Assistant Professor
Ph.D. (2007) University of Wisconsin, Madison
706-542-1887
  • Schmitz Lab Website

  • Research Interests - Population Epigenomics and Mechanisms of Epigenetic Inheritance

    We are interested in determining how phenotypic plasticity and diversity are driven by natural and spontaneous epigenetic variation. Recent advances in genomic technologies are enabling acquisition of sequence-level data at an unprecedented rate and resolution. As a result, genomes for thousands of individuals are being analyzed to determine the total genetic variation present within a species and to determine the impact these variants have on phenotypic variation. Missing from these efforts is the identification of environmentally induced, spontaneous and natural epigenetic alleles (epialleles). We apply epigenomic approaches to populations to study the impact that epialleles have on life history traits and to understand their role in establishing responses to the environment. These epialleles are often associated with changes in their DNA methylation status making their identification possible. Systematically identifying these epialleles, understanding their patterns of heritability, their interaction with genetic variants and their specific roles in controlling gene expression is necessary for a comprehensive understanding of phenotypic variation.

  • Honors/Awards/Professional Service

    • Arabidopsis Biological Resource Center, Advisory Board, 2016 - present
    • Pew Scholar in Biomedical Sciences, 2015 - present
    • DOE Joint Genome Institute, Plant User Advisory Board, 2015 - present
    • Editorial Board Member – Developmental Dynamics, 2015 - present
    • Advisory Editorial Board Member – Trends in Genetics, 2014 - present
    • “40 under 40”, nominated by the Cell editorial board as one of 40 accomplished young scientists shaping current and future trends in science under the age of 40, 2014
    • 7th Annual Young Investigator Award – Genome Technology, 2012
    • K99/R00 Pathway to Independence Award, NIGMS, 2012
  • Grant Support -
    • "Identification and Characterization of Population-wide Epigenetic Variation,” NIH
    • "Comparative-, Functional-, and Epi-Genomics of Legumes and Nodule Formation,” NSF
    • “Harnessing epigenomic reprogramming to improve bioenergy trait performance,” JGI/CSP
    • "Small RNA directed Natural Epigenetic Variation." Pew Charitable Trusts
    • "ECA-PGR: Somatic Genetic and Epigenetic Variations in Long-lived Perennial Trees and their Interactions with the Environment" NSF
    • "EAGER: Site-specific engineering of DNA methylation states in plant genomes" NSF
Selected Publications: 
  • Bewick AJ and Schmitz RJ. (2017) Gene body DNA methylation in plants. Current Opinion in Plant Biology (in press)

  • Lu Z, Hofmeister BT, DuBois R, Vollmers C, Schmitz RJ. (2017) Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. Nucleic Acids Research (in press)

  • Bewick AJ, Vogel KJ, Moore AJ, Schmitz RJ (2017) Sociality and DNA methylation are not evolutionary dependent. Molecular Biology and Evolution

  • Hossain MS, Kawakatsu T, Kim KD, Ning Z, Nguyen CT, Khan SM, Hernandez NG, Batek JM, Joshi T, Schmutz J, Schmitz RJ, Xu D, Grimwood J, Jackson SA, Ecker JR, Stacey G. (2017) Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs in response to heat stress. New Phytologist (in press)

  • Niederhuth CE and Schmitz RJ (2017) Putting methylation in context: from genomes to gene expression in plants. Biochemica et Biophysica Acta (in press)

  • Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Ecker JR, Briggs SP (2016) Integration of omic networks in a developmental atlas of maize. Science Aug 19:353(6301)

  • Panda K, Ji L, Neumann DA, Daron J, Schmitz RJ, Slotkin RK. (2016) Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylationGenome Biology Aug 9;17(170)

  • Kawakatsu T*, Huang SC*, Jupe F*, Sasaki E*, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, Wang C, Bemm F, Becker C, O’Neil R, O’Malley RC, Quarless DX, 1001 Genomes Consortium, Schork NJ, Weigel D, Nordborg M, Ecker JR (2016) Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell Jul 14;166(2):481-91

