Anti-DNA-RNA Hybrid [S9.6] Antibody

Anti-DNA-RNA Hybrid [S9.6] Antibody

This mouse monoclonal antibody was generated against a ΦX174 bacteriophage-derived synthetic DNA–RNA antigen and recognizes RNA-DNA hybrids of various lengths.

Highlights:

  • Useful in the detection of R-loops
  • High specificity and affinity for DNA-RNA hybrids
  • Does NOT cross-react with single-stranded DNA or double-stranded DNA
  • Minor cross-reaction (~5-fold less) has been observed for AU-rich double-stranded RNA.
  • High affinity binding shown for hybrids of 8, 10, 15, and 23 base pairs in length

Recombinant versions available from our sister company, Absolute Antibody:

DNA-RNA hybrids are a natural occurrence within eukaryotic cells, with levels of these hybrids increasing at sites with high transcriptional activity, such as during transcription initiation, repression, and elongation. Because RNA-DNA hybrids influence genomic instability, the S9.6 antibody is a useful reagent to help study the consequences of R-loops and lesions formed by these hybrids during DNA replication or other cellular processes. In addition, the S9.6 antibody is effective in recognizing RNA-DNA hybridization for microarray studies.

From the laboratory of Stephen H. Leppla, PhD, National Institute of Allergy and Infectious Diseases/NIH.

Catalog Number Product DataSheet Size AVAILABILITY Price Qty
ENH002
Anti-DNA-RNA Hybrid [S9.6] Antibody, 1mg (10x100ug)
1mg (10x100ug) In stock
Regular Price:$3,150.00
On Sale:
ENH001
Anti-DNA-RNA Hybrid [S9.6] Antibody, 100ug
100ug In stock
Regular Price:$360.00
On Sale:
Kf-Ab01137-23.0
Recombinant Anti-[S9.6], Rabbit IgG, 100ug
100ug In stock
Regular Price:$455.00
On Sale:
Kf-Ab01137-1.6
Recombinant Anti-[S9.6], Mouse Fab fragment, His-Tagged, Kappa, 100ug
100ug In stock
Regular Price:$455.00
On Sale:
Kf-Ab01137-24.1
Recombinant Anti-[S9.6], Goat IgG, 100ug
100ug In stock
Regular Price:$455.00
On Sale:
Kf-Ab01137-2.0
Recombinant Anti-[S9.6], Mouse IgG2a, Kappa, 100ug
100ug In stock
Regular Price:$455.00
On Sale:
Specifications

Product Type: Antibody
Name: Anti-DNA-RNA Hybrid [S9.6]
Antigen: S9.6 ΦX174 bacteriophage-derived synthetic DNA–RNA antigen
Isotype: Mouse IgG2a, rabbit IgG, mouse Fab, goat IgG
Clonality: Monoclonal
Fusion Tag(s): Mouse Fab version contains His-tag
Clone Name: S9.6
Reactivity: High specificity and affinity for DNA/RNA hybrids and other A-form nucleic acid hybrids
Immunogen: ΦX174 bacteriophage-derived synthetic DNA/RNA
Species Immunized: BALB/c mouse
Paratope: DYYGSRWFDY (proposed)
Purification Method: Protein A/G
Buffer: ENHOO1: PBS, 0.05% (w/v) Sodium Azide
Ab01137- : PBS with 0.02% Proclin 300
Tested Applications:

Dot Blot Analysis: 0.2 µg/mL.
Affinity Binding Assay: Clone S9.6 bound the DNA-RNA heteropolymer and poly(I)-poly(dC) equally, but 100-fold higher levels of poly(A)-poly(dT) were required to achieve a similar degree of binding. Single-stranded DNA, double-stranded DNA and RNA, and ribosomal RNA were not bound by clone S9.6 (Boguslawski, S.J., et al. (1986). J. Immunol Methods. 89(1):123-130).
Chromatin Immunoprecipitation (ChIP) Analysis: A representative lot detected increased DNA RNA hybrids at four actively transcribed genes upon shRNA-mediated knockdown of BRCA1 or BRCA2, but not PCID2 or RAD51 in HeLa cells (Bhatia, V., et al. (2014). Nature. 511(7509):362-365).
Chromatin Immunoprecipitation (ChIP) Analysis: A representative lot detected R-loops formed over beta-actin gene using HeLa chromatin preparation. RNase H treatment of the chromatin preparation prevented clone S9.6 from immunoprecipitating target chromatin fragments (Skourti-Stathaki, K., et al. (2011). Mol. Cell. 42(6):794-805).
Chromatin Immunoprecipitation-sequencing (ChIP-seq) Analysis: A representative lot detected genome-wide distribution of DNA-RNA hybrids in budding yeast by ChIP-seq analysis (El Hage, A., et al. (2014). PLoS Genet. 10(10):e1004716).
Immunocytochemistry Analysis: Representative lots immunolocalized nuclear R loops by fluorescent immunocytochemistry staining of methanol-fixed H1 human embryonic stem cells (hESCs) and formaldehyde-fixed HeLa cells (Bhatia, V., et al. (2014). Nature. 511(7509):362-365; Ginno, P.A., et al. (2012). Mol. Cell. 45(6):814-825).
