TY - JOUR AU - Esteller, M. PY - 2011 DA - 2011// TI - Non-coding RNAs in human disease JO - Nat Rev Genet VL - 12 UR - https://doi.org/10.1038/nrg3074 DO - 10.1038/nrg3074 ID - Esteller2011 ER - TY - JOUR AU - Salta, E. AU - Strooper, B. PY - 2012 DA - 2012// TI - Non-coding RNAs with essential roles in neurodegenerative disorders JO - Lancet Neurol VL - 11 UR - https://doi.org/10.1016/S1474-4422(11)70286-1 DO - 10.1016/S1474-4422(11)70286-1 ID - Salta2012 ER - TY - JOUR AU - Huttenhofer, A. AU - Schattner, P. AU - Polacek, N. PY - 2005 DA - 2005// TI - Non-coding RNAs: hope or hype? JO - Trends Genet VL - 21 UR - https://doi.org/10.1016/j.tig.2005.03.007 DO - 10.1016/j.tig.2005.03.007 ID - Huttenhofer2005 ER - TY - JOUR AU - Krude, T. AU - Christov, C. P. AU - Hyrien, O. AU - Marheineke, K. PY - 2009 DA - 2009// TI - Y RNA functions at the initiation step of mammalian chromosomal DNA replication JO - J Cell Sci VL - 122 UR - https://doi.org/10.1242/jcs.047563 DO - 10.1242/jcs.047563 ID - Krude2009 ER - TY - JOUR AU - Lerner, M. R. AU - Boyle, J. A. AU - Hardin, J. A. AU - Steitz, J. A. PY - 1981 DA - 1981// TI - Two novel classes of small ribonucleoproteins detected by antibodies associated with lupus erythematosus JO - Science VL - 211 UR - https://doi.org/10.1126/science.6164096 DO - 10.1126/science.6164096 ID - Lerner1981 ER - TY - JOUR AU - Chen, X. AU - Wolin, S. L. PY - 2004 DA - 2004// TI - The Ro 60 kDa autoantigen: insights into cellular function and role in autoimmunity JO - J Mol Med (Berl). VL - 82 UR - https://doi.org/10.1007/s00109-004-0529-0 DO - 10.1007/s00109-004-0529-0 ID - Chen2004 ER - TY - JOUR AU - Hall, A. E. AU - Turnbull, C. AU - Dalmay, T. PY - 2013 DA - 2013// TI - Y RNAs: recent developments JO - Biomol Concepts. VL - 4 UR - https://doi.org/10.1515/bmc-2012-0050 DO - 10.1515/bmc-2012-0050 ID - Hall2013 ER - TY - JOUR AU - Christov, C. P. AU - Gardiner, T. J. AU - Szuts, D. AU - Krude, T. PY - 2006 DA - 2006// TI - Functional requirement of noncoding Y RNAs for human chromosomal DNA replication JO - Mol Cell Biol VL - 26 UR - https://doi.org/10.1128/MCB.01060-06 DO - 10.1128/MCB.01060-06 ID - Christov2006 ER - TY - JOUR AU - Gardiner, T. J. AU - Christov, C. P. AU - Langley, A. R. AU - Krude, T. PY - 2009 DA - 2009// TI - A conserved motif of vertebrate Y RNAs essential for chromosomal DNA replication JO - RNA VL - 15 UR - https://doi.org/10.1261/rna.1472009 DO - 10.1261/rna.1472009 ID - Gardiner2009 ER - TY - JOUR AU - Kowalski, M. P. AU - Krude, T. PY - 2015 DA - 2015// TI - Functional roles of non-coding Y RNAs JO - Int J Biochem Cell Biol VL - 66 UR - https://doi.org/10.1016/j.biocel.2015.07.003 DO - 10.1016/j.biocel.2015.07.003 ID - Kowalski2015 ER - TY - JOUR AU - Collart, C. AU - Christov, C. P. AU - Smith, J. C. AU - Krude, T. PY - 2011 DA - 2011// TI - The midblastula transition defines the onset of Y RNA-dependent DNA replication in Xenopus laevis JO - Mol Cell Biol VL - 31 UR - https://doi.org/10.1128/MCB.05411-11 DO - 10.1128/MCB.05411-11 ID - Collart2011 ER - TY - JOUR AU - Perreault, J. AU - Perreault, J. P. AU - Boire, G. PY - 2007 DA - 2007// TI - Ro-associated Y RNAs in metazoans: evolution and diversification JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm084 DO - 10.1093/molbev/msm084 ID - Perreault2007 ER - TY - JOUR AU - Mosig, A. AU - Guofeng, M. AU - Stadler, B. M. AU - Stadler, P. F. PY - 2007 DA - 2007// TI - Evolution of the vertebrate Y RNA cluster JO - Theory Biosci VL - 126 UR - https://doi.org/10.1007/s12064-007-0003-y DO - 10.1007/s12064-007-0003-y ID - Mosig2007 ER - TY - JOUR AU - Farris, A. D. AU - Koelsch, G. AU - Pruijn, G. J. AU - Venrooij, W. J. AU - Harley, J. B. PY - 1999 DA - 1999// TI - Conserved features of Y RNAs revealed by automated phylogenetic secondary structure analysis JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.4.1070 DO - 10.1093/nar/27.4.1070 ID - Farris1999 ER - TY - JOUR AU - Wang, I. AU - Kowalski, M. P. AU - Langley, A. R. AU - Rodriguez, R. AU - Balasubramanian, S. AU - Hsu, S. T. PY - 2014 DA - 2014// TI - Nucleotide contributions to the structural integrity and DNA replication initiation activity of noncoding y RNA JO - Biochemistry VL - 53 UR - https://doi.org/10.1021/bi500470b DO - 10.1021/bi500470b ID - Wang2014 ER - TY - JOUR AU - Debatisse, M. AU - Berry, M. AU - Buttin, G. PY - 1982 DA - 1982// TI - Stepwise isolation and properties of unstable Chinese hamster cell variants that overproduce adenylate deaminase JO - Mol Cell Biol VL - 2 UR - https://doi.org/10.1128/MCB.2.11.1346 DO - 10.1128/MCB.2.11.1346 ID - Debatisse1982 ER - TY - JOUR AU - Baron, B. AU - Fernandez, M. A. AU - Carignon, S. AU - Toledo, F. AU - Buttin, G. AU - Debatisse, M. PY - 1996 DA - 1996// TI - GNAI3, GNAT2, AMPD2, GSTM are clustered in 120 kb of Chinese hamster chromosome 1q JO - Mamm Genome VL - 7 UR - https://doi.org/10.1007/s003359900127 DO - 10.1007/s003359900127 ID - Baron1996 ER - TY - JOUR AU - Toledo, F. AU - Baron, B. AU - Fernandez, M. A. AU - Lachages, A. M. AU - Mayau, V. AU - Buttin, G. PY - 1998 DA - 1998// TI - oriGNAI3: a narrow zone of preferential replication initiation in mammalian cells identified by 2D gel and competitive PCR replicon mapping techniques JO - Nucleic Acids Res VL - 26 UR - https://doi.org/10.1093/nar/26.10.2313 DO - 10.1093/nar/26.10.2313 ID - Toledo1998 ER - TY - JOUR AU - Anglana, M. AU - Apiou, F. AU - Bensimon, A. AU - Debatisse, M. PY - 2003 DA - 2003// TI - Dynamics of DNA replication in mammalian somatic cells: nucleotide pool modulates origin choice and interorigin spacing JO - Cell VL - 114 UR - https://doi.org/10.1016/S0092-8674(03)00569-5 DO - 10.1016/S0092-8674(03)00569-5 ID - Anglana2003 ER - TY - JOUR AU - Fernandez, M. A. AU - Baron, B. AU - Prigent, M. AU - Toledo, F. AU - Buttin, G. AU - Debatisse, M. PY - 1997 DA - 1997// TI - Matrix attachment regions and transcription units in a polygenic mammalian locus overlapping two isochores JO - J Cell Biochem VL - 67 UR - https://doi.org/3.0.CO;2-C DO - 3.0.CO;2-C ID - Fernandez1997 ER - TY - STD TI - Balani VA, de Lima Neto QA, Takeda KI, Gimenes F, Fiorini A, Debatisse M, et al. Replication origins oriGNAI3 and oriB of the mammalian AMPD2 locus nested in a region of straight DNA flanked by intrinsically bent DNA sites. BMB Rep. 2010;43(11):744–9. doi:10.5483/BMBRep.2010.43.11.744. ID - ref21 ER - TY - JOUR AU - Lima Neto, Q. A. AU - Rando, F. S. AU - Freitas, D. V. AU - Rodrigues, L. F. AU - Rosado, F. R. AU - Fiorini, A. PY - 2014 DA - 2014// TI - Straight core structure of DNA replication origins in the mammalian AMPD2 locus JO - Biochemistry (Mosc). VL - 79 UR - https://doi.org/10.1134/S0006297914010064 DO - 10.1134/S0006297914010064 ID - Lima Neto2014 ER - TY - JOUR AU - Farris, A. D. AU - O’Brien, C. A. AU - Harley, J. B. PY - 1995 DA - 1995// TI - Y3 is the most conserved small RNA component of Ro ribonucleoprotein complexes in vertebrate species JO - Gene VL - 154 UR - https://doi.org/10.1016/0378-1119(94)00823-B DO - 10.1016/0378-1119(94)00823-B ID - Farris1995 ER - TY - JOUR AU - Pruijn, G. J. AU - Wingens, P. A. AU - Peters, S. L. AU - Thijssen, J. P. AU - Venrooij, W. J. PY - 1993 DA - 1993// TI - Ro RNP associated Y RNAs are highly conserved among mammals JO - Biochim Biophys Acta VL - 1216 UR - https://doi.org/10.1016/0167-4781(93)90006-Y DO - 10.1016/0167-4781(93)90006-Y ID - Pruijn1993 ER - TY - JOUR AU - Dereeper, A. AU - Guignon, V. AU - Blanc, G. AU - Audic, S. AU - Buffet, S. AU - Chevenet, F. PY - 2008 DA - 2008// TI - Phylogeny.fr: robust phylogenetic analysis for the non-specialist JO - Nucleic Acids Res VL - 36 UR - https://doi.org/10.1093/nar/gkn180 DO - 10.1093/nar/gkn180 ID - Dereeper2008 ER - TY - JOUR AU - Dereeper, A. AU - Audic, S. AU - Claverie, J. M. AU - Blanc, G. PY - 2010 DA - 2010// TI - BLAST-EXPLORER helps you building datasets for phylogenetic analysis JO - BMC Evol Biol. VL - 10 UR - https://doi.org/10.1186/1471-2148-10-8 DO - 10.1186/1471-2148-10-8 ID - Dereeper2010 ER - TY - JOUR AU - Schramm, L. AU - Hernandez, N. PY - 2002 DA - 2002// TI - Recruitment of RNA polymerase III to its target promoters JO - Genes Dev VL - 16 UR - https://doi.org/10.1101/gad.1018902 DO - 10.1101/gad.1018902 ID - Schramm2002 ER - TY - JOUR AU - Larkin, M. A. AU - Blackshields, G. AU - Brown, N. P. AU - Chenna, R. AU - McGettigan, P. A. AU - McWilliam, H. PY - 2007 DA - 2007// TI - Clustal W and Clustal X version 2.0 JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm404 DO - 10.1093/bioinformatics/btm404 ID - Larkin2007 ER - TY - JOUR AU - Oler, A. J. AU - Alla, R. K. AU - Roberts, D. N. AU - Wong, A. AU - Hollenhorst, P. C. AU - Chandler, K. J. PY - 2010 DA - 2010// TI - Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors JO - Nat Struct Mol Biol VL - 17 UR - https://doi.org/10.1038/nsmb.1801 DO - 10.1038/nsmb.1801 ID - Oler2010 ER - TY - JOUR AU - Szuts, D. AU - Kitching, L. AU - Christov, C. AU - Budd, A. AU - Peak-Chew, S. AU - Krude, T. PY - 2003 DA - 2003// TI - RPA is an initiation factor for human chromosomal DNA replication JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg269 DO - 10.1093/nar/gkg269 ID - Szuts2003 ER - TY - JOUR AU - Szuts, D. AU - Christov, C. AU - Kitching, L. AU - Krude, T. PY - 2005 DA - 2005// TI - Distinct populations of human PCNA are required for initiation of chromosomal DNA replication and concurrent DNA repair JO - Exp Cell Res VL - 311 UR - https://doi.org/10.1016/j.yexcr.2005.09.009 DO - 10.1016/j.yexcr.2005.09.009 ID - Szuts2005 ER - TY - JOUR AU - Krude, T. PY - 2000 DA - 2000// TI - Initiation of human DNA replication in vitro using nuclei from cells arrested at an initiation-competent state JO - J Biol Chem VL - 275 UR - https://doi.org/10.1074/jbc.275.18.13699 DO - 10.1074/jbc.275.18.13699 ID - Krude2000 ER - TY - JOUR AU - Keller, C. AU - Hyrien, O. AU - Knippers, R. AU - Krude, T. PY - 2002 DA - 2002// TI - Site-specific and temporally controlled initiation of DNA replication in a human cell-free system JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.10.2114 DO - 10.1093/nar/30.10.2114 ID - Keller2002 ER - TY - JOUR AU - Marheineke, K. AU - Hyrien, O. AU - Krude, T. PY - 2005 DA - 2005// TI - Visualization of bidirectional initiation of chromosomal DNA replication in a human cell free system JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki994 DO - 10.1093/nar/gki994 ID - Marheineke2005 ER - TY - JOUR AU - Popenda, M. AU - Szachniuk, M. AU - Antczak, M. AU - Purzycka, K. J. AU - Lukasiak, P. AU - Bartol, N. PY - 2012 DA - 2012// TI - Automated 3D structure composition for large RNAs JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks339 DO - 10.1093/nar/gks339 ID - Popenda2012 ER - TY - STD TI - Sponer J, Otyepka M, Banas P, Reblova K, Walter NG. Chapter 6 molecular dynamics simulations of RNA molecules. Innovations in biomolecular modeling and simulations, vol. 2. The Royal Society of Chemistry; 2012. p. 