  • 1001 Genome Consortium (2016) 1135 sequenced natural inbred lines reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell Jul 14;166(2):481-91

  • Bewick AJ, Niederhuth CE, Rohr NA, Griffin PT, Leebens-Mack J, Schmitz RJ (2016) The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants. bioRxiv

  • Hohos NM, Lee KJ, Ji L, Yu M, Kandasamy KM, Phillips BG, Baile CA, He C, Schmitz RJ, Meagher RB. (2016) DNA cytosine hydroxymethylation levels are distinct among peripheral blood leukocytes. Journal of Immunological Methods Sep;436;1-15

  • Jordan WT and Schmitz RJ. (2016) The shocking consequences of hybrid epigenomes. Genome Biology May 5;17(1):85

  • Reynolds DL, Hofmeister BT, Cliffe L, Siegal TN, Anderson BA, Beverley SM, Schmitz RJ, Sabatini R. (2016). Base J represses genes at the end of polycistronic gene cluster in Leishmania major by promoting RNAP II termination. Molecular Microbiology Aug;101(4):559-74

  • Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker JR. (2016) Epigenomic profiling reveals unique cell-type specific patterns of DNA methylation in the root meristem. Nature Plants May(2):e16058

  • Yu P, Ji L, Lee KJ, Yu M, He C, Ambati S, McKinney EC, Jackson C, Baile CA, Schmitz RJ, Meagher RB (2016) Subsets of visceral adipose tissue nuclei and distinct levels of 5-hydroxymethylation. PLOS ONE May 12;11(5):e0154949

  • Griffin PT, Niederhuth CE, Schmitz RJ (2016) A comparative analysis of 5-azacytidine and zebularine induced DNA demethylation. G3 - Genes Genomes Genetics (in press)

  • Niederhuth CE*, Bewick AJ*, Ji L, Alabday M, Kim KD, Page JT, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ (2016) Widespread natural variation of DNA methylation within angiosperms. bioRxiv

  • Bewick AJ*, Ji L*, Niederhuth CE*, Willing EM*, Hofmeister BT, Shi X, Wang L, Lu Z, Rohr NA, Hartwig B, Kiefer C, Deal RB, Schmutz J, Grimwood J, Stroud H, Jacobsen SE, Schneeberger K, Zhang X, Schmitz RJ (2016) On the Origin and Evolutionary Consequences of Gene Body DNA Methylation. Proc Natl Acad Sci Aug 9;113(32):9111-6

  • Seymour M*, Ji L*, Santos AM, Kamei M, Sasaki T, Basenko EY, Schmitz RJ, Zhang X, Lewis ZA. (2016) Histone H1 limits DNA methylation in Neurospora crassa. G3 - Genes Genomes Genetics Jul 7;6(7):1879-89

  • Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Cannon EKS, Liu X, Gao D, Clevenger J, Dash S, Ren L, Moretzsohn MC, Shirasawa K, Huang W, Vidigal B, Abernathy B, Chu Y, Niederhuth CE, Umale P, Araújo ACG, Kozik A, Kim KD, Burow MD, Varshney RK, Wang X, Zhang X, Barkley N, Guimarães PM, Isobe S, Guo S, Liao B, Stalker HT, Schmitz RJ, Scheffler BE, Leal-Bertioli SCM, Xun X , Jackson SA, Michelmore R, Ozias-Akins P (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nature Genetics April;48(4):438-446

  • Reynolds D, Hofmeister B, Cliffe L, Alabady M, Siegel NT, Schmitz RJ, Sabatini R. (2016) Histone variant 3 regulates RNA polymerase II transcription termination and dual strand transcription of siRNA loci in Trypanosoma brucei. PLOS Genetics Jan 21;12(1):e1005758