Immunoprecipitation Analysis: A representative lot immunoprecipitated in vitro transcribed R-loop substrate (DNA-RNA hybrid), but not doouble-stranded DNA (dsDNA) (Ginno, P.A., et al. (2012). Mol. Cell. 45(6):814-825).
See also: S9.6 Publications by Application
Storage: -20C (avoid repeated freeze-thaw cycles)
Shipped: Cold packs

Provider
From the laboratory of Stephen H. Leppla, PhD, National Institute of Allergy and Infectious Diseases/NIH.
References

PDF Anti-DNA-RNA Hybrid [S9.6] Antibody - Publications by Application »

  1. Phillips DD, Garboczi DN, Singh K, Hu Z, Leppla SH, Leysath CE. The sub-nanomolar binding of DNA-RNA hybrids by the single-chain Fv fragment of antibody S9.6. J Mol Recognit. 2013 Aug;26(8):376-81.
  2. Boguslawski SJ, Smith DE, Michalak MA, Mickelson KE, Yehle CO, Patterson WL, Carrico RJ. Characterization of monoclonal antibody to DNA.RNA and its application to immunodetection of hybrids. J Immunol Methods. 1986 May 1;89(1):123-30.
  3. Yehle CO, Patterson WL, Boguslawski SJ, Albarella JP, Yip KF, Carrico RJ. A solution hybridization assay for ribosomal RNA from bacteria using biotinylated DNA probes and enzyme-labeled antibody to DNA:RNA. Mol Cell Probes. 1987 Jun;1(2):177-93.
  4. Miller CA, Patterson WL, Johnson PK, Swartzell CT, Wogoman F, Albarella JP, Carrico RJ. Detection of bacteria by hybridization of rRNA with DNA-latex and immunodetection of hybrids. J Clin Microbiol. 1988 Jul;26(7):1271-6.
  5. Casebolt DB, Stephensen CB. Monoclonal antibody solution hybridization assay for detection of mouse hepatitis virus infection. J Clin Microbiol. 1992 Mar;30(3):608-12.
  6. Hu Z, Zhang A, Storz G, Gottesman S, Leppla SH. An antibody-based microarray assay for small RNA detection. Nucleic Acids Res. 2006 Apr 13;34(7):e52.
  7. Székvölgyi L, Rákosy Z, Bálint BL, Kókai E, Imre L, Vereb G, Bacsó Z, Goda K, Varga S, Balázs M, Dombrádi V, Nagy L, Szabó G. Ribonucleoprotein-masked nicks at 50-kbp intervals in the eukaryotic genomic DNA. Proc Natl Acad Sci U S A. 2007 Sep 18;104(38):14964-9.
  8. Dutrow N, Nix DA, Holt D, Milash B, Dalley B, Westbroek E, Parnell TJ, Cairns BR. Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping. Nat Genet. 2008 Aug;40(8):977-86.
  9. Pohjoismäki JL, Holmes JB, Wood SR, Yang MY, Yasukawa T, Reyes A, Bailey LJ, Cluett TJ, Goffart S, Willcox S, Rigby RE, Jackson AP, Spelbrink JN, Griffith JD, Crouch RJ, Jacobs HT, Holt IJ. Mammalian mitochondrial DNA replication intermediates are essentially duplex but contain extensive tracts of RNA/DNA hybrid. J Mol Biol. 2010 Apr 16;397(5):1144-55.
  10. El Hage A, French SL, Beyer AL, Tollervey D. Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis. Genes Dev. 2010 Jul 15;24(14):1546-58.
  11. Sípová H, Zhang S, Dudley AM, Galas D, Wang K, Homola J. Surface plasmon resonance biosensor for rapid label-free detection of microribonucleic acid at subfemtomole level. Anal Chem. 2010 Dec 15;82(24):10110-5.
  12. Skourti-Stathaki K, Proudfoot NJ, Gromak N. Human senataxin resolves RNA/DNA hybrids formed at transcriptional pause sites to promote Xrn2-dependent termination. Mol Cell. 2011 Jun 24;42(6):794-805.
  13. Ginno PA, Lott PL, Christensen HC, Korf I, Chédin F. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell. 2012 Mar 30;45(6):814-25.
  14. Tran HV, Piro B, Reisberg S, Duc HT, Pham MC. Antibodies directed to RNA/DNA hybrids: an electrochemical immunosensor for microRNAs detection using graphene-composite electrodes. Anal Chem. 2013 Sep 3;85(17):8469-74.
  15. Rigby RE, Webb LM, Mackenzie KJ, Li Y, Leitch A, Reijns MA, Lundie RJ, Revuelta A, Davidson DJ, Diebold S, Modis Y, Macdonald AS, Jackson AP. RNA:DNA hybrids are a novel molecular pattern sensed by TLR9. EMBO J. 2014 Mar 18;33(6):542-58.
  16. 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. 2014 Oct 30;10(10):e1004716.
