Convergent Transcription Induces Dynamic DNA Methylation at disiRNA Loci

PLoS Genetics

Volumn 9, Issue 9, 2013, Pages

  Dang, Yunkun ^a   Li, Liande ^a   Guo, Wei ^a   Xue, Zhihong ^a   Liu, Yi ^a  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DISIRNA LOCI DNA METHYLATION; DNA METHYLATION; HISTONE MODIFICATION; NEUROSPORA; NONHUMAN; NUCLEOTIDE SEQUENCE; PROMOTER REGION; REGULATORY MECHANISM; TRANSCRIPTION INITIATION; TRANSCRIPTION TERMINATION;

DNA METHYLATION; DNA, FUNGAL; EPIGENESIS, GENETIC; GENE SILENCING; MUTATION; NEUROSPORA CRASSA; REPETITIVE SEQUENCES, NUCLEIC ACID; RIBONUCLEASE III; RNA INTERFERENCE; RNA, SMALL UNTRANSLATED;

EID: 84884683575     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003761     Document Type: Article

References (49)

1. Freitag M, Selker EU, (2005) Controlling DNA methylation: many roads to one modification. Curr Opin Genet Dev 15: 191-199.
2. Suzuki MM, Bird A, (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9: 465-476.
3. Wu SC, Zhang Y, (2010) Active DNA demethylation: many roads lead to Rome. Nat Rev Mol Cell Biol 11: 607-620.
4. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, et al. (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297: 1833-1837.
5. Buhler M, Moazed D, (2007) Transcription and RNAi in heterochromatic gene silencing. Nat Struct Mol Biol 14: 1041-1048.
6. Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, et al. (2004) RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303: 672-676.
7. He XJ, Chen T, Zhu JK, (2011) Regulation and function of DNA methylation in plants and animals. Cell Res 21: 442-465.
8. Haag JR, Pikaard CS, (2011) Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol 12: 483-492.
9. Aravin AA, Sachidanandam R, Bourc'his D, Schaefer C, Pezic D, et al. (2008) A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell 31: 785-799.
10. Kuramochi-Miyagawa S, Watanabe T, Gotoh K, Totoki Y, Toyoda A, et al. (2008) DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev 22: 908-917.
11. Selker EU, Fritz DY, Singer MJ, (1993) Dense nonsymmetrical DNA methylation resulting from repeat-induced point mutation in Neurospora. Science 262: 1724-1728.
12. Lewis ZA, Honda S, Khlafallah TK, Jeffress JK, Freitag M, et al. (2009) Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Genome Res 19: 427-437.
13. Rountree MR, Selker EU, (2010) DNA methylation and the formation of heterochromatin in Neurospora crassa. Heredity (Edinb) 105: 38-44.
14. Cambareri EB, Jensen BC, Schabtach E, Selker EU, (1989) Repeat-induced G-C to A-T mutations in Neurospora. Science 244: 1571-1575.
15. Tamaru H, Zhang X, McMillen D, Singh PB, Nakayama J, et al. (2003) Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat Genet 34: 75-79.
16. Tamaru H, Selker EU, (2001) A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414: 277-283.
17. Kouzminova E, Selker EU, (2001) dim-2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora. EMBO J 20: 4309-4323.
18. Freitag M, Hickey PC, Khlafallah TK, Read ND, Selker EU, (2004) HP1 is essential for DNA methylation in neurospora. Mol Cell 13: 427-434.
19. Honda S, Selker EU, (2008) Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa. Molecular and cellular biology 28: 6044-6055.
20. Freitag M, Lee DW, Kothe GO, Pratt RJ, Aramayo R, et al. (2004) DNA methylation is independent of RNA interference in Neurospora. Science 304: 1939.
21. Dang Y, Yang Q, Xue Z, Liu Y, (2011) RNA interference in fungi: pathways, functions, and applications. Eukaryot Cell 10: 1148-1155.
22. Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, et al. (2010) Diverse Pathways Generate MicroRNA-like RNAs and Dicer-Independent Small Interfering RNAs in Fungi. Mol Cell 38: 803-814.
23. Zhao Y, Shen Y, Yang S, Wang J, Hu Q, et al. (2010) Ubiquitin ligase components Cullin4 and DDB1 are essential for DNA methylation in Neurospora crassa. J Biol Chem 285: 4355-4365.