  • Basenko EY, Kamei M, Ji L, Schmitz RJ, Lewis ZA (2016) The LSH/DDM1 homolog MUS-30 is required for genome stability, but not for DNA methylation in Neurospora crassa. PLOS Genetics Jan 15;12(1):e1005790

  • Bewick AJ, Hofmeister BT, Lee KJ, Zhang X, Hall DW, Schmitz RJ (2016) FASTmC: a suite of predictive models for non-reference-based estimations of DNA methylation. G3 - Genes Genomes Genetics Feb 17;6(2):447-52

  •  Li Q, Gent JI, Zynda G, Song J, Makarevitch I, Hirsch CD, Hirsch CN, Dawe RK, Madzima TF, McGinnis KM, Lisch D,Schmitz RJ, Vaughn MW, Springer NM (2015) RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome. Proc Natl Acad Sci Nov 24;112(47):14728-33

  • Basenko E, Sasaki T, Ji L, Prybol CJ, Burckhardt RM, Schmitz RJ, Lewis ZA. (2015) Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth. Proc Natl Acad Sci Nov 17;112(46):E6339-48

  • Cunningham CB, Ji L, Wiberg RAW, Shelton J, McKinney EC, Parker DJ, Meagher RB, Benowitz KM, Roy-Zokan EM, Ritchie MG, Brown SJ, Schmitz RJ, Moore AJ. (2015) The genome and methylome of a beetle with complex social behavior, Nicrophorus vespilloides (Coleoptera: Silphidae). Genome Biology & Evolution Oct 9;7(12):3383-9

  • Christensen SA, Huffaker A, Kaplan A, Sims J, Ziemann S, Doehlemann G, Ji L, Schmitz RJ, Kolomeits MV, Alborn HT, Mori N, Ni X, Byers S, Abdo Z, Schmelz EA (2015) Maize death acids, 9-lipoxygenase derived cyclopentenones and derivatives, display activity as cytotoxic phytoalexins and transcriptional mediators. Proc Natl Acad Sci Sep 8;112(36):11407-12

  • Nagel DH, Doherty CJ, Pruneda-Paz JL, Schmitz RJ, Ecker JR, Kay SA (2015) Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proc Natl Acad Sci Aug 25;112(34):E4802-10

  • Yu M*, Ji L*, Neumann DA, Chung D, Groom J, Westpheling J, He C‡, Schmitz RJ‡. (2015) Base-resolution detection ofN4-methylcytosine in genomic DNA using 4mC-Tet-Assisted-Bisulfite-sequencing. Nucleic Acids Research Dec 2;43(21):e148

  • Rancour DM, Hatfield RD, Marita JM, Rohr NA, Schmitz RJ. (2015) Cell wall composition and digestibility alterations in Brachypodium distachyon achieved through reduced expression of the UDP-arabinopyranose mutaseFront. Plant Sci.6:446

  • van der Graaf A, Wardenaar R, Neumann DA, Taudt A, Shaw RG, Jansen RC, Schmitz RJ‡, Colomé-Tatché M‡, Johannes F‡. (2015) Rate, spectrum, and evolutionary dynamics of spontaneous epimutations. Proc Natl Acad Sci. May 26;112(21):6676-81

  • Bewick AJ and Schmitz RJ. (2015) Epigenetics in the wild. eLife 2015;4:e07808

  • Jacobs TB, LaFayette PR, Schmitz RJ Parrott WA. (2015) Targeted genome modifications in soybean with CRISPR/Cas9. BMC Biotechnology. March(15):16

  • Ji L, Neumann DA, Schmitz RJ. (2015) Crop Epigenomics: Identifying, Unlocking and Harnessing Cryptic Variation in Crop Genomes. Molecular Plant. Jun;8(6):860-870

  • Vlachogiannis G, Niederhuth CE, Tuna S, Stathopoulou A, Viiri K, de Rooij DG, Jenner RG, Schmitz RJ, Ooi, STK. (2015) The Dnmt3L ADD domain controls cytosine methylation establishment during spermatogenesis. Cell Reports. Feb(10):944–56

