A conserved motif of vertebrate Y RNAs essential for chromosomal DNA replication

RNA

Volumn 15, Issue 7, 2009, Pages 1375-1385

  Gardiner, Timothy J ^a   Christov, Christo P ^a   Langley, Alexander R ^a   Krude, Torsten ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Cell free system; DNA replication; Evolution; Noncoding RNA; Y RNA

Indexed keywords

DOUBLE STRANDED RNA; OLIGONUCLEOTIDE; RNA;

ARTICLE; CELL CYCLE G1 PHASE; CELL FREE SYSTEM; CHROMOSOME; DNA REPLICATION; GENETIC CONSERVATION; HUMAN; HUMAN CELL; IN VITRO STUDY; MOLECULAR EVOLUTION; MUTANT; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; VERTEBRATE; WILD TYPE;

ANIMALS; BASE SEQUENCE; CAENORHABDITIS ELEGANS; CELL-FREE SYSTEM; CHROMOSOMES, HUMAN; COMPUTATIONAL BIOLOGY; DEINOCOCCUS; DNA REPLICATION; G1 PHASE; HELA CELLS; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; RNA INTERFERENCE; RNA, DOUBLE-STRANDED; RNA, UNTRANSLATED; VERTEBRATES;

VERTEBRATA;

EID: 67649312284     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1472009     Document Type: Article

References (48)

