Is Rna Used As A Template Fror Dna

Nature. Author manuscript; available in PMC 2007 December 7.

Published in terminal edited course as:

PMCID: PMC2121219

NIHMSID: NIHMS33473

RNA-templated DNA repair

Francesca Storici

¹ Laboratory of Molecular Genetics, National Institute of Environmental Wellness Sciences (NIH, DHHS), Inquiry Triangle Park, N Carolina 27709, USA

Katarzyna Bebenek

¹ Laboratory of Molecular Genetics, National Plant of Environmental Wellness Sciences (NIH, DHHS), Research Triangle Park, North Carolina 27709, United states

Thomas A. Kunkel

¹ Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences (NIH, DHHS), Research Triangle Park, North Carolina 27709, USA

Dmitry A. Gordenin

¹ Laboratory of Molecular Genetics, National Establish of Environmental Health Sciences (NIH, DHHS), Research Triangle Park, Due north Carolina 27709, USA

Michael A. Resnick

¹ Laboratory of Molecular Genetics, National Found of Environmental Health Sciences (NIH, DHHS), Research Triangle Park, North Carolina 27709, USA

Abstract

RNA tin can deed every bit a template for DNA synthesis in the reverse transcription of retroviruses and retrotransposons¹ and in the elongation of telomeres². Despite its abundance in the nucleus, there has been no evidence for a direct function of RNA every bit a template in the repair of any chromosomal Deoxyribonucleic acid lesions, including Dna double-strand breaks (DSBs), which are repaired in most organisms by homologous recombination or past non-homologous terminate joiningⁱⁱⁱ. An indirect role for RNA in Deoxyribonucleic acid repair, following opposite transcription and formation of a complementary DNA, has been observed in the non-homologous joining of DSB ends^iv ^, ⁵. In the yeast Saccharomyces cerevisiae, in which homologous recombination is efficient³, RNA was shown to mediate recombination, just only indirectly through a cDNA intermediate^half-dozen ^, ^seven generated by the reverse transcriptase role of Ty retrotransposons in Ty particles in the cytoplasm⁸. Although pairing between duplex DNA and single-strand (ss)RNA can occur in vitro ⁹ ^, ¹⁰ and in vivo ¹¹, direct homologous commutation of genetic information betwixt RNA and Dna molecules has not been observed. Nosotros show here that RNA can serve as a template for DNA synthesis during repair of a chromosomal DSB in yeast. The repair was accomplished with RNA oligonucleotides complementary to the cleaved ends. This and the ascertainment that fifty-fifty yeast replicative Dna polymerases such as α and δ can copy brusk RNA template tracts in vitro demonstrate that RNA can transfer genetic information in vivo through directly homologous interaction with chromosomal DNA.

Nosotros predicted that if RNA could participate directly in the repair of a chromosomal DSB, this would require Dna synthesis on the RNA template. Such activity might be mediated by a reverse transcriptase able to function in the nucleus on the chromosome or possibly by a DNA polymerase. In RNA–protein complexes from LINE1 retrotransposons, retrotranscription tin be primed in the nucleus by the 3′ end of a chromosomal intermission¹². Even so, intermission repair using LINE1 elements does not require RNA/DNA complementarity and is, therefore, mutagenic. On the other mitt, information technology is unclear if DNA polymerases actually possess RNA-templated DNA synthesis activity in vivo, despite the ability of Escherichia coli Pol I (ref. 13), mammalian Pol γ (ref. 14), and human Deoxyribonucleic acid politician-η-ι and -κ (ref. 15) to synthesize Dna on RNA templates in vitro. Here nosotros explore the possibility that a DSB tin be repaired past homologous RNA and that chromosomal DNA synthesis can occur on RNA templates in the yeast S. cerevisiae.