  17. Yeo AJ, Becherel OJ, Luff JE, Cullen JK, Wongsurawat T, Jenjaroenpun P,Kuznetsov VA, McKinnon PJ, Lavin MF. R-loops in proliferating cells but not in the brain: implications for AOA2 and other autosomal recessive ataxias. PLoS One. 2014 Mar 17;9(3):e90219. View Article
  18. Bhatia V, Barroso SI, García-Rubio ML, Tumini E, Herrera-Moyano E, Aguilera A. BRCA2 prevents R-loop accumulation and associates with TREX-2 mRNA export factor PCID2. Nature. 2014 Jul 17;511(7509):362-5.
  19. Koo CX, Kobiyama K, Shen YJ, LeBert N, Ahmad S, Khatoo M, Aoshi T, Gasser S, Ishii KJ. RNA polymerase III regulates cytosolic RNA:DNA hybrids and intracellular microRNA expression. J Biol Chem. 2015 Mar 20;290(12):7463-73. doi: 10.1074/jbc.M115.636365. Epub 2015 Jan 26.
  20. Jenjaroenpun P, Wongsurawat T, Yenamandra SP, Kuznetsov VA. QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences. Nucleic Acids Res. 2015 Nov 16;43(20):10081. View Article
  21. Aronica L, Kasparek T, Ruchman D, Marquez Y, Cipak L, Cipakova I, Anrather D, Mikolaskova B, Radtke M, Sarkar S, Pai CC, Blaikley E, Walker C, Shen KF, Schroeder R, Barta A, Forsburg SL, Humphrey TC. The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast. Nucleic Acids Res. 2015 Dec 17. pii: gkv1473. View Article
  22. Bersani F, Lee E, Kharchenko PV, Xu AW, Liu M, Xega K, MacKenzie OC, Brannigan BW, Wittner BS, Jung H, Ramaswamy S, Park PJ, Maheswaran S, Ting DT, Haber DA. Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer. Proc Natl Acad Sci U S A. 2015 Dec 8;112(49):15148-53. doi: 10.1073/pnas.1518008112. Epub 2015 Nov 2. PubMed PMID: 26575630; PubMed Central PMCID: PMC4679016. View Article
  23. Chen PB, Chen HV, Acharya D, Rando OJ, Fazzio TG. R loops regulate promoter-proximal chromatin architecture and cellular differentiation. Nat Struct Mol Biol. 2015 Dec;22(12):999-1007. View Article
  24. Starokadomskyy P, Gemelli T, Rios JJ, Xing C, Wang RC, Li H, Pokatayev V, Dozmorov I, Khan S, Miyata N, Fraile G, Raj P, Xu Z, Xu Z, Ma L, Lin Z, Wang H, Yang Y, Ben-Amitai D, Orenstein N, Mussaffi H, Baselga E, Tadini G, Grunebaum E, Sarajlija A, Krzewski K, Wakeland EK, Yan N, de la Morena MT, Zinn AR, Burstein E. DNA polymerase-α regulates the activation of type I interferons through cytosolic RNA:DNA synthesis. Nat Immunol. 2016 May;17(5):495-504. doi: 10.1038/ni.3409. PubMed PMID: 27019227; PubMed Central PMCID: PMC4836962. View Article
  25. Krishnan S, Petchiappan A, Singh A, Bhatt A, Chatterji D. R-loop induced stress response by second (p)ppGpp synthetase in Mycobacterium smegmatis: functional and domain interdependence. Mol Microbiol. 2016 Oct;102(1):168-82. doi: 10.1111/mmi.13453. PubMed PMID: 27349932. View Article
  26. Wiedemann EM, Peycheva M, Pavri R. DNA Replication Origins in Immunoglobulin Switch Regions Regulate Class Switch Recombination in an R-Loop-Dependent Manner. Cell Rep. 2016 Dec 13;17(11):2927-2942. View Article
  27. Torrente-Rodríguez RM, Ruiz-Valdepeñas Montiel V, Campuzano S, Farchado-Dinia M, Barderas R, San Segundo-Acosta P, Montoya JJ, Pingarron JM. Fast Electrochemical miRNAs Determination in Cancer Cells and Tumor Tissues with Antibody-Functionalized Magnetic Microcarriers. ACS Sensors. 2016 Jun 10;1(7):896-903. View Article
  28. Abraham KJ, Chan JN, Salvi JS, Ho B, Hall A, Vidya E, Guo R, Killackey SA, LiuN, Lee JE, Brown GW, Mekhail K. Intersection of calorie restriction and magnesiumin the suppression of genome-destabilizing RNA-DNA hybrids. Nucleic Acids Res.2016 Aug 29. pii: gkw752. View Article
  29. Lima WF, Murray HM, Damle SS, Hart CE, Hung G, De Hoyos CL, Liang XH, Crooke ST. Viable RNaseH1 knockout mice show RNaseH1 is essential for R loop processing, mitochondrial and liver function. Nucleic Acids Res. 2016 Apr 29. View Article
