Homologous recombination as a mechanism to recognize repetitive DNA sequences in an RNAi pathway

Genes and Development

Volumn 27, Issue 2, 2013, Pages 145-150

  Zhang, Zhenyu ^a   Chang, Shwu Shin ^a   Zhang, Zhenying ^b   Xue, Zhihong ^a   Zhang, Hanxing ^b   Li, Shaojie ^b   Liu, Yi ^a  

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

^b INSTITUTE OF MICROBIOLOGY   (China)

Author keywords

DNA damage; Homologous recombination; qiRNA; Quelling; Repetitive sequences; RNAi

Indexed keywords

FUNGAL DNA; FUNGAL RNA; RIBOSOME DNA; SMALL INTERFERING RNA;

ARTICLE; CELL CYCLE G1 PHASE; CELL CYCLE S PHASE; CHROMATIN; CONTROLLED STUDY; DNA DAMAGE; DNA SEQUENCE; DNA SPLICING; DOUBLE STRANDED DNA BREAK; GENETIC ANALYSIS; GENETIC SCREENING; NEUROSPORA; NONHUMAN; PRIORITY JOURNAL; RNA INTERFERENCE; RNA SPLICING; TRANSGENE;

EID: 84873048282     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.209494.112     Document Type: Article

References (39)

1. Brewer BJ, Fangman WL. (1987). The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51: 463-471.
2. Buhler M, Moazed D. (2007). Transcription and RNAi in heterochromatic gene silencing. Nat Struct Mol Biol 14: 1041-1048.
3. Bzymek M, Lovett ST. (2001). Instability of repetitive DNA sequences: The role of replication in multiple mechanisms. Proc Natl Acad Sci 98: 8319-8325.
4. Calzada A, Hodgson B, Kanemaki M, Bueno A, Labib K. (2005). Molecular anatomy and regulation of a stable replisome at a paused eukaryotic DNA replication fork. Genes Dev 19: 1905-1919.
5. Catalanotto C, Nolan T, Cogoni C. (2006). Homology effects in Neurospora crassa. FEMS Microbiol Lett 254: 182-189.
6. Cecere G, Cogoni C. (2009). Quelling targets the rDNA locus and functions in rDNA copy number control. BMC Microbiol 9: 44.
7. Chang SS, Zhang Z, Liu Y. (2012). RNA interference pathways in fungi: Mechanisms and functions. Annu Rev Microbiol 66: 305-323.
8. Cheng P, He Q, He Q, Wang L, Liu Y. (2005). Regulation of the Neurospora circadian clock by an RNA helicase. Genes Dev 19: 234-241.
9. Clapier CR, Cairns BR. (2009). The biology of chromatin remodeling complexes. Annu Rev Biochem 78: 273-304.
10. Cogoni C, Macino G. (1999a). Gene silencing in Neurospora crassa requires a protein homologous to RNA-dependent RNA polymerase. Nature 399: 166-169.
11. Cogoni C, Macino G. (1999b). Posttranscriptional gene silencing in Neurospora by a RecQ DNA helicase. Science 286: 2342-2344.
12. Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, Litvinkova L, Weiss RL, Borkovich KA, Dunlap JC. (2006). A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Natl Acad Sci 103: 10352-10357.
13. De Muyt A, Jessop L, Kolar E, Sourirajan A, Chen J, Dayani Y, Lichten M. (2012). BLM helicase ortholog Sgs1 is a central regulator of meiotic recombination intermediate metabolism. Mol Cell 46: 43-53.
14. Francia S, Michelini F, Saxena A, Tang D, de Hoon M, Anelli V, Mione M, Carninci P, d'Adda di Fagagna F. (2012). Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature 488: 231-235.
15. Ghildiyal M, Zamore PD. (2009). Small silencing RNAs: An expanding universe. Nat Rev Genet 10: 94-108.
16. Huang J, Brito IL, Villen J, Gygi SP, Amon A, Moazed D. (2006). Inhibition of homologous recombination by a cohesin-associated clamp complex recruited to the rDNA recombination enhancer. Genes Dev 20: 2887-2901.
17. Ishibashi K, Suzuki K, Ando Y, Takakura C, Inoue H. (2006). Nonhomologous chromosomal integration of foreign DNA is completely dependent on MUS-53 (human Lig4 homolog) in Neurospora. Proc Natl Acad Sci 103: 14871-14876.
