DNMT3L Interacts with Piwi and Modulates the Expression of piRNAs in Transgenic Drosophila

References

• Kanherkar RR , Bhatia-DeyN, CsokaAB. Epigenetics across the human lifespan. Front. Cell Dev. Biol.2, 49 (2014).
   PubMed Web of Science ®Google Scholar
• Rivera CM , RenB. Mapping human epigenomes. Cell155(1), 39–55 (2013).
   PubMed Web of Science ®Google Scholar
• Danchin É , CharmantierA, ChampagneFA, MesoudiA, PujolB, BlanchetS. Beyond DNA: integrating inclusive inheritance into an extended theory of evolution. Nat. Rev. Genet.12(7), 475–486 (2011).
   PubMed Web of Science ®Google Scholar
• Sasaki H , MatsuiY. Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat. Rev. Genet.9(2), 129–140 (2008).
   PubMed Web of Science ®Google Scholar
• Jirtle RL , SkinnerMK. Environmental epigenomics and disease susceptibility. Nat. Rev. Genet.8(4), 253–262 (2007).
   PubMed Web of Science ®Google Scholar
• Zhang X , HoSM. Epigenetics meets endocrinology. J. Mol. Endocrinol.46(1), R11–32 (2011).
   PubMed Web of Science ®Google Scholar
• Heard E , MartienssenRA. Transgenerational epigenetic inheritance: myths and mechanisms. Cell157(1), 95 (2014).
   PubMed Web of Science ®Google Scholar
• Lind MI , SpagopoulouF. Evolutionary consequences of epigenetic inheritance. Heredity121(3), 205–209 (2018).
   PubMed Web of Science ®Google Scholar
• Cecere G . Small RNAs in epigenetic inheritance: from mechanisms to trait transmission. FEBS Lett.595(24), 2953–2977 (2021).
   PubMed Web of Science ®Google Scholar
• Thamban T , AgarwaalV, BasuAet al. Epigenetic inheritance across multiple generations. In: Transgenerational Epigenetics(2nd Edition). Academic Press, 401–420 (2019).
   Google Scholar
• Le Thomas A , StuweE, LiSet al. Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing. Genes Dev.28(15), 1667 (2014).
   PubMed Web of Science ®Google Scholar
• Bregliano JC , PicardG, BuchetonA, PelissonA, LavigeJM, L’HeritierP. Hybrid dysgenesis in Drosophila melanogaster. Science207(4431), 606–611 (1980).
   PubMed Web of Science ®Google Scholar
• Weick EM , MiskaEA. piRNAs: from biogenesis to function. Development141(18), 3458–3471 (2014).
   PubMed Web of Science ®Google Scholar
• Deplus R , BrennerC, BurgersWAet al. Dnmt3L is a transcriptional repressor that recruits histone deacetylase. Nucleic Acids Res.30(17), 3831 (2002).
   PubMed Web of Science ®Google Scholar
• Lees-Murdock DJ , ShovlinTC, GardinerT, DeFelici M, WalshCP. DNA methyltransferase expression in the mouse germ line during periods of de novo methylation. Dev. Dyn.232(4), 992–1002 (2005).
   PubMed Web of Science ®Google Scholar
• Ooi SKT , QiuC, BernsteinEet al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature448(7154), 714–717 (2007).
   PubMed Web of Science ®Google Scholar
• Suetake I , ShinozakiF, MiyagawaJ, TakeshimaH, TajimaS. DNMT3L stimulates the DNA methylation activity of DNMT3A and DNMT3B through a direct interaction. J. Biol. Chem.279(26), 27816–27823 (2004).
   PubMed Web of Science ®Google Scholar
• Bourc’his D , XuGL, LinCS, BollmanB, BestorTH. DNMT3L and the establishment of maternal genomic imprints. Science294(5551), 2536–2539 (2001).
   PubMed Web of Science ®Google Scholar
• Basu A , TomarA, DasariV, MishraRK, KhoslaS. DNMT3L enables accumulation and inheritance of epimutations in transgenic Drosophila. Sci. Rep.6, 19572 (2016).
   PubMed Web of Science ®Google Scholar
• Wickersheim ML , BlumenstielJP. Terminator oligo blocking efficiently eliminates rRNA from Drosophila small RNA sequencing libraries. BioTechniques55(5), 269–272 (2013).
   PubMed Web of Science ®Google Scholar
• Krzywinski M , ScheinJ, BirolIet al. Circos: an information aesthetic for comparative genomics. Genome Res.19(9), 1639–1645 (2009).
   PubMed Web of Science ®Google Scholar
• Brennecke J , MaloneCD, AravinAA, SachidanandamR, StarkA, HannonGJ. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science322(5906), 1387–1392 (2008).
   PubMed Web of Science ®Google Scholar
• Aravin AA , SachidanandamR, Bourc’hisDet al. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol. Cell31(6), 785–799 (2008).
   PubMed Web of Science ®Google Scholar
• Chédin F . The DNMT3 family of mammalian de novo DNA methyltransferases. Prog. Mol. Biol. Transl. Sci.101, 255–285 (2011).
   PubMed Web of Science ®Google Scholar
• Juliano C , WangJ, LinH. Uniting germline and stem cells: the function of Piwi proteins and the piRNA pathway in diverse organisms. Annu. Rev. Genet.45, 447–469 (2011).