  30. Starokadomskyy P, Gemelli T, Rios JJ, Xing C, Wang RC, Li H, Pokatayev V, Dozmorov I, Khan S, Miyata N, Fraile G, Raj P, Xu Z, Xu Z, Ma L, Lin Z, Wang H, Yang Y, Ben-Amitai D, Orenstein N, Mussaffi H, Baselga E, Tadini G, Grunebaum E, Sarajlija A, Krzewski K, Wakeland EK, Yan N, de la Morena MT, Zinn AR, Burstein E. DNA polymerase-? regulates the activation of type I interferons throughcytosolic RNA:DNA synthesis. Nat Immunol. 2016 Mar 28. View Article
  31. Li L, Matsui M, Corey DR. Activating frataxin expression by repeat-targeted nucleic acids. Nat Commun. 2016 Feb 4;7:10606. doi: 10.1038/ncomms 10606. View Article
  32. Zhang R, Wu J, Ferrandon S, Glowacki KJ, Houghton JA. Targeting GLI by GANT61 involves mechanisms dependent on inhibition of both transcription and DNA licensing. Oncotarget. 2016 Dec 6;7(49):80190-80207. View Article
  33. Molès JP, Griez A, Guilhou JJ, Girard C, Nagot N, Van de Perre P, Dujols P. Cytosolic RNA:DNA Duplexes Generated by Endogenous Reverse Transcriptase Activity as Autonomous Inducers of Skin Inflammation in Psoriasis. PLoS One. 2017 Jan 17;12(1):e0169879. doi: 10.1371/journal.pone.0169879. PubMed PMID: 28095445; PubMed Central PMCID: PMC5240966. View Article
  34. Jangi M, Fleet C, Cullen P, Gupta SV, Mekhoubad S, Chiao E, Allaire N, Bennett CF, Rigo F, Krainer AR, Hurt JA, Carulli JP, Staropoli JF. SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage. Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):E2347-E2356. doi: 10.1073/pnas.1613181114. PubMed PMID: 28270613. View Article
  35. Lim J, Giri PK, Kazadi D, Laffleur B, Zhang W, Grinstein V, Pefanis E, Brown LM, Ladewig E, Martin O, Chen Y, Rabadan R, Boyer F, Rothschild G, Cogné M, Pinaud E, Deng H, Basu U. Nuclear Proximity of Mtr4 to RNA Exosome Restricts DNA Mutational Asymmetry. Cell. 2017 Apr 20;169(3):523-537.e15. View Article
  36. Chang EY, Novoa CA, Aristizabal MJ, Coulombe Y, Segovia R, Chaturvedi R, Shen Y, Keong C, Tam AS, Jones SJM, Masson JY, Kobor MS, Stirling PC. RECQ-like helicases Sgs1 and BLM regulate R-loop-associated genome instability. J Cell Biol. 2017 Dec 4;216(12):3991-4005. View Article
  37. Sagie S, Toubiana S, Hartono SR, Katzir H, Tzur-Gilat A, Havazelet S, Francastel C, Velasco G, Chédin F, Selig S. Telomeres in ICF syndrome cells are vulnerable to DNA damage due to elevated DNA:RNA hybrids. Nat Commun. 2017 Jan 24;8:14015. doi: 10.1038/ncomms14015. PubMed PMID: 28117327; PubMed Central PMCID: PMC5286223. View Article
  38. Sridhara SC, Carvalho S, Grosso AR, Gallego-Paez LM, Carmo-Fonseca M, de Almeida SF. Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation. Cell Rep. 2017 Jan 10;18(2):334-343. doi: 10.1016/j.celrep.2016.12.050. PubMed PMID: 28076779. View Article
  39. Min J, Wright WE, Shay JW. Alternative Lengthening of Telomeres Mediated by Mitotic DNA Synthesis Engages Break-Induced Replication Processes. Mol Cell Biol. 2017 Sep 26;37(20). pii: e00226-17. View Article
  40. Jiang YF, Lin SS, Chen JM, Tsai HZ, Hsieh TS, Fu CY. Electron tomographic analysis reveals ultrastructural features of mitochondrial cristae architecture which reflect energetic state and aging. Sci Rep. 2017 Mar 30;7:45474. View Article
  41. Chen L, Chen JY, Zhang X, Gu Y, Xiao R, Shao C, Tang P, Qian H, Luo D, Li H, Zhou Y, Zhang DE, Fu XD. R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters. Mol Cell. 2017 Nov 16;68(4):745-757.e5. View Article
  42. Carolina A Novoa, Emily Yun-Chia Chang, Maria J Aristizabal, Yan Coulombe, Romulo Segovia, Yaoqing Shen, Christelle Keong, Steven JM Jones, Jean-Yves Masson, Michael S Kobor, Peter C Stirling. Conserved roles of RECQ-like helicases Sgs1 and BLM in preventing R-loop induced genome instability. bioRxiv. doi: https://doi.org/10.1101/119677. View Article
  43. Shafiq S, Chen C, Yang J, Cheng L, Ma F, Widemann E, Sun Q. DNA Topoisomerase 1 prevents R-loop accumulation to modulate auxin-regulated root development in rice. Mol Plant. 2017 Apr 12. pii: S1674-2052(17)30102-8. doi: 10.1016/j.molp.2017.04.001. [Epub ahead of print] PubMed PMID: 28412545. View Article
