Frederic Chedin • UC Davis Profiles (original) (raw)

  1. Protein-mediated stabilization and nicking of the nontemplate DNA strand dramatically affect R-loop formation in vitro. Proc Natl Acad Sci U S A. 2025 Sep 23; 122(38):e2509309122. Holleman E, Catley TE, Sereiva T, Hartono SR, Pyne ALB, Chédin F. PMID: 40966285; PMCID: PMC12478114.
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  2. Profiling Genome-Wide DNA Methylation in Children with Autism Spectrum Disorder and in Children with Fragile X Syndrome. Genes (Basel). 2022 10 04; 13(10). Jasoliya M, Gu J, AlOlaby RR, Durbin-Johnson B, Chedin F, Tassone F. PMID: 36292679; PMCID: PMC9602177.
    View in: PubMed Mentions: 5 Fields:
    Translation:HumansCells
  3. Mapping R-Loops and RNA:DNA Hybrids with S9.6-Based Immunoprecipitation Methods. J Vis Exp. 2021 08 24; (174). Sanz LA, Castillo-Guzman D, Chédin F. PMID: 34515688; PMCID: PMC9676068.
    View in: PubMed Mentions: 7 Fields:
    Translation:HumansCells
  4. PRMT1-dependent regulation of RNA metabolism and DNA damage response sustains pancreatic ductal adenocarcinoma. Nat Commun. 2021 07 30; 12(1):4626. Giuliani V, Miller MA, Liu CY, Hartono SR, Class CA, Bristow CA, Suzuki E, Sanz LA, Gao G, Gay JP, Feng N, Rose JL, Tomihara H, Daniele JR, Peoples MD, Bardenhagen JP, Geck Do MK, Chang QE, Vangamudi B, Vellano C, Ying H, Deem AK, Do KA, Genovese G, Marszalek JR, Kovacs JJ, Kim M, Fleming JB, Guccione E, Viale A, Maitra A, Emilia Di Francesco M, Yap TA, Jones P, Draetta G, Carugo A, Chedin F, Heffernan TP. PMID: 34330913; PMCID: PMC8324870.
    View in: PubMed Mentions: 35 Fields:
    Translation:HumansAnimalsCells
  5. Defining R-loop classes and their contributions to genome instability. DNA Repair (Amst). 2021 10; 106:103182. Castillo-Guzman D, Chédin F. PMID: 34303066; PMCID: PMC8691176.
    View in: PubMed Mentions: 61 Fields:
    Translation:HumansAnimalsCells
  6. Emerging roles for R-loop structures in the management of topological stress. J Biol Chem. 2020 04 03; 295(14):4684-4695. Chedin F, Benham CJ. PMID: 32107311; PMCID: PMC7135976.
    View in: PubMed Mentions: 60 Fields:
    Translation:AnimalsCells
  7. Ultra-deep Coverage Single-molecule R-loop Footprinting Reveals Principles of R-loop Formation. J Mol Biol. 2020 03 27; 432(7):2271-2288. Malig M, Hartono SR, Giafaglione JM, Sanz LA, Chedin F. PMID: 32105733; PMCID: PMC7669280.
    View in: PubMed Mentions: 54 Fields:
    Translation:HumansCells
  8. Characterization of R-Loop Structures Using Single-Molecule R-Loop Footprinting and Sequencing. Methods Mol Biol. 2020; 2161:209-228. Malig M, Chedin F. PMID: 32681515; PMCID: PMC7669279.
    View in: PubMed Mentions: 7 Fields:
    Translation:HumansCells
  9. The extruded non-template strand determines the architecture of R-loops. Nucleic Acids Res. 2019 07 26; 47(13):6783-6795. Carrasco-Salas Y, Malapert A, Sulthana S, Molcrette B, Chazot-Franguiadakis L, Bernard P, Chédin F, Faivre-Moskalenko C, Vanoosthuyse V. PMID: 31066439; PMCID: PMC6648340.
