Frederic Chedin

Title(s)Professor, Molecular and Cellular Biology
SchoolCollege of Biological Sciences
Address335 Briggs Hall
CA 95616
Phone530-752-1800
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    Collapse Research 
    Collapse Research Activities and Funding
    Understanding the mechanisms underlying R-loop biogenesis and resolution in mammals
    NIH R35GM139549Jan 1, 2021 - Dec 31, 2025
    Role: Principal Investigator
    Genomic profiling of pathological R-loop formation in human diseases.
    NIH R01GM120607Sep 23, 2016 - Jul 31, 2021
    Role: Principal Investigator
    Epigenetic regulation of the FMR1 gene
    NIH R01GM113929Sep 21, 2015 - Dec 31, 2019
    Role: Co-Principal Investigator
    R-loop formation protects CpG islands against epigenetic silencing.
    NIH R01GM094299Aug 1, 2010 - Jul 31, 2017
    Role: Principal Investigator
    Training Program in Molecular and Cellular Biology
    NIH T32GM007377Jul 1, 1983 - Jun 30, 2024
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. 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: 2     Fields:    Translation:HumansCells
    2. 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: 17     Fields:    Translation:HumansAnimalsCells
    3. 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: 38     Fields:    Translation:AnimalsCells
    4. 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: 28     Fields:    Translation:HumansCells
    5. 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: 2     Fields:    Translation:HumansCells
    6. 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: 17     Fields:    Translation:Cells
    7. 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: 20     Fields:    Translation:HumansAnimalsCells
    8. 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: 92     Fields:    Translation:HumansAnimalsCells
    9. 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: 51     Fields:    Translation:Cells
    10. 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: 76     Fields:    Translation:HumansCells
    11. 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.
      View in: PubMed   Mentions:    Fields:    
    12. 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: 73     Fields:    Translation:AnimalsCells
    13. Hybrids in the chromatin. Nat Plants. 2017 09; 3(9):692-693. Chédin F. PMID: 28848239.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    14. 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: 94     Fields:    Translation:HumansAnimalsCells
    15. 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: 52     Fields:    Translation:HumansCells
    16. 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: 125     Fields:    Translation:AnimalsCells
    17. 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: 143     Fields:    Translation:HumansCells
    18. 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: 268     Fields:    Translation:HumansAnimalsCells
    19. 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: 248     Fields:    Translation:HumansCells
    20. 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: 33     Fields:    Translation:HumansAnimalsCells
    21. 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: 86     Fields:    Translation:HumansCells
    22. 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. .
      View in: Publisher Site   Mentions:
    23. 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: 115     Fields:    Translation:HumansCells
    24. 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: 136     Fields:    Translation:HumansAnimalsCells
    25. 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
    26. 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: 85     Fields:    Translation:HumansAnimalsCells
    27. 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: 29     Fields:    Translation:HumansAnimalsCells
    28. 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: 203     Fields:    Translation:HumansCells
    29. 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: 440     Fields:    Translation:HumansAnimalsCells
    30. 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: 29     Fields:    Translation:HumansCells
    31. 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: 105     Fields:    Translation:HumansAnimalsCells
    32. 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: 70     Fields:    Translation:HumansAnimals
    33. 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: 67     Fields:    Translation:HumansAnimalsCells
    34. 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
    35. 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
    36. 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: 76     Fields:    Translation:HumansCells
    37. 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
    38. 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: 90     Fields:    Translation:HumansAnimalsCells
    39. 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: 377     Fields:    Translation:HumansAnimalsCells
    40. 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: 190     Fields:    Translation:HumansCells
    41. 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
    42. 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: 42     Fields:    Translation:Cells
    43. 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: 31     Fields:    Translation:Cells
    44. 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: 31     Fields:    Translation:Cells
    45. 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
    46. 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
    47. 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: 3     Fields:    Translation:Cells
    48. 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: 35     Fields:    Translation:Cells
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