1. Arias EE, Walter JC. 2007. Strength in numbers: Preventing rereplication via multiple mechanisms in eukaryotic cells. Genes & Dev 21: 497-518. (Pubitemid 46409465)
2. Bartel DP. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297. (Pubitemid 38167318)
3. Bell SP, Dutta A. 2002. DNA replication in eukaryotic cells. Annu Rev Biochem 71: 333-374. (Pubitemid 34800224)
4. Chen X, Wolin SL. 2004. The Ro 60 kDa autoantigen: Insights into cellular function and role in autoimmunity. J Mol Med 82: 232-239. (Pubitemid 38553651)
5. Chen X, Quinn AM, Wolin SL. 2000. Ro ribonucleoproteins contribute to the resistance of Deinococcus radiodurans to ultraviolet irradiation. Genes & Dev 14: 777-782. (Pubitemid 30214997)
6. Chen X, Smith JD, Shi H, Yang DD, Flavell RA, Wolin SL. 2003. The Ro autoantigen binds misfolded U2 small nuclear RNAs and assists mammalian cell survival after UV irradiation. Curr Biol 13: 2206-2211. (Pubitemid 38024948)
7. Chen X, Wurtmann EJ, Van Batavia J, Zybailov B, Washburn MP, Wolin SL. 2007. An ortholog of the Ro autoantigen functions in 23S rRNA maturation in D. radiodurans. Genes & Dev 21: 1328-1339. (Pubitemid 46871037)
8. Christov CP, Gardiner TJ, Szüts D, Krude T. 2006. Functional requirement of noncoding Y RNAs for human chromosomal DNA replication. Mol Cell Biol 26: 6993-7004. (Pubitemid 44387647)
9. Christov CP, Trivier E, Krude T. 2008. Noncoding human Y RNAs are overexpressed in tumours and required for cell proliferation. Br J Cancer 98: 981-988. (Pubitemid 351341611)
10. Clamp M, Cuff J, Searle SM, Barton GJ. 2004. The Jalview Java alignment editor. Bioinformatics 20: 426-427. (Pubitemid 38262778)
11. Costa S, Blow JJ. 2007. The elusive determinants of replication origins. EMBO Rep 8: 332-334. (Pubitemid 46511032)
12. DePamphilis ML, Blow JJ, Ghosh S, Saha T, Noguchi K, Vassilev A. 2006. Regulating the licensing of DNA replication origins in metazoa. Curr Opin Cell Biol 18: 231-239.
13. Du T, Zamore PD. 2005. microPrimer: The biogenesis and function of microRNA. Development 132: 4645-4652. (Pubitemid 41685275)
14. Fabini G, Rutjes SA, Zimmermann C, Pruijn GJ, Steiner G. 2000. Analysis of the molecular composition of Ro ribonucleoprotein complexes. Identification of novel Y RNA-binding proteins. Eur J Biochem 267: 2778-2789. (Pubitemid 30304276)
15. Fabini G, Raijmakers R, Hayer S, Fouraux MA, Pruijn GJ, Steiner G. 2001. The heterogeneous nuclear ribonucleoproteins I and K interact with a subset of the ro ribonucleoprotein-associated Y RNAs in vitro and in vivo. J Biol Chem 276: 20711-20718. (Pubitemid 37411160)
16. Farris AD, Koelsch G, Pruijn GJ, van Venrooij WJ, Harley JB. 1999. Conserved features of Y RNAs revealed by automated phylogenetic secondary structure analysis. Nucleic Acids Res 27: 1070-1078. (Pubitemid 29209511)
17. Farris AD, O'Brien CA, Harley JB. 1995. Y3 is the most conserved small RNA component of Ro ribonucleoprotein complexes in vertebrate species. Gene 154: 193-198.
18. Fouraux MA, Bouvet P, Verkaart S, van Venrooij WJ, Pruijn GJ. 2002. Nucleolin associates with a subset of the human Ro ribonucleoprotein complexes. J Mol Biol 320: 475-488. (Pubitemid 34753975)
19. Fuchs G, Stein AJ, Fu C, Reinisch KM, Wolin SL. 2006. Structural and biochemical basis for misfolded RNA recognition by the Ro autoantigen. Nat Struct Mol Biol 13: 1002-1009. (Pubitemid 44684852)
20. Gilbert DM. 2001. Making sense of eukaryotic DNA replication origins. Science 294: 96-100. (Pubitemid 32952956)
21. Green CD, Long KS, Shi H, Wolin SL. 1998. Binding of the 60-kDa Ro autoantigen to Y RNAs: Evidence for recognition in the major groove of a conserved helix. RNA 4: 750-765. (Pubitemid 28317824)
22. Hendrick JP, Wolin SL, Rinke J, Lerner MR, Steitz JA. 1981. Ro small cytoplasmic ribonucleoproteins are a subclass of La ribonucleoproteins: Further characterization of the Ro and La small ribonucleoproteins from uninfected mammalian cells. Mol Cell Biol 1: 1138-1149. (Pubitemid 12178359)
23. Hogg JR, Collins K. 2007. Human Y5 RNA specializes a Ro ribonucleoprotein for 5S ribosomal RNA quality control. Genes & Dev 21: 3067-3072. (Pubitemid 350223524)
24. Hogg JR, Collins K. 2008. Structured noncoding RNAs and the RNP Renaissance. Curr Opin Chem Biol 12: 684-689.