  44. Esanov R, Cabrera GT, Andrade NS, Gendron TF, Brown RH Jr, Benatar M, Wahlestedt C, Mueller C, Zeier Z. A C9ORF72 BAC mouse model recapitulates key epigenetic perturbations of ALS/FTD. Mol Neurodegener. 2017 Jun 12;12(1):46. doi: 10.1186/s13024-017-0185-9. PubMed PMID: 28606110. View Article
  45. Brönner C, Salvi L, Zocco M, Ugolini I, Halic M. Accumulation of RNA on chromatin disrupts heterochromatic silencing. Genome Res. 2017 Jul;27(7):1174-1183. View Article
  46. Bonnet A, Grosso AR, Elkaoutari A, Coleno E, Presle A, Sridhara SC, Janbon G, Géli V, de Almeida SF, Palancade B. Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability. Mol Cell. 2017 Aug 17;67(4):608-621.e6. View Article
  47. Velazquez Camacho O, Galan C, Swist-Rosowska K, Ching R, Gamalinda M, Karabiber F, De La Rosa-Velazquez I, Engist B, Koschorz B, Shukeir N, Onishi-Seebacher M, van de Nobelen S, Jenuwein T. Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation. Elife. 2017 Aug 1;6. pii: e25293. View Article
  48. Su XA, Freudenreich CH. Cytosine deamination and base excision repair cause R-loop-induced CAG repeat fragility and instability in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2017 Sep 18. pii: 201711283. View Article
  49. Lang KS, Hall AN, Merrikh CN, Ragheb M, Tabakh H, Pollock AJ, Woodward JJ, Dreifus JE, Merrikh H. Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis. Cell. 2017 Aug 10;170(4):787-799.e18. View Article
  50. Walker C, Herranz-Martin S, Karyka E, Liao C, Lewis K, Elsayed W, Lukashchuk V, Chiang SC, Ray S, Mulcahy PJ, Jurga M, Tsagakis I, Iannitti T, Chandran J, Coldicott I, De Vos KJ, Hassan MK, Higginbottom A, Shaw PJ, Hautbergue GM, Azzouz M, El-Khamisy SF. C9orf72 expansion disrupts ATM-mediated chromosomal break repair. Nat Neurosci. 2017 Sep;20(9):1225-1235. View Article
  51. Jones SE, Fleuren EDG, Frankum J, Konde A, Williamson CT, Krastev DB, Pemberton HN, Campbell J, Gulati A, Elliott R, Menon M, Selfe JL, Brough R, Pettitt SJ, Niedzwiedz W, van der Graaf WTA, Shipley J, Ashworth A, Lord CJ. ATR is a therapeutic target in synovial sarcoma. Cancer Res. 2017 Oct 16. pii: canres.2056.2017. View Article
  52. Dumelie JG, Jaffrey SR. Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq. Elife. 2017 Oct 26;6. pii:e28306. View Article
  53. Qian Z, Zhurkin VB, Adhya S. DNA-RNA interactions are critical for chromosome condensation in Escherichia coli. Proc Natl Acad Sci U S A. 2017 Oct 30. pii: 201711285. View Article
  54. Vargas E, Torrente-Rodríguez RM, Ruiz-Valdepeñas Montiel V, Povedano E, Pedrero M, Montoya JJ, Campuzano S, Pingarrón JM. Magnetic Beads-Based Sensor with Tailored Sensitivity for Rapid and Single-Step Amperometric Determination of miRNAs. Int J Mol Sci. 2017 Nov 9;18(11). pii: E2151. View Article
  55. Watanabe T, Marotta M, Suzuki R, Diede SJ, Tapscott SJ, Niida A, Chen X, Mouakkad L, Kondratova A, Giuliano AE, Orsulic S, Tanaka H. Impediment of Replication Forks by Long Non-coding RNA Provokes Chromosomal Rearrangements by Error-Prone Restart. Cell Rep. 2017 Nov 21;21(8):2223-2235. View Article
  56. Choi J, Hwang SY, Ahn K. Interplay between RNASEH2 and MOV10 controls LINE-1 retrotransposition. Nucleic Acids Res. 2018 Jan 5. View Article
  57. Komseli ES, Pateras IS, Krejsgaard T, Stawiski K, Rizou SV, Polyzos A, Roumelioti FM, Chiourea M, Mourkioti I, Paparouna E, Zampetidis CP, Gumeni S, Trougakos IP, Pefani DE, O'Neill E, Gagos S, Eliopoulos AG, Fendler W, Chowdhury D, Bartek J, Gorgoulis VG. A prototypical non-malignant epithelial model to study genome dynamics and concurrently monitor micro-RNAs and proteins in situ during oncogene-induced senescence. BMC Genomics. 2018 Jan 10;19(1):37. View Article
