Addendum: Ribose-seq: global mapping of ribonucleotides embedded in genomic DNA (Nature Methods, (2019), 10.1038/nmeth.3259);Ribose-seq: Global mapping of ribonucleotides embedded in genomic DNA

Nature Methods

Volumn 12, Issue 3, 2015, Pages 251-257

  Koh, Kyung Duk ^a   Balachander, Sathya ^a   Hesselberth, Jay R ^b   Storici, Francesca ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS DNA; CYTIDINE; FUNGAL DNA; GENOMIC DNA; GUANOSINE; MITOCHONDRIAL DNA; RIBONUCLEOTIDE; RIBOSE; RIBOSOME DNA; SINGLE STRANDED DNA; TRANSFER RNA; URACIL DNA GLYCOSIDASE;

ARABIDOPSIS THALIANA; ARTICLE; DNA BASE COMPOSITION; DNA DETERMINATION; DNA LIBRARY; DNA REPLICATION; GENE MAPPING; HIGH THROUGHPUT SEQUENCING; MITOCHONDRIAL GENOME; NONHUMAN; PRIORITY JOURNAL; RIBOSE SEQUENCE LIBRARY; SACCHAROMYCES CEREVISIAE; FUNGAL GENOME; GC RICH SEQUENCE; GENETIC PROCEDURES; GENETICS; METABOLISM; PROCEDURES;

SACCHAROMYCES CEREVISIAE;

DNA REPLICATION; DNA, FUNGAL; DNA, MITOCHONDRIAL; GC RICH SEQUENCE; GENETIC TECHNIQUES; GENOME, FUNGAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; RIBONUCLEOTIDES; SACCHAROMYCES CEREVISIAE; URACIL-DNA GLYCOSIDASE;

EID: 84923844518     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/s41592-019-0505-9     Document Type: Erratum

References (57)

