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Research: Three-dimensional genome organization and gene expression in stem cells and cancer cells

Assistant Professor of Biochemistry & Biophysics
Joint Appointment in Biology
Member, Integrative Prog for Biological & Genome Sciences
Member, Lineberger Comprehensive Cancer Center

(PhD – University of California San Diego)


Trained Faculty Mentor endorsed by Office of Graduate Ed UNC Chapel Hill& Mental Health First Aid


  • NIH Maximizing Investigators’ Research Award (MIRA), National Institute of General Medical Sciences, 2017
  • Kimmel Scholar, Sidney Kimmel Foundation for Cancer Research, 2016
  • Ruth L. Kirschstein Postdoctoral Fellowship from the National Cancer Institute, 2012-2015
  • Whitehead Institute Postdoctoral Association Education Award, 2012
  • International Society for Stem Cell Research (ISSCR) Travel Award, 2012


The folding pattern of the genome plays an important role in gene regulation. Recent technological advancements have allowed for mapping of genome organization at high resolution. However, these maps are just the first step toward understanding how the looping of DNA in three-dimensional space controls gene regulation during development and disease.

Our laboratory is investigating the function of DNA loops involving genes and their transcriptional regulatory elements. A major question is how a specific regulatory element finds its correct target gene and is prevented from acting on thousands of other genes in the genome. To answer this question we combine genomic approaches (ChIP-Seq, ChIA-PET) and genome editing tools (CRISPR) to study the epigenetic mechanisms by which transcriptional regulatory elements control gene expression in embryonic stem cells. Our current research efforts are divided into 3 areas: 1) Characterizing the folding pattern of the genome 2) Dynamics of three-dimensional genome organization as embryonic stem cells differentiate into other cell types and 3) Functional analysis of altered chromosome structure in cancer and developmental disorders.


  • Dowen JM*, Fan ZP*, Hnisz D*, Ren G*, Abraham BJ, Zhang L, Weintraub AS, Schujiers J, Lee TI, Zhao K and Young RA. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. (2014) Cell. Oct 9;159(2):374-387. PMCID: 25303531 * these authors contributed equally
  • Dowen JM and Young RA. SMC complexes link gene expression and genome architecture. (2014) Curr Opin Genet Dev. Apr;25:131-137. PMCID: PMC4045092
  • Dowen, JM, Bilodeau, S, Orlando, DO, Hubner, MR, Abraham, BJ, Spector, DL, Young, RA. (2013) Multiple Structural Maintenance of Chromosome Complexes at Transcriptional Regulatory Elements. Stem Cell Reports. Nov;19(1):1-8. PMCID: PMC3841252
  • Dowen, RH, Pelizzola, M, Schmitz, RJ, Lister, R, Dowen, JM, Nery, JR, Dixon, JE, Ecker, JR. (2012) Widespread dynamic DNA methylation in response to biotic stress. PNAS. Aug;7 109(32):12858-12859. PMCID: PMC3420206
  • Dowen, JM, Putnam, CD, Kolodner, RD. (2010) Functional studies and homology modeling of Msh2-Msh3 predict that mispair recognition involves DNA bending and strand separation. Mol Cell Biol. Jul;30(13):3321-8. PMCID: PMC2897569
  • Harrington, JM, Kolodner, RD. (2007) Saccharomyces cerevisiae Msh2-Msh3 acts in repair of specific base-base mispairs. Mol Cell Biol. Sep;27(18):6546-54. PMCID: PMC2099603
  • Vieira AR, Avila JR, Daack-Hirsch S, Dragan E, Félix TM, Rahimov F, Harrington J, Schultz RR, Watanabe Y, Johnson M, Fang J, O’Brien SE, Orioli IM, Castilla EE, Fitzpatrick DR, Jiang R, Marazita ML, Murray JC. (2005) Medical sequencing of candidate genes for nonsyndromic cleft lip and palate. PLoS Genet. Dec;1(6):e64. PMCID: PMC1298935
Jill Dowen
  • Phone Number

    (919) 962-8132 (Office Phone)

  • Address

    250 Bell Tower Drive, CB 7100

    3360 Genome Sciences Building

    Chapel Hill, NC 27599-7100