We first investigated DNA synthesis across a brusque RNA tract during the repair of a chromosomal DSB, using the capacity of ssDNA oligonucleotides to serve as a template for efficient DSB repair^sixteen ^, ¹⁷. A site-specific DSB was induced within the LEU2 gene by overexpression of HO endonuclease¹⁸. Following DSB consecration, cells were transformed with ssDNA oligonucleotides that were designed (see Fig. 1) to bring together LEU2 ends and introduce a unique, in-frame 12-base insert containing 0, 4, 6 or 12 RNA bases (a, b, c and d, respectively), or a half-dozen-base insert with 0 or 6 RNA bases (e and f). To attain DSB repair and restore a functional LEU2 gene, the insert sequence must exist used equally a template. Remarkably, repair by b (containing four ribonucleotides) was simply a factor of 3 lower than repair by the DNA-only control (a). The frequencies decreased with increasing RNA-tract length (b, c, d, Fig. 1). The advent of the oligonucleotide sequence in the Leu⁺ transformants (see 'Verification' in Supplementary Table 2a) suggests that the RNA-containing molecules participate direct in the repair. This contrasts with the ascertainment that two ribonucleotides at the mating type locus of Schizosaccharomyces pombe seem to block DNA replication and lead to a site-specific DSB^xix. Withal, the reduced transformation frequency with increased size of RNA might exist due to a higher likelihood of replication arrest. If so, it is unlikely that cDNA generated by Ty reverse transcriptase of the RNA-containing oligonucleotides would be the source of DSB repair.

An external file that holds a picture, illustration, etc. Object name is nihms33473f1.jpg

Repair of a DSB by RNA-containing oligonucleotides

The diagram shows the broken LEU2 chromosomal Dna along with the oligonucleotides containing Deoxyribonucleic acid (D; blue) or RNA (R; red) sequences that were used to repair the DSB, and corresponding frequencies of LEU2 repair. The HO cutting site (124 bp) is split in two halves shown equally thicker short black lines (non to scale). Oligonucleotides are shown every bit lines with arrows at the three′ stop; nucleotide inserts are shown equally thick lines; dotted lines indicate not-homologous tails. Potential for homologous pairing is presented as brusk, thin parallel vertical lines. Numbers of nucleotides homologous to the LEU2 sequence are indicated in foursquare brackets. Insertions are indicated by 'ins::'; a comma separates DNA from RNA bases within the insertions; a hyphen separates the different parts of the oligonucleotides. Oligonucleotide sequences are given in Supplementary Tabular array 1. Presented are numbers of Leu⁺ transformants per ten⁷ viable cells resulting from targeting by 1 or 5* (side by side column) nmoles of oligonucleotides a to southward. Targeting frequencies with a pair of oligonucleotides (connected past braces) are shown in parentheses. Confidence intervals, also as results of sequence verification are provided in Supplementary Table 2a.

To exclude this possibility, that RNA-containing oligonucleotides were copied into cDNA earlier interacting with the DSB ends, we used our recent finding that a DSB can actuate strand-biased targeting by ssDNA oligonucleotides with homology to a afar site¹⁷. Because many kilobases (kb) of the five′ strand tin be degraded before repairⁱⁱⁱ, at that place is a bias for the oligonucleotide complementary to the 3′ strand. If a cDNA intermediate were formed from ssRNA-containing oligonucleotides, the observed bias should be opposite to that with the corresponding ssDNA oligonucleotides, and there would be no bias if dsDNA were formed. As shown in Fig. 2, targeting with RNA-containing oligonucleotides was biased in favour of the oligonucleotide complementary to the 3′ stop of the intermission, similar to Deoxyribonucleic acid-just oligonucleotides. No bias was detected without DSB consecration (Supplementary Tabular array iii). Transfer of the BamHello site contained in R.w and R.c (Fig. 2a) was confirmed in 28/xxx transformants. Nosotros conclude that yeast cells take the ability to use RNA embedded in DNA as a template within the chromosome.