129–55. ID - ref36 ER - TY - JOUR AU - Halder, S. AU - Bhattacharyya, D. PY - 2013 DA - 2013// TI - RNA structure and dynamics: a base pairing perspective JO - Prog Biophys Mol Biol VL - 113 UR - https://doi.org/10.1016/j.pbiomolbio.2013.07.003 DO - 10.1016/j.pbiomolbio.2013.07.003 ID - Halder2013 ER - TY - JOUR AU - Clarke, P. A. AU - Mathews, M. B. PY - 1995 DA - 1995// TI - Interactions between the double-stranded RNA binding motif and RNA: definition of the binding site for the interferon-induced protein kinase DAI (PKR) on adenovirus VA RNA JO - RNA VL - 1 ID - Clarke1995 ER - TY - JOUR AU - Tian, B. AU - Mathews, M. B. PY - 2003 DA - 2003// TI - Phylogenetics and functions of the double-stranded RNA-binding motif: a genomic survey JO - Prog Nucleic Acid Res Mol Biol VL - 74 UR - https://doi.org/10.1016/S0079-6603(03)01012-2 DO - 10.1016/S0079-6603(03)01012-2 ID - Tian2003 ER - TY - JOUR AU - Tian, B. AU - Bevilacqua, P. C. AU - Diegelman-Parente, A. AU - Mathews, M. B. PY - 2004 DA - 2004// TI - The double-stranded-RNA-binding motif: interference and much more JO - Nat Rev Mol Cell Biol VL - 5 UR - https://doi.org/10.1038/nrm1528 DO - 10.1038/nrm1528 ID - Tian2004 ER - TY - JOUR AU - Zuker, M. PY - 2003 DA - 2003// TI - Mfold web server for nucleic acid folding and hybridization prediction JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg595 DO - 10.1093/nar/gkg595 ID - Zuker2003 ER - TY - JOUR AU - Darty, K. AU - Denise, A. AU - Ponty, Y. PY - 2009 DA - 2009// TI - VARNA: interactive drawing and editing of the RNA secondary structure JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp250 DO - 10.1093/bioinformatics/btp250 ID - Darty2009 ER - TY - JOUR AU - Pronk, S. AU - Pall, S. AU - Schulz, R. AU - Larsson, P. AU - Bjelkmar, P. AU - Apostolov, R. PY - 2013 DA - 2013// TI - GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt055 DO - 10.1093/bioinformatics/btt055 ID - Pronk2013 ER - TY - JOUR AU - Hornak, V. AU - Abel, R. AU - Okur, A. AU - Strockbine, B. AU - Roitberg, A. AU - Simmerling, C. PY - 2006 DA - 2006// TI - Comparison of multiple Amber force fields and development of improved protein backbone parameters JO - Proteins. VL - 65 UR - https://doi.org/10.1002/prot.21123 DO - 10.1002/prot.21123 ID - Hornak2006 ER - TY - JOUR AU - Jha, S. AU - Coveney, P. V. AU - Laughton, C. A. PY - 2005 DA - 2005// TI - Force field validation for nucleic acid simulations: comparing energies and dynamics of a DNA dodecamer JO - J Comput Chem VL - 26 UR - https://doi.org/10.1002/jcc.20300 DO - 10.1002/jcc.20300 ID - Jha2005 ER - TY - BOOK AU - Sambrook, J. AU - Russell, D. W. PY - 2001 DA - 2001// TI - Molecular cloning: a laboratory manual PB - Cold Spring Harbor Laboratory Press CY - Cold Spring Harbor ID - Sambrook2001 ER - TY - JOUR AU - Sal, G. AU - Manfioletti, G. AU - Schneider, C. PY - 1989 DA - 1989// TI - The CTAB-DNA precipitation method: a common mini-scale preparation of template DNA from phagemids, phages or plasmids suitable for sequencing JO - Biotechniques VL - 7 ID - Sal1989 ER - TY - JOUR AU - Silva, W. A. AU - Costa, M. C. AU - Valente, V. AU - Sousa, J. F. AU - Paco-Larson, M. L. AU - Espreafico, E. M. PY - 2001 DA - 2001// TI - PCR template preparation for capillary DNA sequencing JO - Biotechniques. VL - 30 ID - Silva2001 ER - TY - JOUR AU - Zhang, A. T. AU - Langley, A. R. AU - Christov, C. P. AU - Kheir, E. AU - Shafee, T. AU - Gardiner, T. J. PY - 2011 DA - 2011// TI - Dynamic interaction of Y RNAs with chromatin and initiation proteins during human DNA replication JO - J Cell Sci VL - 124 UR - https://doi.org/10.1242/jcs.086561 DO - 10.1242/jcs.086561 ID - Zhang2011 ER -