  58. Iijima K, Kobayashi J, Ishizaka Y. Structural alteration of DNA induced by viral protein R of HIV-1 triggers the DNA damage response. Retrovirology. 2018 Jan 16;15(1):8. View Article
  59. Okamoto Y, Iwasaki WM, Kugou K, Takahashi KK, Oda A, Sato K, Kobayashi W, Kawai H, Sakasai R, Takaori-Kondo A, Yamamoto T, Kanemaki MT, Taoka M, Isobe T, Kurumizaka H, Innan H, Ohta K, Ishiai M, Takata M. Replication stress induces accumulation of FANCD2 at central region of large fragile genes. Nucleic Acids Res. 2018 Jan 31. View Article
  60. Lu WT, Hawley BR, Skalka GL, Baldock RA, Smith EM, Bader AS, Malewicz M, Watts FZ, Wilczynska A, Bushell M. Drosha drives the formation of DNA:RNA hybrids around DNA break sites to facilitate DNA repair. Nat Commun. 2018 Feb 7;9(1):532. View Article
  61. Raghunathan N, Kapshikar RM, Leela JK, Mallikarjun J, Bouloc P, Gowrishankar J. Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli. Nucleic Acids Res. 2018 Feb 21. View Article
  62. Brustel J, Kozik Z, Gromak N, Savic V, Sweet SMM. Large XPF-dependent deletions following misrepair of a DNA double strand break are prevented by the RNA:DNA helicase Senataxin. Sci Rep. 2018 Mar 1;8(1):3850. View Article
  63. Chen L, Chen JY, Huang YJ, Gu Y, Qiu J, Qian H, Shao C, Zhang X, Hu J, Li H, He S, Zhou Y, Abdel-Wahab O, Zhang DE, Fu XD. The Augmented R-Loop Is a Unifying Mechanism for Myelodysplastic Syndromes Induced by High-Risk Splicing Factor Mutations. Mol Cell. 2018 Feb 1;69(3):412-425.e6. View Article
  64. Postberg J, Jönsson F, Weil PP, Bulic A, Juranek SA, Lipps HJ. 27nt-RNAs guide histone variant deposition via 'RNA-induced DNA replication interference' and thus transmit parental genome partitioning in Stylonychia. Epigenetics Chromatin. 2018 Jun 12;11(1):31. View Article
  65. Andrews AM, McCartney HJ, Errington TM, D'Andrea AD, Macara IG. A senataxin-associated exonuclease SAN1 is required for resistance to DNA interstrand cross-links. Nat Commun. 2018 Jul 3;9(1):2592. View Article
  66. Kannan A, Bhatia K, Branzei D, Gangwani L. Combined deficiency of Senataxin and DNA-PKcs causes DNA damage accumulation and neurodegeneration in spinal muscular atrophy. Nucleic Acids Res. 2018 Jul 16. View Article
  67. Chen Y, Li J, Cao F, Lam J, Cheng CCY, Yu CH, Huen MSY. Nucleolar residence of the seckel syndrome protein TRAIP is coupled to ribosomal DNA transcription. Nucleic Acids Res. 2018 Aug 27. View Article
  68. Majerska J, Feretzaki M, Glousker G, Lingner J. Transformation-induced stress at telomeres is counteracted through changes in the telomeric proteome including SAMHD1. Life Sci Alliance. 2018 Jul 17;1(4):e201800121. View Article
  69. Teng Y, Yadav T, Duan M, Tan J, Xiang Y, Gao B, Xu J, Liang Z, Liu Y, Nakajima S, Shi Y, Levine AS, Zou L, Lan L. ROS-induced R loops trigger a transcription-coupled but BRCA1/2-independent homologous recombination pathway through CSB. Nat Commun. 2018 Oct 8;9(1):4115. View Article
  70. Chakraborty P, Huang JTJ, Hiom K. DHX9 helicase promotes R-loop formation in cells with impaired RNA splicing. Nat Commun. 2018 Oct 19;9(1):4346.View Article
  71. Abu Diab M, Mor-Shaked H, Cohen E, Cohen-Hadad Y, Ram O, Epsztejn-Litman S, Eiges R. The G-rich Repeats in FMR1 and C9orf72 Loci Are Hotspots for Local Unpairing of DNA. Genetics. 2018 Nov 5. pii: genetics.301672.2018. View Article
  72. Ostrowski LA, Hall AC, Szafranski KJ, Oshidari R, Abraham KJ, Chan JNY, Krustev C, Zhang K, Wang A, Liu Y, Guo R, Mekhail K. Conserved Pbp1/Ataxin-2 regulates retrotransposon activity and connects polyglutamine expansion-driven protein aggregation to lifespan-controlling rDNA repeats. Commun Biol. 2018 Nov 5;1:187.View Article
  73. Landsverk HB, Sandquist LE, Sridhara SC, Rødland GE, Sabino JC, de Almeida SF, Grallert B, Trinkle-Mulcahy L, Syljuåsen RG. Regulation of ATR activity via the RNA polymerase II associated factors CDC73 and PNUTS-PP1. Nucleic Acids Res. 2018 Dec 12. View Article