An external file that holds a picture, illustration, etc. Object name is nihms33473f2.jpg

Strand bias of oligonucleotide targeting to sites distant from the DSB

a, System to discover oligonucleotide strand bias in yeast diploid strains. Ane copy of chromosome Vii with the TRP5 locus inactivated by a 31 bp frameshift insertion plus an I-SceI-induced DSB either 10 kb upstream or downstream¹⁷. The Trp⁺ phenotype can be restored by the oligonucleotides R.w or R.c (corresponding to the 'Watson' or 'Crick' strand in the TRP5 coding sequence), containing six central bases of RNA, or simply DNA (D.w and D.c), while the intact copy of chromosome VII, in which TRP5 is replaced by LEU2, provides a template for repair of the DSB. A restriction site created by the oligonucleotides is indicated by an asterisk b, Number of Trp⁺ transformants per x^seven viable cells resulting from targeting 1 nmole of R.west, R.c, D.westward or D.c following DSB induction. Presented are mean + s.d. from half dozen independent experiments.

Nosotros then examined repair by RNA-only molecules that were homologous to both sides of a DSB. Equally shown in Fig. i, the Leu⁺ transformation frequency with five nmoles of oligonucleotides h or i reached 5 × 10⁻⁷, and restoration of LEU2 sequence was precise (in 26/27 clones tested). In the absence of oligonucleotides, the frequency of Leu⁺ colonies was ~1 × ten^−eight and in all tested isolates (xvi/16) the Leu⁺ phenotype was due to imprecise non-homologous finish joining causing small insertions or deletions (Supplementary Table 2a). Thus, ssRNA oligonucleotides are estimated to increase the precise repair of a DSB in LEU2 by over 500-fold. Similar RNA oligonucleotides containing two-base substitutions in the centre (k and l) gave comparable Leu⁺ transformation frequencies (Fig. 1). The mutations were precisely transferred (Supplementary Table 2a), indicating DNA synthesis beyond the RNA templates.

Several oligonucleotides were used to better understand DSB repair by RNA. The minimum size for repair by RNA-merely molecules was greater than 45 bases (grand.45 and fifty.45 in Supplementary Tabular array 2a). The repair was enhanced past the presence of Dna at one end of the RNA oligonucleotides, regardless of whether the DNA was homologous (one thousand, n, o and p) or non-homologous (r and s) to the DSB ends. Repair frequencies by oligonucleotides that required DNA synthesis through long RNA tracts were much lower than those of corresponding oligonucleotides requiring less synthesis on RNA (Fig. 1, compare northward with p; likewise compare b, c, d and f). RNA oligonucleotides containing DNA homologous to a DSB end at their 5′ (m) or 3′ terminate (n) were over 100 and 1,000-fold more efficient, respectively, than the RNA-only molecules (Fig. ane). 1 possible explanation is that rather than simply enhancing annealing, the homologous Dna tin provide a Deoxyribonucleic acid duplex region close to the 3′ end of the pause that could facilitate polymerase binding (compare north with m and with o). Information technology is also possible that the DNA end could prevent cease-degradation, specially from the 3′ end (compare m with n, and o with r and s) (Fig. 1). In understanding with the protection idea, the presence of a 20-base non-homologous DNA tail at the 3′ finish of an oligonucleotide containing 60 nucleotides of homologous RNA (r and s), but non a iii-nucleotide tail (r3), increased repair past a factor of 100 when compared with the RNA-only oligonucleotides (k and 50) containing an fifty-fifty longer RNA stretch of homology (Fig. 1 and Supplementary Table 2a). The transformation differences associated with the longer DNA tail could be due to protection from 3′ → five′ exoRNases, which have a major role in RNA surveillance²⁰. Deletion of the non-essential three′ → 5′ exoRNase RRP6 did not increase transformation with an RNA-only oligonucleotide (thou) (Supplementary Tabular array 4). All the same, because most 3′ → five′ exoRNases are coded by essential genes in yeast, further genetic studies are required to examine the potential involvement of these enzymes. Considering RNA-templated repair must involve RNA–Deoxyribonucleic acid duplex intermediates, we also examined the possible function of RNases H1 (RNH1) and H2 (RNH35), which can efficiently degrade messenger RNA paired with DNA^eleven. There was no increase in RNA oligonucleotide-mediated repair for the single or the double mutants (Supplementary Table 4).