1. Williams, J.S. & Kunkel, T.A. Ribonucleotides in DNA: origins, repair and consequences. DNA Repair (Amst.) 19, 27-37 (2014
2. Grossman, L.I., Watson, R. & Vinograd, J. The presence of ribonucleotides in mature closed-circular mitochondrial DNA. Proc. Natl. Acad. Sci. USA 70, 3339-3343 (1973
3. Vengrova, S. & Dalgaard, J.Z. The wild-Type Schizosaccharomyces pombe mat1 imprint consists of two ribonucleotides. EMBO Rep. 7, 59-65 (2006
4. Potenski, C.J. & Klein, H.L. How the misincorporation of ribonucleotides into genomic DNA can be both harmful and helpful to cells. Nucleic Acids Res. 42, 10226-10234 (2014
5. Clausen, A.R., Zhang, S., Burgers, P.M., Lee, M.Y. & Kunkel, T.A. Ribonucleotide incorporation, proofreading and bypass by human DNA polymerase delta. DNA Repair (Amst.) 12, 121-127 (2013
6. Kasiviswanathan, R. & Copeland, W.C. Ribonucleotide discrimination and reverse transcription by the human mitochondrial DNA polymerase. J. Biol. Chem. 286, 31490-31500 (2011
7. Nick McElhinny, S.A., et al. Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases. Proc. Natl. Acad. Sci. USA 107, 4949-4954 (2010
8. McDonald, J.P., Vaisman, A., Kuban, W., Goodman, M.F. & Woodgate, R. Mechanisms employed by Escherichia coli to prevent ribonucleotide incorporation into genomic DNA by pol V. PLoS Genet. 8, e1003030 (2012
9. Zhu, H. & Shuman, S. Bacterial nonhomologous end joining ligases preferentially seal breaks with a 3'-OH monoribonucleotide. J. Biol. Chem. 283, 8331-8339 (2008
10. Rumbaugh, J.A., Murante, R.S., Shi, S. & Bambara, R.A. Creation and removal of embedded ribonucleotides in chromosomal DNA during mammalian Okazaki fragment processing. J. Biol. Chem. 272, 22591-22599 (1997
11. Randerath, K., et al. Formation of ribonucleotides in DNA modified by oxidative damage in vitro and in vivo. Characterization by 32P-postlabeling. Mutat. Res. 275, 355-366 (1992
12. Cerritelli, S.M. & Crouch, R.J. Ribonuclease H: the enzymes in eukaryotes. FEBS J. 276, 1494-1505 (2009
13. Sparks, J.L., et al. RNase H2-initiated ribonucleotide excision repair. Mol. Cell 47, 980-986 (2012
14. Reijns, M.A., et al. Enzymatic removal of ribonucleotides from DNA is essential for mammalian genome integrity and development. Cell 149, 1008-1022 (2012
15. Lujan, S.A., Williams, J.S., Clausen, A.R., Clark, A.B. & Kunkel, T.A. Ribonucleotides are signals for mismatch repair of leading-strand replication errors. Mol. Cell 50, 437-443 (2013
16. Williams, J.S., et al. Topoisomerase 1-mediated removal of ribonucleotides from nascent leading-strand DNA. Mol. Cell 49, 1010-1015 (2013
17. Yao, N.Y., Schroeder, J.W., Yurieva, O., Simmons, L.A. & O'Donnell, M.E. Cost of rNTP/dNTP pool imbalance at the replication fork. Proc. Natl. Acad. Sci. USA 110, 12942-12947 (2013
18. Chiu, H.C., et al. RNA intrusions change DNA elastic properties and structure. Nanoscale 6, 10009-10017 (2014
19. Caldecott, K.W. Molecular biology. Ribose-An internal threat to DNA. Science 343, 260-261 (2014
20. Kim, N., et al. Mutagenic processing of ribonucleotides in DNA by yeast topoisomerase I. Science 332, 1561-1564 (2011
21. Potenski, C.J., Niu, H., Sung, P. & Klein, H.L. Avoidance of ribonucleotide-induced mutations by RNase H2 and Srs2-Exo1 mechanisms. Nature 511, 251-254 (2014
22. Cho, J.E., Kim, N., Li, Y.C. & Jinks-Robertson, S. Two distinct mechanisms of Topoisomerase 1-dependent mutagenesis in yeast. DNA Repair (Amst.) 12, 205-211 (2013
23. Crow, Y.J., et al. Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutieres syndrome and mimic congenital viral brain infection. Nat. Genet. 38, 910-916 (2006
24. Schutz, K., Hesselberth, J.R. & Fields, S. Capture and sequence analysis of RNAs with terminal 2', 3'-cyclic phosphates. RNA 16, 621-631 (2010
25. Remus, B.S. & Shuman, S. Distinctive kinetics and substrate specificities of plant and fungal tRNA ligases. RNA 20, 462-473 (2014
26. Cooper, D.A., Jha, B.K., Silverman, R.H., Hesselberth, J.R. & Barton, D.J. Ribonuclease L and metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs. Nucleic Acids Res. 42, 5202-5216 (2014
27. Krokan, H.E., Drablos, F. & Slupphaug, G. Uracil in DNA-occurrence, consequences and repair. Oncogene 21, 8935-8948 (2002
28. Lindahl, T., Ljungquist, S., Siegert, W., Nyberg, B. & Sperens, B. DNA N-glycosidases: properties of uracil-DNA glycosidase from Escherichia coli. J. Biol. Chem. 252, 3286-3294 (1977
