Frederic Chedin

image of Frederic Chedin

Professor

Departments

UC Davis Genome Center
Molecular & Cellular Biology

Offices and Labs

335 BRIGGS HALL
530-752-1800
329 Briggs Hall
530-752-8224

Degrees

1995 PhD DNA recombination in Bacteria University of Paris - France
1991 MS DNA repair and recombination University of Paris - France

Research Interests

R-loop biology in mammals

 

I am focused on understanding the formation, function, and resolution of R-loop structures, a class of non-B DNA structures formed upon the annealing of an RNA strand to one strand of the DNA duplex. Genome-wide mapping data from my laboratory established that R-loop structures are the most abundant non-B DNA structures in mammalian genomes and suggests that they represent a novel type of cis-acting DNA element. Our main research themes are:

  • Developing and improving genomics technologies to map R-loop formation.
  • Analyzing the relationship between R-loop structures and chromatin states, including histone modifications and DNA methylation.
  • Understanding the mechanisms by which R-loops are formed, sensed, and dynamically resolved.
  •  Elucidating how dysfunctions in R-loop metabolism is linked to human diseases, in particular neurodevelopmental and neurodegenerative disorders.

 

To address these topics, my group makes use of innovative (epi)genomics tools, mammalian cell culture assays, biochemical assays, proteomic methods, and computational approaches.

Awards

Basil O'Connor Starter Research Scholar Award - March of dimes foundation - 2005-2007
CONquer CancER Now Award - Concern Foundation - 2006-2008
Hartwell Foundation Investigator - 2012-2015

Department and Center Affiliations

Department of Molecular and Cellular Biology
UC Davis Genome Center

ProfessionalSocieties

DNA Methylation Society
American Society of Human Genetics

CBS Grad Group Affiliations

Integrated Genetics and Genomics
Biochemistry, Molecular, Cellular and Developmental Biology

Specialties / Focus

Integrated Genetics and Genomics
  • Chromosome Biology
  • Human Genetics and Genomics
  • Computational Biology
  • Integrated Genetics and Genomics
  • Epigenomics
Biochemistry, Molecular, Cellular and Developmental Biology
  • Molecular Genetics
  • Chromosome Dynamics and Nuclear Function
  • DNA Repair
  • Gene Regulation
  • Genomics, Proteomics and Metabolomics
  • RNA

Labs

Chedin Lab - 332 Briggs Hall website
  • Lionel Sanz: Postdoctoral researcher / Stella Hartono, and John Smolka: graduate students / Staff Research Associate: Xiaoqin Xu / Undergraduate researchers: Kimmey Berg, Abby Lepinsky, Jenna Giafaglione, Tom Schwarz

Courses

MCB 162 Human Genetics (Fall)
MCB 214 Molecular Biology (Spring)
GGG 205 Lab Rotation (Fall-Winter)

Publications

  • Lim Y.W., Sanz L., Xu X., Hartono S.R., and Chédin F. (2015). DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi-Goutières syndrome. eLife. In press

  • Yang Y.Z., McBride K., Hensley K., Yue L., Chédin F., and Bedford M.T. (2014). Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R-loop accumulation. Molecular Cell. 53(3):484-497.

  • Loomis E.W., Sanz L.A., Chédin F., and Hagerman P.J. (2014). Transcription-associated R-loop formation across the human FMR1 CGG-repeat region. PLoS Genetics. 10(4):e1004294

  • Powell W. T., Coulson R., Crary F. K., Wong S., Gonzales M. L., Adams S., Yasui D.H., Chédin F., and LaSalle J. M. (2013). Topotecan stabilizes R-loops to inhibit transcription in the Prader-Willi/Angelman imprinted locus. Proceedings of the National Academy of Sciences USA; 110(34):13938-13943

  • Ginno P. A., Lim Y.W., Lott P., Korf I., and Chédin* F. (2013). GC skew at the 5’ and 3’ Ends of Human Genes Links R-loop Formation to Epigenetic Regulation and Transcription Termination. (2013). Genome Research. 23(10):1590-1600

  • Gordon C.A., Hartono S.R., and Chédin* F. (2013) Inactive DNMT3B splice variants modulate de novo DNA methylation. PLoS One 2013 Jul 19;8(7):e69486.

  • Ginno P. A., Lott P., Christensen H. C., Korf I., and Chédin* F. (2012) R-loop formation is a distinctive characteristic of unmethylated human CpG islands. Molecular Cell, 45(6):814-825.