18. Kelman Z. (1997). PCNA: Structure, functions and interactions. Oncogene 14: 629-640.
19. Krings G, Bastia D. (2004). swi1-and swi3-dependent and independent replication fork arrest at the ribosomal DNA of Schizosaccharomyces pombe. Proc Natl Acad Sci 101: 14085-14090.
20. Lee HC, Chang SS, Choudhary S, Aalto AP, Maiti M, Bamford DH, Liu Y. (2009). qiRNA is a new type of small interfering RNA induced by DNA damage. Nature 459: 274-277.
21. Lee HC, Aalto AP, Yang Q, Chang SS, Huang G, Fisher D, Cha J, Poranen MM, Bamford DH, Liu Y. (2010). The DNA/RNA-dependent RNA polymerase QDE-1 generates aberrant RNA and dsRNA for RNAi in a process requiring replication protein A and a DNA helicase. PLoS Biol 8: e1000496.
22. 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.
23. Michalik KM, Bottcher R, Forstemann K. (2012). A small RNA response at DNA ends in Drosophila. Nucleic Acids Res 40: 9596-9603.
24. Mohanty BK, Bairwa NK, Bastia D. (2006). The Tof1p-Csm3p protein complex counteracts the Rrm3p helicase to control replication termination of Saccharomyces cerevisiae. Proc Natl Acad Sci 103: 897-902.
25. Nolan T, Braccini L, Azzalin G, De Toni A, Macino G, Cogoni C. (2005). The post-transcriptional gene silencing machinery functions independently of DNA methylation to repress a LINE1-like retrotransposon in Neurospora crassa. Nucleic Acids Res 33: 1564-1573.
26. Nolan T, Cecere G, Mancone C, Alonzi T, Tripodi M, Catalanotto C, Cogoni C. (2008). The RNA-dependent RNA polymerase essential for post-transcriptional gene silencing in Neurospora crassa interacts with replication protein A. Nucleic Acids Res 36: 532-538.
27. Romano N, Macino G. (1992). Quelling: Transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol 6: 3343-3353.
28. Sancar A, Lindsey-Boltz LA, Unsal-Kacmaz K, Linn S. (2004). Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu Rev Biochem 73: 39-85.
29. Sijen T, Plasterk RH. (2003). Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi. Nature 426: 310-314.
30. Siomi MC, Saito K, Siomi H. (2008). How selfish retrotransposons are silenced in Drosophila germline and somatic cells. FEBS Lett 582: 2473-2478.
31. Srivastava VK, Pall ML, Schroeder AL. (1988). Deoxyribonucleoside triphosphate pools in Neurospora crassa: Effects of histidine and hydroxyurea. Mutat Res 200: 45-53.
32. Sung P, Klein H. (2006). Mechanism of homologous recombination: Mediators and helicases take on regulatory functions. Nat Rev Mol Cell Biol 7: 739-750.
33. Vader G, Blitzblau HG, Tame MA, Falk JE, Curtin L, Hochwagen A. (2011). Protection of repetitive DNA borders from self-induced meiotic instability. Nature 477: 115-119.
34. van Attikum H, Fritsch O, Gasser SM. (2007). Distinct roles for SWR1 and INO80 chromatin remodeling complexes at chromosomal doublestrand breaks. EMBO J 26: 4113-4125.
35. Vignali M, Hassan AH, Neely KE, Workman JL. (2000). ATP-dependent chromatin-remodeling complexes. Mol Cell Biol 20: 1899-1910.
36. Vincent JA, Kwong TJ, Tsukiyama T. (2008). ATP-dependent chromatin remodeling shapes the DNA replication landscape. Nat Struct Mol Biol 15: 477-484.
37. Wang X, Hsueh YP, Li W, Floyd A, Skalsky R, Heitman J. (2010). Sexinduced silencing defends the genome of Cryptococcus neoformans via RNAi. Genes Dev 24: 2566-2582.
38. Wei W, Ba Z, Gao M, Wu Y, Ma Y, Amiard S, White CI, Rendtlew Danielsen JM, Yang YG, Qi Y. (2012). A role for small RNAs in DNA double-strand break repair. Cell 149: 101-112.
39. Zou H, Rothstein R. (1997). Holliday junctions accumulate in replication mutants via a RecA homolog-independent mechanism. Cell 90: 87-96.