noto T, et al. Study of an RNA helicase implicates small RNA-noncoding RNA interactions in programmed DNA elimination in Tetrahymena. Genes Dev. 2008 Aug;22(16):2228–2241.
  • Wiley EA, Horrell S, Yoshino A, et al. Diversification of HP1-like chromo domain proteins in tetrahymena thermophila. J Eukaryot Microbiol. 2018 Jan;65(1):104–116.
  • Suhren JH, Noto T, Kataoka K, et al. Negative regulators of an RNAi-heterochromatin positive feedback loop safeguard somatic genome integrity in tetrahymena. Cell Rep. 2017 Mar;18(10):2494–2507.
  • Shieh AWY, Chalker DL. LIA5 is required for nuclear reorganization and programmed DNA rearrangements occurring during tetrahymena macronuclear differentiation. PLoS One. 2013 Sep;8(9):e75337–e75337.
  • Lin I-T, Chao J-L, Yao M-C. An essential role for the DNA breakage-repair protein Ku80 in programmed DNA rearrangements in tetrahymena thermophila. Mol Biol Cell. 2012 Apr;23(11):2213–2225.
  • Lin CYG, Chao JL, Tsai HK, et al. Setting boundaries for genome-wide heterochromatic DNA deletions through flanking inverted repeats in tetrahymena thermophila. Nucleic Acids Res. 2019;47(10):5181–5192.
  • Zhang X-H, Tee LY, Wang X-G, et al. Off-target effects in CRISPR/Cas9-mediated genome engineering. Mol Ther Nucleic Acids. 2015 Jan;4:e264.
  • Horlbeck MA, Witkowsky LB, Guglielmi B, et al. Nucleosomes impede Cas9 access to DNA in vivo and in vitro. Elife. 2016 Mar;5:e12677.
  • Charlesworth CT, Deshpande PS, Dever DP, et al. Identification of preexisting adaptive immunity to Cas9 proteins in humans. Nat. Med. 2019;25(2):249–254.
  • Vogt A, Mochizuki K. A domesticated piggyBac transposase interacts with heterochromatin and catalyzes reproducible DNA elimination in tetrahymena. PLoS Genet. 2013 Dec;9(12):e1004032.