    View in: PubMed Mentions: 23 Fields:
    Translation:Cells
  10. Dimethyl fumarate dosing in humans increases frataxin expression: A potential therapy for Friedreich's Ataxia. PLoS One. 2019; 14(6):e0217776. Jasoliya M, Sacca F, Sahdeo S, Chedin F, Pane C, Brescia Morra V, Filla A, Pook M, Cortopassi G. PMID: 31158268; PMCID: PMC6546270.
    View in: PubMed Mentions: 26 Fields:
    Translation:HumansAnimalsCells
  11. High-resolution, strand-specific R-loop mapping via S9.6-based DNA-RNA immunoprecipitation and high-throughput sequencing. Nat Protoc. 2019 06; 14(6):1734-1755. Sanz LA, Chédin F. PMID: 31053798; PMCID: PMC6615061.
    View in: PubMed Mentions: 147 Fields:
    Translation:HumansAnimalsCells
  12. Interplay between DNA sequence and negative superhelicity drives R-loop structures. Proc Natl Acad Sci U S A. 2019 03 26; 116(13):6260-6269. Stolz R, Sulthana S, Hartono SR, Malig M, Benham CJ, Chedin F. PMID: 30850542; PMCID: PMC6442632.
    View in: PubMed Mentions: 75 Fields:
    Translation:Cells
  13. DNA Topoisomerase I differentially modulates R-loops across the human genome. Genome Biol. 2018 07 30; 19(1):100. Manzo SG, Hartono SR, Sanz LA, Marinello J, De Biasi S, Cossarizza A, Capranico G, Chedin F. PMID: 30060749; PMCID: PMC6066927.
    View in: PubMed Mentions: 98 Fields:
    Translation:HumansCells
  14. Author Correction: Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis. Nat Commun. 2018 03 30; 9:16211. Zhang X, Chiang HC, Wang Y, Zhang C, Smith S, Zhao X, Nair SJ, Michalek J, Jatoi I, Lautner M, Oliver B, Wang H, Petit A, Soler T, Brunet J, Mateo F, Angel Pujana M, Poggi E, Chaldekas K, Isaacs C, Peshkin BN, Ochoa O, Chedin F, Theoharis C, Sun LZ, Curiel TJ, Elledge R, Jin VX, Hu Y, Li R. PMID: 29600804; PMCID: PMC5882462.
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  15. The Affinity of the S9.6 Antibody for Double-Stranded RNAs Impacts the Accurate Mapping of R-Loops in Fission Yeast. J Mol Biol. 2018 02 02; 430(3):272-284. Hartono SR, Malapert A, Legros P, Bernard P, Chédin F, Vanoosthuyse V. PMID: 29289567; PMCID: PMC5987549.
    View in: PubMed Mentions: 92 Fields:
    Translation:AnimalsCells
  16. Hybrids in the chromatin. Nat Plants. 2017 09; 3(9):692-693. Chédin F. PMID: 28848239.
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    Translation:Cells
  17. Attenuation of RNA polymerase II pausing mitigates BRCA1-associated R-loop accumulation and tumorigenesis. Nat Commun. 2017 06 26; 8:15908. Zhang X, Chiang HC, Wang Y, Zhang C, Smith S, Zhao X, Nair SJ, Michalek J, Jatoi I, Lautner M, Oliver B, Wang H, Petit A, Soler T, Brunet J, Mateo F, Angel Pujana M, Poggi E, Chaldekas K, Isaacs C, Peshkin BN, Ochoa O, Chedin F, Theoharis C, Sun LZ, Curiel TJ, Elledge R, Jin VX, Hu Y, Li R. PMID: 28649985; PMCID: PMC5490191.
    View in: PubMed Mentions: 112 Fields:
    Translation:HumansAnimalsCells
  18. Telomeres in ICF syndrome cells are vulnerable to DNA damage due to elevated DNA:RNA hybrids. Nat Commun. 2017 01 24; 8:14015. Sagie S, Toubiana S, Hartono SR, Katzir H, Tzur-Gilat A, Havazelet S, Francastel C, Velasco G, Chédin F, Selig S. PMID: 28117327; PMCID: PMC5286223.