29. Fasullo, M., Tsaponina, O., Sun, M. & Chabes, A. Elevated dNTP levels suppress hyper-recombination in Saccharomyces cerevisiae S-phase checkpoint mutants. Nucleic Acids Res. 38, 1195-1203 (2010
30. Williams, J.S., et al. Proofreading of ribonucleotides inserted into DNA by yeast DNA polymerase varepsilon. DNA Repair (Amst.) 11, 649-656 (2012
31. Foury, F., Roganti, T., Lecrenier, N. & Purnelle, B. The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae. FEBS Lett. 440, 325-331 (1998
32. Gerhold, J.M., Aun, A., Sedman, T., Joers, P. & Sedman, J. Strand invasion structures in the inverted repeat of Candida albicans mitochondrial DNA reveal a role for homologous recombination in replication. Mol. Cell 39, 851-861 (2010
33. Yabuki, N., Terashima, H. & Kitada, K. Mapping of early firing origins on a replication profile of budding yeast. Genes Cells 7, 781-789 (2002
34. Moraes, C.T. What regulates mitochondrial DNA copy number in animal cells? Trends Genet. 17, 199-205 (2001
35. Szostak, J.W. & Wu, R. Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae. Nature 284, 426-430 (1980
36. Hani, J. & Feldmann, H. tRNA genes and retroelements in the yeast genome. Nucleic Acids Res. 26, 689-696 (1998
37. Mieczkowski, P.A., Lemoine, F.J. & Petes, T.D. Recombination between retrotransposons as a source of chromosome rearrangements in the yeast Saccharomyces cerevisiae. DNA Repair (Amst.) 5, 1010-1020 (2006
38. El Hage, A., Webb, S., Kerr, A. & Tollervey, D. Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria. PLoS Genet. 10, e1004716 (2014
39. Barrett, T., et al. NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res. 41, D991-D995 (2013
40. Clausen, A.R., et al. Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation. Nat. Struct. Molec. Biol. doi: 10.1038/nsmb.2957 (26 January 2015
41. Reijns, M.A.M., et al. Lagging strand replication shapes the mutational landscape of the genome. Nature doi: 10.1038/nature14183 (26 January 2015
42. Daigaku, Y., et al. A global profile of replicative polymerase usage. Nat. Struct. Mol. Biol. (in the press
43. Clark, A.B., et al. Functional analysis of human MutSa and MutSβ complexes in yeast. Nucleic Acids Res. 27, 736-742 (1999
44. Morrison, A., Bell, J.B., Kunkel, T.A. & Sugino, A. Eukaryotic DNA polymerase amino acid sequence required for 3' 5' exonuclease activity. Proc. Natl. Acad. Sci. USA 88, 9473-9477 (1991
45. Jin, Y.H., et al. The 3'5' exonuclease of DNA polymerase d can substitute for the 5' flap endonuclease Rad27/Fen1 in processing Okazaki fragments and preventing genome instability. Proc. Natl. Acad. Sci. USA 98, 5122-5127 (2001
46. Storici, F., Bebenek, K., Kunkel, T.A., Gordenin, D.A. & Resnick, M.A. RNA-Templated DNA repair. Nature 447, 338-341 (2007
47. Pursell, Z.F., Isoz, I., Lundstrom, E.B., Johansson, E. & Kunkel, T.A. Yeast DNA polymerase e participates in leading-strand DNA replication. Science 317, 127-130 (2007
48. Kokoska, R.J., McCulloch, d. & Kunkel, T.A. The efficiency and specificity of apurinic/apyrimidinic site bypass by human DNA polymerase and Sulfolobus solfataricus Dpo4. J. Biol. Chem. 278, 50537-50545 (2003
49. Kuchta, R.D. & Stengel, G. Mechanism and evolution of DNA primases. Biochim. Biophys. Acta 1804, 1180-1189 (2010
50. Smith, C.W.J. RNA-Protein Interactions: A Practical Approach 1st edn. (Oxford Univ. Press, New York, 1998
51. Lhomme, J., Constant, J.F. & Demeunynck, M. Abasic DNA structure, reactivity, and recognition. Biopolymers 52, 65-83 (1999
52. Bailly, V. & Verly, W.G. Possible roles of β-elimination and d-elimination reactions in the repair of DNA containing AP (apurinic/apyrimidinic) sites in mammalian cells. Biochem. J. 253, 553-559 (1988
53. Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010
54. Dale, R.K., Pedersen, B.S. & Quinlan, A.R. Pybedtools: a flexible Python library for manipulating genomic data sets and annotations. Bioinformatics 27, 3423-3424 (2011
55. Siow, C.C., Nieduszynska, S.R., Muller, C.A. & Nieduszynski, C.A. OriDB, the DNA replication origin database updated and extended. Nucleic Acids Res. 40, D682-D686 (2012
56. Zhang, Y., et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008
57. Sokal, R.R. & Rohlf, F.J. Biometry: The Principles and Practice of Statistics in Biological Research 3rd edn. (W.H. Freeman, New York, 1995