Dr. Eric M. Mendenhall

ASSOCIATE Professor, Biological Sciences Department


The goal of our lab is to define the function of the non-coding genome, the mere 99% of the mammalian genome that does not directly code for a protein. Our work focuses on: (i) the identification and functional characterization of candidate distal enhancers, and their associated chromatin states; (ii) combined computational and molecular approaches to uncover the importance of the underlying DNA sequence in establishing chromatin or DNA methylation states; (iii) the therapeutic potential of locus specific epigenome modifications, using the CFTR locus (found mutated in patients with Cystic Fibrosis) as one therapeutically relevant target locus.

We utilize a number of synthetic biology tools, including CRISPR/Cas9 genome and epigenome engineering, synthetic DNA libraries and combines these with next-generation sequencing to assign biological functions to non-coding regions of the genome.


  • Ph.D., Molecular and Cellular Biology, University of Minnesota, 2006

Classes Taught


  • “CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA- binding proteins.” Genome Research. Savic D, Partridge E.C., Newberry K.M., Smith S.B., Meadows S.K., Roberts B.S., Mackiewicz M., Mendenhall E.M.*, Myers, R.M.* (2015).

    “Htt CAG repeat expansion confers pleiotropic gains of mutant huntingtin function in chromatin regulation.” Human Molecular Genetics. Biagioli M., Ferrari F., Mendenhall E.M., Zhang Y., Erdin S., Vijayvargia R., Vallabh S.M., Solomos N., Manavalan P., Ragavendran A., Ozsolak F., Lee J.M., Talkowski M.E., Gusella J.F., Macdonald M.E., Park P.J., Seong I.S. (2015).

    “Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis.” Genome Research. Attanasio C., Nord A.S., Zhu Y., Blow M.J., Biddie S.C., Mendenhall E.M., C., Hosseini R., Akiyama J.A., Holt A., Plajzer-Frick I., Shoukry M., Afzal V., Ren B., Bernstein, Rubin E.M., Visel A., Pennacchio L.A. (2014).
  • "Locus-specific chromatin inactivation at endogenous enhancers with programmable TALE-LSD1 fusions." Nature Biotechnology. Mendenhall E.M., Williamson K.E, Reyon D., Zou J.Y., Ram O., Joung J.K., Bernstein B.E. (2013).
  • "Protein Binding in High Definition." Genome Biology. Jan; 27;13(1):139. Mendenhall E.M., Bernstein B.E. (2012).
  • "GC-rich sequence elements recruit PRC2 in mammalian ES cells." PLoS Genetics. Dec 9;6(12):e1001244 PMCID: PMC3000368. Mendenhall E.M., Koche R.P., Truong T., Zhou V.W., Issac B., Chi A.S., Ku M., Bernstein B.E. (2010).
  • "Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains." PLoS Genetics. Oct; 4 (10):e100242. Ku M., Koche R.P., Rheinbay E., Mendenhall E.M., Endoh M., Mikkelsen T.S., Presser A., Nusbaum C., Xie X., Chi A.S., Adli M., Kasif S., Ptaszek L.M., Cowan C.A., Lander E.S., Koseki H., Bernstein B.E. (2008).
  • "Chromatin state maps: new technologies, new insights." Current Opinion in Genetics & Development. Apr; 18(2):109-115. Mendenhall E.M., Bernstein BE. (2008).
  • "Genome-wide maps of chromatin state in pluripotent and lineage-committed cells." Nature. Aug 2;448(7153):553-60. Mikkelsen T.S., Ku M., Jaffe D.B., Issac B., Lieberman E., Giannoukos G., Alvarez P., Brockman W., Kim T.K., Koche R.P., Lee W., Mendenhall E., O’Donovan A., Presser A., Russ C., Xie X., Meissner A., Wernig M., Jaenisch R., Nusbaum C., Lander E.S., Bernstein B.E. (2007).
  • "Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome." PLOS One. Dec 20 (1):e104. Pickart M.A., Klee E.W., Nielsen A.L., Sivasubbu S., Mendenhall E.M., Bill B.R., Chen E., Eckfeldt C.E., Knowlton M., Robu M.E., Larson J.D., Deng Y., Schimmenti L.A., Ellis L.B., Verfaillie C.M., Hammerschmidt M., Farber S.A., Ekker S.C. (2006).
  • "The Molecular Repertoire of the Almighty Stem Cell." Nature Reviews Molecular Cellular Biology. Sept 6:726-737. Eckfeldt C.E., Mendenhall E.M., Verfaillie C.M. (2005).
  • "Functional Analysis of Hematopoietic Stem Cell Gene Expression Using Zebrafish." PLOS Biology. Aug 3(8) e254. Eckfeldt C.E.*, Mendenhall E.M.*, Pickart M.A., Ekker S.C., Verfaillie C.M. (2005).
  • "Characterization of Expanded Intermediate Cell Mass in Zebrafish Chordin Morphant Embryos." Developmental Biology. Jan 1:277(1):235-254. Leung A.Y., Mendenhall E.M., Kwan T.T., Liang R., Eckfeldt C.E., Hammerschmidt M., Grindle S., Ekker S.C., Verfaillie C.M. (2005).