  • Lane AK, Niederhuth CE, Ji L, Schmitz RJ. (2015) pENCODE: A Plant Encyclopedia of DNA Elements. Annual Review of Genetics. Volume 48, Issue 1

  • Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR. (2015) MethylC-seq: Base resolution whole genome bisulfite sequencing library preparation. Nature Protocols. Feb(10):475–483

  • Ji L, Sasaki T, Sun X, Ma P, Lewis ZA, Schmitz RJ. (2014) Methylated DNA is over-represented in whole-genome bisulfite sequencing data. Frontiers in Genetics. 5:341. doi: 10.3389/fgene.2014.00341\

  • West PT, Li Q, Ji L, Eichten SR, Song J, Vaughn MW, Schmitz RJ, Springer, NM. (2014) Genomic distribution of H3K9me2 and DNA methylation in a maize genomePLOS ONEAug;9(8):e105267

  • Dinh TT, Gao L, Liu X, O’Leary M, Zhao Y, Li D, Le B, Schmitz RJ, Manavella P, Li S, Weigel D, Pontes O, Ecker JR, Chen X. (2014) DNA Topoisomerase 1α promotes RNA-directed DNA methylation and histone lysine 9 dimethylation at transposable elements in ArabidopsisPLoS Genetics. Jul;7(10):e1004446

  • Eichten S, Schmitz RJ‡, Springer NM‡. (2014) Epigenetics; beyond chromatin modifications and complex gene regulatory systems. Plant Physiology. Jul 165(3):933-947.

  • Schmitz RJ. (2014) The Secret Garden - Epigenetic Alleles Underlie Complex Traits. Science. March(343):1082.

  • Wang Y, Gu X, Yuan W, Schmitz RJ, He Y. (2014) Photoperiodic Control of the Floral Transition through a Distinct Polycomb Repressive ComplexDevelopmental Cell. Mar(28):1-10.

  • Valdes-Lopez O*, Khan SM*, Schmitz RJ, Cui S, Qiu J, Zhu M, Cheng JJ, Joshi T, Xu D, Diers B, Ecker JR, Stacey G. (2014) Genotypic variation of gene expression during the soybean innate immunity response. Plant Genetic Resources. 12(S1):S27-30.

  • Niederhuth CE and Schmitz RJ. (2014) Covering your bases: Inheritance of DNA methylation in plant genomesMolecular Plant. Mar;7(3):472-80.

  • Schmitz RJ‡ and Zhang X‡. (2014) Chapter XI: Decoding epigenomes of herbaceous land plants. Advances in Botanical Research: Genomes of Herbaceous Land Plants. Volume 69.

  • Hua ZH, Pool JE, Schmitz RJ, Schultz MD, Shiu SH, Ecker JR‡, Vierstra RD‡. (2013) Epigenomic programming contributes to the genomic drift evolution of the F-box protein superfamily in Arabidopsis. Proc Natl Acad Sci. Oct;110(42):16927-32.

  • Schmitz RJ*, He Y*, Valdes-Lopez O, Khan S, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G‡, Ecker JR‡. (2013) Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred populationGenome Research. Oct(23):1663-67.

  • Chung WY, Schmitz RJ, Biorac T, Ye D, Dudas M, Meredith GD, Adams CC, Ecker JR, Zhang MQ. (2013) Constructing hepitypes: phasing local genotype and DNA methylation. JNSNE. Aug:2(4):335-346.

  • Chang KN, Zhong S, Weirauch MT, Hong G, Pelizzola M, Li H, Huang SC, Schmitz RJ, Urich MA, Kue D, Nery J, Qiao H, Yang A, Jamali A, Ideker T, Ren B, Bar-Joseph Z, Hughes TR, Ecker JR (2013) Temporal transcriptional responses to ethylene gas drives growth hormone cross-regulation in Arabidopsis. eLIFE. Jun;2:e00675.

  • Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker JR. (2013) Response to perspective: "Separation anxiety: An analysis of ethylene-induced cleavage of EIN2." Plant Signaling & Behavior. Aug:8(8):127-8.

  • Schmitz RJ*, Schultz MD*, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A†, McCosh RB, Chen H, Schork NJ, Ecker JR. (2013) Patterns of Population Epigenomic Diversity. Nature. Mar;495(7440):193-8.

  • Woodson JD*, Perez-Ruiz JM*, Schmitz RJ, Ecker JR, Chory J. (2013) Sigma factor mediated plastid retrograde signals control nuclear gene expression. The Plant Journal. Jan;73(1):1-13. PMCID: PMC3605210

  • Vollmers C*, Schmitz RJ*, Nathanson J, Yeo G, Ecker JR, Panda S. (2012) Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. Cell Metabolism. Dec;16(6):833-45. PMCID: PMC3541940

  • Schultz MD*, Schmitz RJ*, Ecker JR. (2012) "Leveling" the playing field for analysis of single base resolution DNA methylomes. Trends in Genetics. Dec;28(12):583-5. PMCID: PMC3523709

  • Qiao H, Shen Z, Huang SS, Schmitz RJ, Urich MA, Briggs SP, Ecker JR. (2012) Processing and Subcellular Trafficking of ER-Tethered EIN2 Control Response to Ethylene Gas. Science. Oct;338(6105):390-3. PMCID: PMC3523706

  • Dowen RJ, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR. (2012) Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci. Jun;109(32):E2183-91. PMCID: PMC3420206

  • Johnson, DBF, Wang C, Xu J, Schultz MD, Schmitz RJ, Ecker JR, Wang L. (2012) Release factor one is not essential for Escherichia coli. ACS Chemical Biology. Jul;7(8):1337-44. PMCID: PMC3423824

  • Li L, Ljung K, Breton G, Schmitz RJ, Pruneda-Paz J, Cowing-Vitron C, Cole BJ, Ivans LJ, Pedmale U, Jung HS, Ecker JR, Kay SA, Chory J. (2012) Linking photoreceptor excitation to changes in plant architecture. Genes & Development. Apr;26(8):785-90. PMCID: PMC3337452

  • Kurihara Y, Schmitz RJ, Nery JR, Schultz MD, Kurihara E, Morosawa T, Tanaka M, Toyoda T, Seki M, Ecker JR. (2012) Surveillance and degradation of 3’ non-coding transcripts requires FIERY1 and XRN3 in Arabidopsis thaliana. G3 - Genes Genomes Genetics. PMCID: PMC3337477

  • Schmitz RJ, Ecker JR. (2012) Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends in Plant Sciences. Mar;17(3):149-54. PMCID: PMC3645451

  • Hotto, A, Schmitz RJ, Fei Z, Ecker JR, Stern D. (2011) Unexpected diversity of chloroplast non-coding RNAs as revealed by deep sequencing of the Arabidopsis transcriptome. G3 - Genes Genomes Genetics. Dec;1(7):559-70. PMCID: PMC3276175

  • Schmitz RJ, Schultz MD, Lewsey MG, O’Malley RC, Urich MA†, Lilbiger O, Schork NJ, Ecker JR. (2011) Transgenerational epigenetic instability is a source of novel methylation variants. Science. Oct;334(6045):369-373. PMCID: PMC3210014

  • Johnson DBF, Xu J, Shen Z, Takimoto J, Schultz MD, Schmitz RJ, Ecker JR, Briggs SP, Wang L. (2011) RF1 Knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nature Chemical Biology. Sep;7(11):779-86. PMCID: PMC3201715

  • Arabidopsis Interactome Mapping Consortium. (2011) Evidence for network evolution in an Arabidopsis interacome map. Science. Jul;333(6042):601-7. PMCID: PMC3170756