Targeting of RNA oligonucleotides was stimulated by the DSB by at least 100-fold (compare n or r added to cells in galactose medium to induce the HO-endonculease versus no galactose, Supplementary Tables 2a and b) and occurred independently from the strand invasion part of Rad51 (Supplementary Table 4). The targeting was as well independent of chromosomal locus considering a DSB induced inside TRP5 was too precisely repaired by RNA oligonucleotides (T2 and T4 in Supplementary Table 2c).

Except for telomerase genes, the but genes in yeast known to lawmaking for reverse transcriptases are those contained in Ty elements. Deletion of the SPT3 factor, which is essential for transposition and transcription of Ty1 and Ty2 elements^iv ^, ²¹, did not touch RNA-templated repair (Supplementary Tabular array 5). Nosotros conclude that Ty reverse transcription has at most a pocket-sized function in DSB repair events mediated past a homologous RNA template. Deletion of telomerase genes EST2 or EST1 (ref. 22) also did not affect transformation by the RNA-containing oligonucleotides (Supplementary Table five). This contrasts with the potent stimulation of Ty cDNA synthesis and transposition in an est2-nix mutant⁸.

It is also possible that Deoxyribonucleic acid synthesis during RNA-templated repair is accomplished past DNA polymerases. However, deletion of individual nonessential yeast DNA polymerase genes (POL4, REV1, REV3, RAD30 or MIP1)²³, equally well as double and triple deletion mutants of translesion Dna polymerase REV1, REV3 and RAD30 genes, did not alter transformation by RNA-containing oligonucleotides (Supplementary Tabular array 5). We conclude that the power to synthesize Deoxyribonucleic acid on an RNA tract during repair could be a redundant office amid polymerases and/or a function of i or more essential replicative Dna polymerases.

Nosotros therefore examined the power of yeast Dna polymerases α and δ to copy templates with sequences respective to oligonucleotides a and b containing 0 or 4 RNA bases (Fig. 3a and Supplementary Table one). Both polymerases copied all 4 ribonucleotides and generated full-length products (Fig. 3b; compare lanes eight and 9, and 14 and 15). Synthesis by Pol α, merely not past Pol δ (non shown), was stimulated past Mn²⁺ (Fig. 3b, lanes 2–3 versus 8–nine). These polymerases as well partially copied a template (Iv) in which the RNA tract starts at the beginning single-strand template position (Fig. 3b, lanes 11 and 17). Greater extension occurred when synthesis started from a Deoxyribonucleic acid tract (for example, substrate Iii, lanes x and 16, and substrate Two containing a iv ribonucleotide tract (R 4), lanes 9 and 15). Although non tested, the Deoxyribonucleic acid polymerase co-gene proliferating cell nuclear antigen might enhance synthesis farther, considering PCNA enhances Pol δ processivity when copying DNA. On an RNA-simply template (V), Pol α incorporated up to 12 bases in the presence of Mn²⁺ (lane vi), and both polymerases added a nucleotide with or without the presence of a downstream oligonucleotide (Dw), which created a gap, if Mg²⁺ was present (Fig. 3b, lanes 12 and 18, and Fig. 3c). When the efficiency of copying the iv-nucleotide template tract was determined (as described in Section 3.ane in ref. 24), Pol δ extended 80% of the products beyond R four and 76% of the products beyond the equivalent D 4 tract. Thus, the RNA tract was copied by Politico δ every bit efficiently as the corresponding DNA tract. Interestingly, in one case the R4 tract was copied by Pol δ, further elongation was impeded past the presence of the RNA–DNA duplex upstream of the Pol δ active site (for case, see band highlighted with a blackness asterisk in Fig. 3b, lane 15). Pol α too copied the R4 tract, simply less efficiently (27% of products beyond R4 compared with 92% of products beyond D4). Moreover, Politico α required 20-fold more than binding–synthesis-dissociation cycles (adamant as described²⁴) than Pol δ to completely bypass R4. Thus, Pol δ may be the more likely candidate for contrary transcriptional repair of a DSB in vivo. Information technology will be interesting to assess the effects of specific replicative DNA polymerase mutants on DSB repair past RNA-containing molecules.