   PubMed Web of Science ®Google Scholar
• Iwasaki YW , MuranoK, IshizuHet al. Piwi modulates chromatin accessibility by regulating multiple factors including histone H1 to repress transposons. Mol. Cell63(3), 408–419 (2016).
   PubMed Web of Science ®Google Scholar
• Basu A . Role of DNA Methyltransferase DNMT3L in Development. ( PhD thesis, CDFD & Manipal Academy of Higher Education, India). (2016). http://hdl.handle.net/10603/148253
   Google Scholar
• Nagamori I , KobayashiH, NishimuraTet al. Relationship between PIWIL4-mediated H3K4me2 demethylation and piRNA-dependent DNA methylation. Cell Rep.25(2), 350–356 (2018).
   PubMed Web of Science ®Google Scholar
• Gebert D , HewelC, RosenkranzD. Unitas: the universal tool for annotation of small RNAs. BMC Genomics18(1), 1–14 (2017).
   PubMedGoogle Scholar
• Basu A , TomarA, KhoslaS. Expression data from third instar Drosophila larvae. Gene Expression Omnibus (GEO) database (accession number GSE68861) (2015). www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68861 (Accessed 15September2023).
   Google Scholar
• Casier K , BoivinA, CarréC, TeyssetL. Environmentally-induced transgenerational epigenetic inheritance: implication of PIWI interacting RNAs. Cells8(9), 1108 (2019).
   PubMed Web of Science ®Google Scholar
• Grentzinger T , ArmeniseC, BrunCet al. piRNA-mediated transgenerational inheritance of an acquired trait. Genome Res.22(10), 1877–1888 (2012).
   PubMed Web of Science ®Google Scholar
• Ashe A , SapetschnigA, WeickEMet al. piRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans. Cell150(1), 88–99 (2012).
   PubMed Web of Science ®Google Scholar
• Hergeth SP , SchneiderR. The H1 linker histones: multifunctional proteins beyond the nucleosomal core particle. EMBO Rep.16(11), 1439–1453 (2015).
   PubMed Web of Science ®Google Scholar
• Izzo A , KamieniarzK, SchneiderR. The histone H1 family: specific members, specific functions?Biol. Chem.389(4), 333–343 (2008).
   PubMed Web of Science ®Google Scholar
• Robinson PJ , RhodesD. Structure of the ‘30 nm’ chromatin fibre: a key role for the linker histone. Curr. Opin. Struct. Biol.16(3), 336–343 (2006).
   PubMed Web of Science ®Google Scholar
• Thoma F , KollerT, KlugA. Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J. Cell Biol.83(2 Pt 1), 403–427 (1979).
   PubMed Web of Science ®Google Scholar
• Li G , ReinbergD. Chromatin higher-order structures and gene regulation. Curr. Opin. Genet. Dev.21(2), 175 (2011).
   PubMed Web of Science ®Google Scholar
• Oudelaar AM , HiggsDR. The relationship between genome structure and function. Nat. Rev. Genet.22(3), 154–168 (2020).
   PubMed Web of Science ®Google Scholar
• Cox DN , ChaoA, BakerJ, ChangL, QiaoD, LinH. A novel class of evolutionarily conserved genes defined by Piwi are essential for stem cell self-renewal. Genes Dev.12(23), 3715 (1998).
   PubMed Web of Science ®Google Scholar
• Aravin AA , HannonGJ, BrenneckeJ. The Piwi–piRNA pathway provides an adaptive defense in the transposon arms race. Science318(5851), 761–764 (2007).
   PubMed Web of Science ®Google Scholar
• Czech B , HannonGJ. One loop to rule them all: the ping-pong cycle and piRNA-guided silencing. Trends Biochem. Sci.41(4), 324 (2016).
   PubMed Web of Science ®Google Scholar
• Ramat A , SimoneligM. Functions of PIWI proteins in gene regulation: new arrows added to the piRNA quiver. Trends Genet.37(2), 188–200 (2021).
   PubMed Web of Science ®Google Scholar
• Wang C , LinH. Roles of piRNAs in transposon and pseudogene regulation of germline mRNAs and lncRNAs. Genome Biol.22(1), 27 (2021).
   PubMed Web of Science ®Google Scholar
• Lee EJ , BanerjeeS, ZhouHet al. Identification of piRNAs in the central nervous system. RNA17(6), 1090–1099 (2011).
   PubMed Web of Science ®Google Scholar
• Perera BPU , TsaiZTY, ColwellMLet al. Somatic expression of piRNA and associated machinery in the mouse identifies short, tissue-specific piRNA. Epigenetics14(5), 504 (2019).
   PubMed Web of Science ®Google Scholar
• Ross RJ , WeinerMM, LinH. PIWI proteins and PIWI-interacting RNAs in the soma. Nature505(7483), 353–359 (2014).
   PubMed Web of Science ®Google Scholar
• Castel SE , MartienssenRA. RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat. Rev. Genet.14(2), 100–112 (2013).
   PubMed Web of Science ®Google Scholar
• Ruthenburg AJ , AllisCD, WysockaJ. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol. Cell.. 25(1), 15–30 (2007).
   PubMed Web of Science ®Google Scholar