    View in: PubMed Mentions: 60 Fields:
    Translation:HumansCells
  19. Nascent Connections: R-Loops and Chromatin Patterning. Trends Genet. 2016 12; 32(12):828-838. Chédin F. PMID: 27793359; PMCID: PMC5123964.
    View in: PubMed Mentions: 146 Fields:
    Translation:AnimalsCells
  20. Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage. Elife. 2016 08 23; 5. Stork CT, Bocek M, Crossley MP, Sollier J, Sanz LA, Chédin F, Swigut T, Cimprich KA. PMID: 27552054; PMCID: PMC5030092.
    View in: PubMed Mentions: 187 Fields:
    Translation:HumansCells
  21. Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals. Mol Cell. 2016 07 07; 63(1):167-78. Sanz LA, Hartono SR, Lim YW, Steyaert S, Rajpurkar A, Ginno PA, Xu X, Chédin F. PMID: 27373332; PMCID: PMC4955522.
    View in: PubMed Mentions: 343 Fields:
    Translation:HumansAnimalsCells
  22. Comprehensive Proteomic Analysis of Mesenchymal Stem Cell Exosomes Reveals Modulation of Angiogenesis via Nuclear Factor-KappaB Signaling. Stem Cells. 2016 Mar; 34(3):601-13. Anderson JD, Johansson HJ, Graham CS, Vesterlund M, Pham MT, Bramlett CS, Montgomery EN, Mellema MS, Bardini RL, Contreras Z, Hoon M, Bauer G, Fink KD, Fury B, Hendrix KJ, Chedin F, El-Andaloussi S, Hwang B, Mulligan MS, Lehtiö J, Nolta JA. PMID: 26782178; PMCID: PMC5785927.
    View in: PubMed Mentions: 291 Fields:
    Translation:HumansCells
  23. GC skew is a conserved property of unmethylated CpG island promoters across vertebrates. Nucleic Acids Res. 2015 Nov 16; 43(20):9729-41. Hartono SR, Korf IF, Chédin F. PMID: 26253743; PMCID: PMC4787789.
    View in: PubMed Mentions: 41 Fields:
    Translation:HumansAnimalsCells
  24. Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi-Goutières syndrome. Elife. 2015 Jul 16; 4. Lim YW, Sanz LA, Xu X, Hartono SR, Chédin F. PMID: 26182405; PMCID: PMC4528086.
    View in: PubMed Mentions: 107 Fields:
    Translation:HumansCells
  25. Chapter 19 Targeting Epigenetics in the Development of New Diagnostic Applications—Lessons from Autoimmune Diseases. . 2015 Jan 1; 409-441. Chen CH, Chedin CF, Chang CC, Leung LP. .
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  26. Transcription-associated R-loop formation across the human FMR1 CGG-repeat region. PLoS Genet. 2014 Apr; 10(4):e1004294. Loomis EW, Sanz LA, Chédin F, Hagerman PJ. PMID: 24743386; PMCID: PMC3990486.
    View in: PubMed Mentions: 143 Fields:
    Translation:HumansCells
  27. Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R loop accumulation. Mol Cell. 2014 Feb 06; 53(3):484-97. Yang Y, McBride KM, Hensley S, Lu Y, Chedin F, Bedford MT. PMID: 24507716; PMCID: PMC3959860.
    View in: PubMed Mentions: 159 Fields:
    Translation:HumansAnimalsCells
  28. An ultrasensitive high throughput screen for DNA methyltransferase 1-targeted molecular probes. PLoS One. 2013; 8(11):e78752. Fagan RL, Wu M, Chédin F, Brenner C. PMID: 24236046; PMCID: PMC3827244.
    View in: PubMed Mentions: 5 Fields:
    Translation:HumansCells
  29. R-loop formation at Snord116 mediates topotecan inhibition of Ube3a-antisense and allele-specific chromatin decondensation. Proc Natl Acad Sci U S A. 2013 Aug 20; 110(34):13938-43. Powell WT, Coulson RL, Gonzales ML, Crary FK, Wong SS, Adams S, Ach RA, Tsang P, Yamada NA, Yasui DH, Chédin F, LaSalle JM. PMID: 23918391; PMCID: PMC3752217.