An external file that holds a picture, illustration, etc. Object name is nihms33473f3.jpg

Synthesis by Pol α and Pol δ across RNA templates

a, Substrates consist of DNA (D; bluish) and/or RNA (R; red) and include primer P (same in all substrates). b, Lanes 1, vii, xiii, template I, no enzyme; lanes ii–half-dozen and viii–12, Pol α products; lanes 14–18, Pol δ products. Reactions use templates: I in lanes 2, eight, 14; 2 in lanes three, ix, 15; Iii in lanes 4, 10 and 16; IV in lanes 5, 11, and 17; and Five in lanes 6, 12, and eighteen. Red asterisks, ribonucleotide positions in template II and first ribonucleotide position in templates Iii and Four. Red arrows, RNA tracts in templates III, IV and V. The black asterisk in lane fifteen marks where Political leader δ was impeded when the RNA–DNA duplex is upstream of the polymerase active site. c, Synthesis on a gapped substrate. Lane ane, template with no enzyme V; lanes 2 and 4, products with template V and indicated enzyme; lanes 3 and 5, products with gapped substrate (V-Dw). Extension of the primer by one nucleotide is shown as +one.

The finding of in vivo and in vitro DNA synthesis on RNA-containing oligonucleotides is relevant to situations where RNA might appear inside DNA in vivo, as shown for the mammalian mitochondrial genome²⁵. The inclusion of RNA bases could occur during normal Deoxyribonucleic acid metabolic reactions, equally indicated by the power of several Deoxyribonucleic acid polymerases to incorporate ribonucleotides in vitro ²⁵ ^, ²⁶ and the power of DNA ligase I to ligate RNA bases into DNA during Okazaki fragment maturation in vitro ²⁷.

The RNA-templated DSB repair presented here is clearly distinct from previously described RNA/cDNA-mediated DSB repair processes^four ^– ⁷ ^, ¹². Nosotros evidence that at that place is no barrier to the direct transfer of data from RNA templates to chromosomal Dna. On the basis of this newly discovered RNA adequacy, we propose that endogenous RNA could have a direct function in repairing lesions during or after transcription, especially given its high local concentration. Our results set the stage for understanding how directly, homology-driven transfer of endogenous RNA information to Dna may occur.

The power of RNA to transfer genetic information to homologous chromosomal DNA could atomic number 82 to new directions in gene targeting, given that RNA can be amplified at will inside cells. Moreover, RNA every bit a homologous template in DNA repair may contribute to both genome integrity and development.

METHODS

DSB induction and targeting with oligonucleotides

The RNA-containing oligonucleotides and the DNA oligonucleotides used to repair the HO or the I-SceI induced DSB, or to target a sequence distant from an induced I-SceI interruption, are described in Supplementary Table ane. DSB induction (Supplementary Methods) and targeting with oligonucleotides (1 or 5 nmoles), using a lithium acetate transformation protocol, were done equally previously described¹⁶ ^, ¹⁷ ^, ²⁸, with the only difference being that cells to exist transformed with RNA-containing oligonucleotides were done five times with RNase-free water to dilute potential traces of RNases. All solutions and equipment used for the transformation were RNase complimentary. Cells from each oligonucleotide transformation were plated to either selective Leu⁻ or Trp⁻ media and to synthetic complete media to determine culture viability. We excluded the possibility that DNA contamination in our RNA-containing oligonucleotides was responsible for the transfer of genetic information (Supplementary Fig. 1). Details about yeast strains are presented in the Supplementary Methods section and genetic standard methods are as described¹⁶ ^, ²⁸.