  74. Bhatia V, Valdés-Sánchez L, Rodriguez-Martinez D, Bhattacharya SS. Formation of 53BP1 foci and ATM activation under oxidative stress is facilitated by RNA:DNA hybrids and loss of ATM-53BP1 expression promotes photoreceptor cell survival in mice. F1000Res. 2018 Aug 10;7:1233. View Article
  75. Briggs E, Crouch K, Lemgruber L, Lapsley C, McCulloch R. Ribonuclease H1-targeted R-loops in surface antigen gene expression sites can direct trypanosome immune evasion. PLoS Genet. 2018 Dec 13. View Article
  76. Okamoto Y, Abe M, Itaya A, Tomida J, Ishiai M, Takaori-Kondo A, Taoka M, Isobe T, Takata M. FANCD2 protects genome stability by recruiting RNA processing enzymes to resolve R-loops during mild replication stress. FEBS J. 2018 Nov 15. View Article
  77. Kuznetsov VA, Bondarenko V, Wongsurawat T, Yenamandra SP, Jenjaroenpun P. Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers. Nucleic Acids Res. 2018 Sep 6;46(15):8023. View Article
  78. Teloni F, Michelena J, Lezaja A, Kilic S, Ambrosi C, Menon S, Dobrovolna J, Imhof R, Janscak P, Baubec T, Altmeyer M. Efficient Pre-mRNA Cleavage Prevents Replication-Stress-Associated Genome Instability. Mol Cell. 2018 Dec 24. View Article
  79. Liang Z, Liang F, Teng Y, Chen X, Liu J, Longerich S, Rao T, Green AM, Collins NB, Xiong Y, Lan L, Sung P, Kupfer GM. Binding of FANCI-FANCD2 Complex to RNA and R-Loops Stimulates Robust FANCD2 Monoubiquitination. Cell Rep. 2019 Jan 15. View Article
  80. Marabitti V, Lillo G, Malacaria E, Palermo V, Sanchez M, Pichierri P, Franchitto A. ATM pathway activation limits R-loop-associated genomic instability in Werner syndrome cells. Nucleic Acids Res. 2019 Apr 23;47(7):3485-3502. View Article
  81. Burger K, Schlackow M, Gullerova M. Tyrosine kinase c-Abl couples RNA polymerase II transcription to DNA double-strand breaks. Nucleic Acids Res. 2019 Jan 22. View Article
  82. Milbury KL, Paul B, Lari A, Fowler C, Montpetit B, Stirling PC. Exonuclease domain mutants of yeast DIS3 display genome instability. Nucleus. 2019 Dec;10(1):21-32. View Article
  83. Alfano L, Caporaso A, Altieri A, Dell'Aquila M, Landi C, Bini L, Pentimalli F, Giordano A. Depletion of the RNA binding protein HNRNPD impairs homologous recombination by inhibiting DNA-end resection and inducing R-loop accumulation. Nucleic Acids Res. 2019 Feb 25. pii: gkz076. View Article
  84. Martinez-Macias MI, Moore DA, Green RL, Gomez-Herreros F, Naumann M, Hermann A, Van Damme P, Hafezparast M, Caldecott KW. FUS (fused in sarcoma) is a component of the cellular response to topoisomerase I-induced DNA breakage and transcriptional stress. Life Sci Alliance. 2019 Feb 26;2(2). pii: e201800222. View Article
  85. Baiersdörfer M, Boros G, Muramatsu H, Mahiny A, Vlatkovic I, Sahin U, Karikó K. A Facile Method for the Removal of dsRNA Contaminant from In Vitro-Transcribed mRNA. Mol Ther Nucleic Acids. 2019 Apr 15;15:26-35. View Article
  86. De Cecco M, Ito T, Petrashen AP, Elias AE, Skvir NJ, Criscione SW, Caligiana A, Brocculi G, Adney EM, Boeke JD, Le O, Beauséjour C, Ambati J, Ambati K, Simon M, Seluanov A, Gorbunova V, Slagboom PE, Helfand SL, Neretti N, Sedivy JM. L1 drives IFN in senescent cells and promotes age-associated inflammation. Nature. 2019 Feb;566(7742):73-78. View Article
  87. Pezone A, Zuchegna C, Tramontano A, Romano A, Russo G, de Rosa M, Vinciguerra M, Porcellini A, Gottesman ME, Avvedimento EV. RNA Stabilizes Transcription-Dependent Chromatin Loops Induced By Nuclear Hormones. Sci Rep. 2019 Mar 8;9(1):3925. View Article
  88. Pérez Di Giorgio JA, Lepage É, Tremblay-Belzile S, Truche S, Loubert-Hudon A, Brisson N. Transcription is a major driving force for plastid genome instability in Arabidopsis. PLoS One. 2019 Apr 3;14(4):e0214552. View Article