24. Selker EU, Stevens JN, (1985) DNA methylation at asymmetric sites is associated with numerous transition mutations. Proc Natl Acad Sci U S A 82: 8114-8118.
25. Margolin BS, Garrett-Engele PW, Stevens JN, Fritz DY, Garrett-Engele C, et al. (1998) A methylated Neurospora 5S rRNA pseudogene contains a transposable element inactivated by repeat-induced point mutation. Genetics 149: 1787-1797.
26. Singer MJ, Marcotte BA, Selker EU, (1995) DNA methylation associated with repeat-induced point mutation in Neurospora crassa. Mol Cell Biol 15: 5586-5597.
27. Honda S, Selker EU, (2008) Direct interaction between DNA methyltransferase DIM-2 and HP1 is required for DNA methylation in Neurospora crassa. Mol Cell Biol 28: 6044-6055.
28. Kramer C, Loros JJ, Dunlap JC, Crosthwaite SK, (2003) Role for antisense RNA in regulating circadian clock function in Neurospora crassa. Nature 421: 948-952.
29. Heintzen C, Liu Y, (2007) The Neurospora crassa circadian clock. Adv Genet 58: 25-66.
30. Yang Q, Li L, Xue Z, Ye Q, Zhang L, et al. (2013) Transcription of the major neurospora crassa microRNA-like small RNAs relies on RNA polymerase III. PLoS Genet 9: e1003227.
31. Maiti M, Lee HC, Liu Y, (2007) QIP, a putative exonuclease, interacts with the Neurospora Argonaute protein and facilitates conversion of duplex siRNA into single strands. Genes Dev 21: 590-600.
32. Selker EU, Tountas NA, Cross SH, Margolin BS, Murphy JG, et al. (2003) The methylated component of the Neurospora crassa genome. Nature 422: 893-897.
33. Selker EU, (1990) Premeiotic instability of repeated sequences in Neurospora crassa. Annual review of genetics 24: 579-613.
34. Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, et al. (2011) Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473: 398-402.
35. Belden WJ, Lewis ZA, Selker EU, Loros JJ, Dunlap JC, (2011) CHD1 remodels chromatin and influences transient DNA methylation at the clock gene frequency. PLoS Genet 7: e1002166.
36. O'Sullivan JM, Tan-Wong SM, Morillon A, Lee B, Coles J, et al. (2004) Gene loops juxtapose promoters and terminators in yeast. Nature genetics 36: 1014-1018.
37. Ansari A, Hampsey M, (2005) A role for the CPF 3′-end processing machinery in RNAP II-dependent gene looping. Genes & development 19: 2969-2978.
38. Tan-Wong SM, Zaugg JB, Camblong J, Xu Z, Zhang DW, et al. (2012) Gene loops enhance transcriptional directionality. Science 338: 671-675.
39. Choudhary S, Lee HC, Maiti M, He Q, Cheng P, et al. (2007) A double-stranded-RNA response program important for RNA interference efficiency. Mol Cell Biol 27: 3995-4005.
40. He Q, Cheng P, Yang Y, Wang L, Gardner KH, et al. (2002) White collar-1, a DNA binding transcription factor and a light sensor. Science 297: 840-843.
41. Davis RL, deSerres D, (1970) Genetic and microbial research techniques for Neurospora crassa. Methods of Enzymology 27A: 79-143.
42. Cheng P, Yang Y, Liu Y, (2001) Interlocked feedback loops contribute to the robustness of the Neurospora circadian clock. Proc Natl Acad Sci U S A 98: 7408-7413.
43. Pomraning KR, Smith KM, Freitag M, (2009) Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 47: 142-150.
44. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, et al. (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37: 853-862.
45. Guo J, Cheng P, Yuan H, Liu Y, (2009) The exosome regulates circadian gene expression in a posttranscriptional negative feedback loop. Cell 138: 1236-1246.
46. Marques JT, Kim K, Wu PH, Alleyne TM, Jafari N, et al. (2010) Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila. Nat Struct Mol Biol 17: 24-30.
47. Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, et al. (2010) Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 16: 991-1006.
48. Zhang L, Chia JM, Kumari S, Stein JC, Liu Z, et al. (2009) A genome-wide characterization of microRNA genes in maize. PLoS Genet 5: e1000716.
49. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12: 1599-1610.