DNA synthesis reactions

Reactions (20 μl) with 5 nM S. cerevisiae Politician α (catalytic subunit), purified as described²⁹, contained twenty mM Tris-HCl (pH8), 10 mM MgCl₂ or 0.5 mM MnCl₂, two mM DTT, 0.2 mg ml⁻¹ BSA, 50 nM dNTPs and 200 nM oligonucleotide substrates prepared as described in Supplementary Table 1. Reactions with the iii-subunit South. cerevisiae Pol δ (gift from P. Thousand. J. Burgers) were the same except for the utilise of twoscore mM Tris (pH viii), v mM MgCl₂, 0.1 mg ml^−ane BSA and 75 mM NaCl. Subsequently a vi min incubation at xxx °C, reaction mixtures were quenched by calculation 20 μl of 99% formamide, five mM EDTA, 0.1% xylene cyanole, 0.1% bromophenol blueish, resolved past electrophoresis in a 12% denaturing polyacrylamide gel and visualized using a Molecular Dynamics PhosphorImager.

Supplementary Material

supplement

Supplementary Information is linked to the online version of the paper at world wide web.nature.com/nature.

Acknowledgments

We thank J. E. Haber for yeast strain YFP17 and P. Thou. J. Burgers for yeast Deoxyribonucleic acid polymerase δ. We thank C. Halweg and Due west. C. Copeland for suggestions; K. L. Adelman, J. Westward. Drake and A. Sugino for critical reading of the manuscript; and J. R. Snipe and G. K. Chan for technical assistance. Inquiry back up was from National Institute of Ecology Wellness Sciences (NIH) intramural research funds.

Footnotes

Author Data Reprints and permissions data is available at www.nature.com/reprints. The authors declare no competing financial interests.

References

1. Baltimore D. Retroviruses and retrotransposons: the role of reverse transcription in shaping the eukaryotic genome. Jail cell. 1985;40:481–482. [PubMed] [Google Scholar]

two. Autexier C, Lue NF. The structure and office of telomerase reverse transcriptase. Annu Rev Biochem. 2006;75:493–517. [PubMed] [Google Scholar]

3. Paques F, Haber JE. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol Mol Biol Rev. 1999;63:349–404. [PMC costless commodity] [PubMed] [Google Scholar]

4. Teng SC, Kim B, Gabriel A. Retrotransposon reverse-transcriptase-mediated repair of chromosomal breaks. Nature. 1996;383:641–644. [PubMed] [Google Scholar]

5. Moore JK, Haber JE. Capture of retrotransposon DNA at the sites of chromosomal double-strand breaks. Nature. 1996;383:644–646. [PubMed] [Google Scholar]

vi. Derr LK, Strathern JN. A role for contrary transcripts in gene conversion. Nature. 1993;361:170–173. [PubMed] [Google Scholar]

7. Nevo-Caspi Y, Kupiec G. cDNA-mediated Ty recombination can take place in the absenteeism of plus-strand cDNA synthesis, but not in the absence of the integrase protein. Curr Genet. 1997;32:32–40. [PubMed] [Google Scholar]

8. Lesage P, Todeschini AL. Happy together: the life and times of Ty retrotransposons and their hosts. Cytogenet Genome Res. 2005;110:70–90. [PubMed] [Google Scholar]

9. Kasahara 1000, Clikeman JA, Bates DB, Kogoma T. RecA poly peptide-dependent R-loop formation in vitro. Genes Dev. 2000;14:360–365. [PMC costless article] [PubMed] [Google Scholar]

10. Zaitsev EN, Kowalczykowski SC. A novel pairing procedure promoted by Escherichia coli RecA protein: inverse Dna and RNA strand commutation. Genes Dev. 2000;14:740–749. [PMC gratis article] [PubMed] [Google Scholar]

eleven. Huertas P, Aguilera A. Cotranscriptionally formed Deoxyribonucleic acid:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol Cell. 2003;12:711–721. [PubMed] [Google Scholar]

12. Morrish TA, et al. Deoxyribonucleic acid repair mediated by endonuclease-independent LINE-1 retrotransposition. Nature Genet. 2002;31:159–165. [PubMed] [Google Scholar]

13. Ricchetti M, Buc H. E coli Dna polymerase I every bit a reverse transcriptase. EMBO J. 1993;12:387–396. [PMC free article] [PubMed] [Google Scholar]