  89. Herold S, Kalb J, Büchel G, Ade CP, Baluapuri A, Xu J, Koster J, Solvie D, Carstensen A, Klotz C, Rodewald S, Schülein-Völk C, Dobbelstein M, Wolf E, Molenaar J, Versteeg R, Walz S, Eilers M. Recruitment of BRCA1 limits MYCN-driven accumulation of stalled RNA polymerase. Nature. 2019 Mar;567(7749):545-549. View Article
  90. Sanz LA, Chédin F. High-resolution, strand-specific R-loop mapping via S9.6-based DNA-RNA immunoprecipitation and high-throughput sequencing. Nat Protoc. 2019 Jun;14(6):1734-1755. View Article
  91. Graf M, Bonetti D, Lockhart A, Serhal K, Kellner V, Maicher A, Jolivet P, Teixeira MT, Luke B. Telomere Length Determines TERRA and R-Loop Regulation through the Cell Cycle. Cell. 2017 Jun 29;170(1):72-85.e14. View Article
  92. Zhu Q, Hoong N, Aslanian A, Hara T, Benner C, Heinz S, Miga KH, Ke E, Verma S, Soroczynski J, Yates JR 3rd, Hunter T, Verma IM. Heterochromatin-Encoded Satellite RNAs Induce Breast Cancer. Mol Cell. 2018 Jun 7;70(5):842-853.e7. View Article
  93. Yang Z, Hou Q, Cheng L, Xu W, Hong Y, Li S, Sun Q. RNase H1 Cooperates with DNA Gyrases to Restrict R-Loops and Maintain Genome Integrity in Arabidopsis Chloroplasts. Plant Cell. 2017 Oct;29(10):2478-2497. View Article
  94. Gorthi A, Romero JC, Loranc E, Cao L, Lawrence LA, Goodale E, Iniguez AB, Bernard X, Masamsetti VP, Roston S, Lawlor ER, Toretsky JA, Stegmaier K, Lessnick SL, Chen Y, Bishop AJR. EWS-FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma. Nature. 2018 Mar 15;555(7696):387-391. View Article
  95. Patel PS, Abraham KJ, Guturi KKN, Halaby MJ, Khan Z, Palomero L, Ho B, Duan S, St-Germain J, Algouneh A, Mateo F, El Ghamrasni S, Barbour H, Barnes DR, Beesley J, Sanchez O, Berman HK, Brown GW, Affar EB, Chenevix-Trench G, Antoniou AC, Arrowsmith CH, Raught B, Pujana MA, Mekhail K, Hakem A, Hakem R. RNF168 regulates R-loop resolution and genomic stability in BRCA1/2-deficient tumors. J Clin Invest. 2021 Feb 1;131(3):e140105. View article 
  96. De Santis I, Zanoni M, Arienti C, Bevilacqua A, Tesei A. Density Distribution Maps: A Novel Tool for Subcellular Distribution Analysis and Quantitative Biomedical Imaging. Sensors (Basel). 2021 Feb 2;21(3):1009. View article
  97. Dobersch S, Rubio K, Singh I, Günther S, Graumann J, Cordero J, Castillo-Negrete R, Huynh MB, Mehta A, Braubach P, Cabrera-Fuentes H, Bernhagen J, Chao CM, Bellusci S, Günther A, Preissner KT, Kugel S, Dobreva G, Wygrecka M, Braun T, Papy-Garcia D, Barreto G. Positioning of nucleosomes containing γ-H2AX precedes active DNA demethylation and transcription initiation. Nat Commun. 2021 Feb 16;12(1):1072.  View article
  98. Kim C, Sung S, Kim JS, Lee H, Jung Y, Shin S, Kim E, Seo JJ, Kim J, Kim D, Niida H, Kim VN, Park D, Lee J. Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells. Nat Commun. 2021 Feb 17;12(1):1097.  View article 
  99. Tesei A, Arienti C, Bossi G, Santi S, De Santis I, Bevilacqua A, Zanoni M, Pignatta S, Cortesi M, Zamagni A, Storci G, Bonafè M, Sarnelli A, Romeo A, Cavallo C, Bartolazzi A, Rossi S, Soriani A, Strigari L. TP53 drives abscopal effect by secretion of senescence-associated molecular signals in non-small cell lung cancer. J Exp Clin Cancer Res. 2021 Mar 5;40(1):89. View article 
  100. Shiromoto Y, Sakurai M, Minakuchi M, Ariyoshi K, Nishikura K. ADAR1 RNA editing enzyme regulates R-loop formation and genome stability at telomeres in cancer cells. Nat Commun. 2021 Mar 12;12(1):1654. View article
  101. Xu C, Wu Z, Duan HC, Fang X, Jia G, Dean C. R-loop resolution promotes co-transcriptional chromatin silencing. Nat Commun. 2021 Mar 19;12(1):1790. View article 
  102. Park K, Ryoo J, Jeong H, Kim M, Lee S, Hwang SY, Ahn J, Kim D, Moon HC, Baek D, Kim K, Park HY, Ahn K. Aicardi-Goutières syndrome-associated gene SAMHD1 preserves genome integrity by preventing R-loop formation at transcription-replication conflict regions. PLoS Genet. 2021 Apr 15;17(4):e1009523.  View article