    View in: PubMed Mentions: 92 Fields:
    Translation:HumansAnimalsCells
  30. Inactive DNMT3B splice variants modulate de novo DNA methylation. PLoS One. 2013; 8(7):e69486. Gordon CA, Hartono SR, Chédin F. PMID: 23894490; PMCID: PMC3716610.
    View in: PubMed Mentions: 33 Fields:
    Translation:HumansAnimalsCells
  31. GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination. Genome Res. 2013 Oct; 23(10):1590-600. Ginno PA, Lim YW, Lott PL, Korf I, Chédin F. PMID: 23868195; PMCID: PMC3787257.
    View in: PubMed Mentions: 238 Fields:
    Translation:HumansCells
  32. R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters. Mol Cell. 2012 Mar 30; 45(6):814-25. Ginno PA, Lott PL, Christensen HC, Korf I, Chédin F. PMID: 22387027; PMCID: PMC3319272.
    View in: PubMed Mentions: 541 Fields:
    Translation:HumansAnimalsCells
  33. ICF syndrome mutations cause a broad spectrum of biochemical defects in DNMT3B-mediated de novo DNA methylation. J Mol Biol. 2011 Jun 24; 409(5):758-72. Moarefi AH, Chédin F. PMID: 21549127.
    View in: PubMed Mentions: 34 Fields:
    Translation:HumansCells
  34. Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein. J Biol Chem. 2011 Jul 08; 286(27):24300-11. Nady N, Lemak A, Walker JR, Avvakumov GV, Kareta MS, Achour M, Xue S, Duan S, Allali-Hassani A, Zuo X, Wang YX, Bronner C, Chédin F, Arrowsmith CH, Dhe-Paganon S. PMID: 21489993; PMCID: PMC3129210.
    View in: PubMed Mentions: 115 Fields:
    Translation:HumansAnimalsCells
  35. The DNMT3 family of mammalian de novo DNA methyltransferases. Prog Mol Biol Transl Sci. 2011; 101:255-85. Chédin F. PMID: 21507354.
    View in: PubMed Mentions: 80 Fields:
    Translation:HumansAnimals
  36. DNMT3L modulates significant and distinct flanking sequence preference for DNA methylation by DNMT3A and DNMT3B in vivo. PLoS Genet. 2010 Sep 09; 6(9):e1001106. Wienholz BL, Kareta MS, Moarefi AH, Gordon CA, Ginno PA, Chédin F. PMID: 20838592; PMCID: PMC2936528.
    View in: PubMed Mentions: 72 Fields:
    Translation:HumansAnimalsCells
  37. A systematic search for DNA methyltransferase polymorphisms reveals a rare DNMT3L variant associated with subtelomeric hypomethylation. Hum Mol Genet. 2009 May 15; 18(10):1755-68. El-Maarri O, Kareta MS, Mikeska T, Becker T, Diaz-Lacava A, Junen J, Nüsgen N, Behne F, Wienker T, Waha A, Oldenburg J, Chédin F. PMID: 19246518.
    View in: PubMed Mentions: 24 Fields:
    Translation:HumansCells
  38. A SPOT on the chromatin landscape? Histone peptide arrays as a tool for epigenetic research. Trends Biochem Sci. 2008 Jul; 33(7):305-13. Nady N, Min J, Kareta MS, Chédin F, Arrowsmith CH. PMID: 18538573.
    View in: PubMed Mentions: 33 Fields:
    Translation:HumansAnimalsCells
  39. Reconstitution and mechanism of the stimulation of de novo methylation by human DNMT3L. J Biol Chem. 2006 Sep 08; 281(36):25893-902. Kareta MS, Botello ZM, Ennis JJ, Chou C, Chédin F. PMID: 16829525.
    View in: PubMed Mentions: 85 Fields:
    Translation:HumansCells
  40. The AddAB helicase/nuclease forms a stable complex with its cognate chi sequence during translocation. J Biol Chem. 2006 Jul 07; 281(27):18610-7. Chédin F, Handa N, Dillingham MS, Kowalczykowski SC. PMID: 16632468.