  • Farrona S, Hurtado L, March-Díaz R, Schmitz RJ, Florencio FJ, Turck F, Amasino RM, Reyes JC. (2011) Brahma is required for proper expression of the floral repressor FLC. PLOS ONE. Mar;6(3). PMCID: PMC3061888

  • Schmitz RJ‡, Zhang X‡. (2011) High-throughput approaches for studying plant epigenomics. Current Opinions in Plant Biology. Apr;14:130-136. PMCID: PMC3112054

  • Belkdhadir Y, Durbak A, Wierzba M, Schmitz RJ, Aquirre A, Michel R, Rowe S, Fujioka S, Tax FE. (2010) Intragenic suppression of a trafficking-defective brassinosteroid receptor mutant in Arabidopsis. Genetics. Aug;185(4):1283-96. PMCID: PMC2927756

  • Schmitz RJ*, Tamada Y*, Doyle MR, Zhang X, Amasino RM. (2009) Histone H2B deubiquitination is required for transcriptional activation of FLOWERING LOCUS C and for proper control of flowering in Arabidopsis. Plant Physiology. Feb;149(2):1196-204. PMCID: PMC2633843

  • Schmitz RJ*, Sung S*, Amasino RM. (2008) Histone arginine methylation is required for vernalization-induced epigenetic silencing of FLC in winter-annual Arabidopsis thaliana. Proc Natl Acad Sci. Jan;15:105(2):411-6. PMCID: PMC2206549

  • Schmitz RJ, Hong L†, Fitzpatrick KE†, Amasino RM. (2007) DICER-LIKE 1 and DICER-LIKE 3 redundantly act to promote flowering via repression of FLOWERING LOCUS C in Arabidopsis thaliana. Genetics. Jun;176(2):1359-62. PMCID: PMC1894598

  • Reeves PA, He Y, Schmitz RJ, Amasino RM, Panella LW, Richards CM. (2007) Evolutionary conservation of the FLC-mediated vernalization response: evidence from the sugar beet (Beta vulgaris). Genetics. May;176(1):295-307.

  • Schmitz RJ and Amasino RM. (2007) Vernalization: a model for investigating epigenetics and eukaryotic gene regulation in plants. Biochemica et Biophysica Acta. Mar/Apr;2(2):127-128.

  • Sung S, Schmitz RJ, Amasino RM. (2007) A role for VIN3-Like genes in environmentally induced epigenetic regulation of floweringPlant Signaling & Behavior. Mar:2(2):127-8.

  • Sung S, Schmitz RJ, Amasino RM. (2006) A PHD finger protein involved in both the vernalization and photoperiod pathways in Arabidopsis. Genes & Development. Dec;20(23):3244-8.

  • Schmitz RJ, Hong L†, Michaels S, Amasino RM. (2005) FRIGIDA-ESSENTIAL 1 interacts genetically with FRIGIDA and FRIGIDA-LIKE 1 to promote the winter-annual habit of Arabidopsis thaliana. Development. Dec;132(24):5471-8.

  • Choe S, Schmitz RJ, Fujioka S, Takatsuto S, Lee MO, Yoshida S, Feldmann KA, Tax FE. (2002) Arabidopsis brassinosteroid-insensitive dwarf12 mutants are semidominant and defective in a glycogen synthase kinase 3 beta-like kinase. Plant Physiology. Nov:130(3):1506-15.

  • Zhao J, Peng P, Schmitz RJ, Decker AD, Tax FE, Li J. (2002) Two putative BIN2 substrates are nuclear components of brassinosteroid signaling. Plant Physiology. Nov;130(3):1221-9.

Research Interests Detail: 

Population epigenomics and mechanisms of epigenetic inheritance: molecular mechanisms of DNA methylation initiation and establishment; how phenotypic plasticity and diversity are driven by epigenetic variation; identification of environmentally induced, spontaneous, and natural epigenetic alleles