14. Murakami Eastward, et al. Characterization of novel opposite transcriptase and other RNA-associated catalytic activities by homo Dna polymerase γ: importance in mitochondrial Dna replication. J Biol Chem. 2003;278:36403–36409. [PubMed] [Google Scholar]

fifteen. Franklin A, Milburn PJ, Blanden RV, Steele EJ. Human Dna polymerase-η, an A-T mutator in somatic hypermutation of rearranged immunoglobulin genes, is a opposite transcriptase. Immunol Cell Biol. 2004;82:219–225. [PubMed] [Google Scholar]

16. Storici F, Durham CL, Gordenin DA, Resnick MA. Chromosomal site-specific double-strand breaks are efficiently targeted for repair past oligonucleotides in yeast. Proc Natl Acad Sci The states. 2003;100:14994–14999. [PMC complimentary commodity] [PubMed] [Google Scholar]

17. Storici F, Snipe RJ, Chan GK, Gordenin DA, Resnick MA. Conservative repair of a chromosomal double-strand interruption by single-strand DNA through two steps of annealing. Mol Jail cell Biol. 2006;26:7645–7657. [PMC free article] [PubMed] [Google Scholar]

18. Paques F, Leung WY, Haber JE. Expansions and contractions in a tandem repeat induced by double-strand intermission repair. Mol Cell Biol. 1998;xviii:2045–2054. [PMC free commodity] [PubMed] [Google Scholar]

19. Vengrova S, Dalgaard JZ. The wild-type Schizosaccharomyces pombe matone imprint consists of ii ribonucleotides. EMBO Rep. 2006;seven:59–65. [PMC costless article] [PubMed] [Google Scholar]

20. Houseley J, LaCava J, Tollervey D. RNA-quality control by the exosome. Nature Rev Mol Cell Biol. 2006;seven:529–539. [PubMed] [Google Scholar]

21. Boeke JD, Styles CA, Fink One thousand. R Saccharomyces cerevisiae SPT3 gene is required for transposition and transpositional recombination of chromosomal Ty elements. Mol Prison cell Biol. 1986;vi:3575–3581. [PMC costless article] [PubMed] [Google Scholar]

22. Smogorzewska A, de Lange T. Regulation of telomerase by telomeric proteins. Annu Rev Biochem. 2004;73:177–208. [PubMed] [Google Scholar]

23. Shcherbakova PV, Kunkel TA. DNA. In: DePamphilis ML, editor. Replication in Eukaryotic Cells and its Relevance to Human being Disease. Cold Bound Harbor Laboratory Press; Common cold Jump Harbor, New York: 2006. pp. 391–410. [Google Scholar]

24. McCulloch SD, Kunkel TA. Multiple solutions to inefficient lesion bypass by T7 Deoxyribonucleic acid polymerase. DNA Repair. 2006;5:1373–1383. [PMC free article] [PubMed] [Google Scholar]

25. Yang MY, et al. Biased incorporation of ribonucleotides on the mitochondrial L-strand accounts for apparent strand-asymmetric Dna replication. Cell. 2002;111:495–505. [PubMed] [Google Scholar]

26. Nick McElhinny SA, Ramsden DA. Polymerase mu is a Deoxyribonucleic acid-directed Dna/RNA polymerase. Mol Prison cell Biol. 2003;23:2309–2315. [PMC costless article] [PubMed] [Google Scholar]

27. Rumbaugh JA, Murante RS, Shi S, Bambara RA. Creation and removal of embedded ribonucleotides in chromosomal Dna during mammalian Okazaki fragment processing. J Biol Chem. 1997;272:22591–22599. [PubMed] [Google Scholar]

28. Storici F, Resnick MA. The delitto perfetto approach to in vivo site-directed mutagenesis and chromosome rearrangements with synthetic oligonucleotides in yeast. Methods Enzymol. 2006;409:329–345. [PubMed] [Google Scholar]

29. Niimi A, et al. Palm mutants in DNA polymerases α and η alter Dna replication fidelity and translesion action. Mol Cell Biol. 2004;24:2734–2746. [PMC free article] [PubMed] [Google Scholar]