25. Krude T. 2000. Initiation of human DNA replication in vitro using nuclei from cells arrested at an initiation-competent state. J Biol Chem 275: 13699-13707. (Pubitemid 30257440)
26. Krude T. 2006. Initiation of chromosomal DNA replication in mammalian cell-free systems. Cell Cycle 5: 2115-2122. (Pubitemid 44553746)
27. Krude T, Christov CP, Hyrien O, Marheineke K. 2009. Y RNA functions at the initiation step of mammalian chromosomal DNA replication. J Cell Sci 122 (in press).
28. Labbe JC, Burgess J, Rokeach LA, Hekimi S. 2000. ROP-1, an RNA quality-control pathway component, affects Caenorhabditis elegans dauer formation. Proc Natl Acad Sci 97: 13233-13238.
29. Lassmann T, Sonnhammer EL. 2005. Kalign - An accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 6: 298. (Pubitemid 41829850)
30. Lerner MR, Boyle JA, Hardin JA, Steitz JA. 1981. Two novel classes of small ribonucleoproteins detected by antibodies associated with lupus erythematosus. Science 211: 400-402. (Pubitemid 11128752)
31. Machida YJ, Hamlin JL, Dutta A. 2005. Right place, right time, and only once: Replication initiation in metazoans. Cell 123: 13-24. (Pubitemid 41414525)
32. Maraia RJ, Sasaki-Tozawa N, Driscoll CT, Green ED, Darlington GJ. 1994. The human Y4 small cytoplasmic RNA gene is controlled by upstream elements and resides on chromosome 7 with all other hY scRNA genes. Nucleic Acids Res 22: 3045-3052. (Pubitemid 24260634)
33. Maraia R, Sakulich AL, Brinkmann E, Green ED. 1996. Gene encoding human Ro-associated autoantigen Y5 RNA. Nucleic Acids Res 24: 3552-3559.
34. Matera AG, Frey MR, Margelot K, Wolin SL. 1995. A perinucleolar compartment contains several RNA polymerase III transcripts as well as the polypyrimidine tract-binding protein, hnRNP I. J Cell Biol 129: 1181-1193.
35. Mathews DH, Sabina J, Zuker M, Turner DH. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288: 911-940. (Pubitemid 29248642)
36. Mosig A, Guofeng M, Stadler BMR, Stadler PF. 2007. Evolution of the vertebrate Y RNA cluster. Theory Biosci 129: 9-14. (Pubitemid 46838774)
37. Perreault J, Perreault JP, Boire G. 2007. The Ro Associated Y RNAs in Metazoans: Evolution and diversification. Mol Biol Evol 24: 1678-1689. (Pubitemid 47236684)
38. Pruijn GJ, Wingens PA, Peters SL, Thijssen JP, van Venrooij WJ. 1993. Ro RNP associated Y RNAs are highly conserved among mammals. Biochim Biophys Acta 1216: 395-401. (Pubitemid 24013516)
39. Simons FH, Rutjes SA, van Venrooij WJ, Pruijn GJ. 1996. The interactions with Ro60 and La differentially affect nuclear export of hY1 RNA. RNA 2: 264-273. (Pubitemid 26371296)
40. Stein AJ, Fuchs G, Fu C, Wolin SL, Reinisch KM. 2005. Structural insights into RNA quality control: The Ro autoantigen binds misfolded RNAs via its central cavity. Cell 121: 529-539. (Pubitemid 40720007)
41. Szüts D, Kitching L, Christov C, Budd A, Peak-Chew S, Krude T. 2003. RPA is an initiation factor for human chromosomal DNA replication. Nucleic Acids Res 31: 1725-1734. (Pubitemid 36336574)
42. Szüts D, Christov C, Kitching L, Krude T. 2005. Distinct populations of human PCNA are required for initiation of chromosomal DNA replication and concurrent DNA repair. Exp Cell Res 311: 240-250. (Pubitemid 41636317)
43. Takeda DY, Dutta A. 2005. DNA replication and progression through S phase. Oncogene 24: 2827-2843. (Pubitemid 40638093)
44. Teunissen SW, Kruithof MJ, Farris AD, Harley JB, Venrooij WJ, Pruijn GJ. 2000. Conserved features of Y RNAs: A comparison of experimentally derived secondary structures. Nucleic Acids Res 28: 610-619. (Pubitemid 30058003)
45. Van Horn DJ, Eisenberg D, O'Brien CA, Wolin SL. 1995. Caenorhabditis elegans embryos contain only one major species of Ro RNP. RNA 1: 293-303.
46. Wolin SL, Cedervall T. 2002. The La protein. Annu Rev Biochem 71: 375-403.
47. Xue D, Shi H, Smith JD, Chen X, Noe DA, Cedervall T, Yang DD, Eynon E, Brash DE, Kashgarian M, et al. 2003. A lupus-like syndrome develops in mice lacking the Ro 60-kDa protein, a major lupus autoantigen. Proc Natl Acad Sci 100: 7503-7508. (Pubitemid 36759999)
48. Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415. (Pubitemid 37442169)