    View in: PubMed Mentions: 28 Fields:
    Translation:Cells
  41. Physical and functional interactions between the human DNMT3L protein and members of the de novo methyltransferase family. J Cell Biochem. 2005 Aug 01; 95(5):902-17. Chen ZX, Mann JR, Hsieh CL, Riggs AD, Chédin F. PMID: 15861382.
    View in: PubMed Mentions: 98 Fields:
    Translation:HumansAnimalsCells
  42. R-loops at immunoglobulin class switch regions in the chromosomes of stimulated B cells. Nat Immunol. 2003 May; 4(5):442-51. Yu K, Chedin F, Hsieh CL, Wilson TE, Lieber MR. PMID: 12679812.
    View in: PubMed Mentions: 413 Fields:
    Translation:HumansAnimalsCells
  43. The DNA methyltransferase-like protein DNMT3L stimulates de novo methylation by Dnmt3a. Proc Natl Acad Sci U S A. 2002 Dec 24; 99(26):16916-21. Chedin F, Lieber MR, Hsieh CL. PMID: 12481029; PMCID: PMC139244.
    View in: PubMed Mentions: 212 Fields:
    Translation:HumansCells
  44. A novel family of regulated helicases/nucleases from Gram-positive bacteria: insights into the initiation of DNA recombination. Mol Microbiol. 2002 Feb; 43(4):823-34. Chédin F, Kowalczykowski SC. PMID: 11929535.
    View in: PubMed Mentions: 43 Fields:
    Translation:AnimalsCells
  45. The Bacillus subtilis AddAB helicase/nuclease is regulated by its cognate Chi sequence in vitro. J Mol Biol. 2000 Apr 21; 298(1):7-20. Chédin F, Ehrlich SD, Kowalczykowski SC. PMID: 10756102.
    View in: PubMed Mentions: 44 Fields:
    Translation:Cells
  46. A five-nucleotide sequence protects DNA from exonucleolytic degradation by AddAB, the RecBCD analogue of Bacillus subtilis. Mol Microbiol. 1998 Sep; 29(6):1369-77. Chédin F, Noirot P, Biaudet V, Ehrlich SD. PMID: 9781875.
    View in: PubMed Mentions: 34 Fields:
    Translation:Cells
  47. Novel homologs of replication protein A in archaea: implications for the evolution of ssDNA-binding proteins. Trends Biochem Sci. 1998 Aug; 23(8):273-7. Chédin F, Seitz EM, Kowalczykowski SC. PMID: 9757822.
    View in: PubMed Mentions: 32 Fields:
    Translation:Cells
  48. Inhibition of a naturally occurring rolling-circle replicon in derivatives of the theta-replicating plasmid pIP501. Mol Microbiol. 1998 Aug; 29(3):709-18. Pujol C, Chédin F, Ehrlich SD, Jannière L. PMID: 9723911.
    View in: PubMed Mentions: 5 Fields:
    Translation:Cells
  49. The recombination hot spot chi is embedded within islands of preferred DNA pairing sequences in the E. coli genome. Cell. 1997 Jul 25; 90(2):205-6. Tracy RB, Chédin F, Kowalczykowski SC. PMID: 9244294.
    View in: PubMed Mentions: 13 Fields:
    Translation:Cells
  50. Apparent and real recombination frequencies in multicopy plasmids: the need for a novel approach in frequency determination. J Bacteriol. 1997 Feb; 179(3):754-61. Chédin F, Dervyn R, Ehrlich SD, Noirot P. PMID: 9006030; PMCID: PMC178757.
    View in: PubMed Mentions: 4 Fields:
    Translation:Cells
  51. Frequency of deletion formation decreases exponentially with distance between short direct repeats. Mol Microbiol. 1994 May; 12(4):561-9. Chédin F, Dervyn E, Dervyn R, Ehrlich SD, Noirot P. PMID: 7934879.
    View in: PubMed Mentions: 40 Fields:
    Translation:Cells

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