Professor UGA Foundation Professorship in Plant Sciences Lars G. Ljungdahl Distinguished Investigator Ph.D. (2007) University of Wisconsin, Madison 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. We are also applying epigenome profiling methods to discover non-coding regulatory elements across numerous plant species. These methods include genome-wide assays to functionally evaluate identified regions using both gain-of-function and loss-of-function approaches. With advances in genome-editing technologies we are beginning to engineer non-coding regulatory elements as well as to use identified sequences to create modular units that can be used to drive transgene expression in a predictable manner. We are taking advantage of single-cell genomic technologies to better understand the link between natural or induced mutation and gene expression variation using a range of plant species. The ability to measure transcript abundance and accessible chromatin regions from thousands of individual cells changes the scale at which we can do molecular genetics. We are innovating multiple new methods that combine single-cell genomics with genetics to explore the link between sequence and trait variation. Honors & Awards ISI Highly Cited Researcher (Top 1% most-cited, for subject area) UGA Creative Research Medal in Natural Sciences and Engineering UGA Foundation Professorship in Plant Sciences Hans Fischer Fellow, Technical University of Munich (2018) Georgia Research Alliance Lars G. Ljungdahl Distinguished Research Investigator Pew Biomedical Scholar (2015-2019) “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 Professional Service Senior Editor, The Plant Cell, 2019 - present Editorial Board Member, Epigenomes, 2018 - present Associate Editor, Current Protocols in Plant Biology, 2018 - present Multinational Arabidopsis Steering Committee (Subcommittee - Epigenetics) ‘17- present DOE Joint Genome Institute, Plant User Advisory Board, 2015 - present Advisory Editorial Board Member – Trends in Genetics, 2014 - present Grant Support "TRTech-PGR: Comprehensive identification and functional characterization of cis-regulatory elements in legumes" National Science Foundation "Investigating the mechanistic origins and functions of gene body DNA methylation" National Science Foundation "Collaborative Research: Mechanisms and manipulation of maize meristem size" National Science Foundation "Collaborative Research: Mechanisms of differentiation and morphogenesis of the ligule/auricle hinge" National Science Foundation "Discovery of gene cis-regulatory DNA elements to improve protein/oil content in soybean" United Soybean Board "BioPoplar: A tunable chassis for diversified bioproduct production" Department of Energy "RESEARCH PGR: Impact of transposable element bursts on the rice genome and epigenome" National Science Foundation Research Research Areas: Genomics and Bioinformatics Molecular Genetics Biotechnology Selected Publications Selected Publications: Cunningham CB, Shelby EA, McKinney EC, Schmitz RJ, Moore AJ, Moore PJ. The role of Dmnt1 during spermatogenesis of the insect Oncopeltus fasciatus. Epigenetics & Chromatin 2023 Mendieta JP, Sangra A, Yan H, Minow MAA, Schmitz RJ. Exploring plant cis-regulatory elements at single-cell resolution: overcoming biological and computational challenges to advance plant research. The Plant Journal 2023 Kieft R, Zhang Y, Yan H, Schmitz RJ, Sabatini R. Knockout of protein phosphatase 1 in Leishmania major reveals its role during RNA polymerase II transcription termination. Nucleic Acids Research 2023 Ivasyk I, Olivos-Cisneros L, Valdés-Rodríguez S, Droual M, Jang H, Schmitz RJ, Kronauer DJC. DNMT1 mutant ants develop normally but have disrupted oogenesis. Nature Communications 2023 Murray A, Vollmers C, Schmitz RJ. Smar2C2: A simple and efficient protocol for the identification of transcription start sites. Current Protocols 2023 Yao N, Zhang Z, You L, Hazarika R, Yu C, Jang H, Smith LM, Ton J, Liu L, Stachowicz J, Reusch TBH, Schmitz RJ, Johannes F. An evolutionary epigenetic clock in plants. bioRxiv 2023 Zee A, Deng DZQ, Adams M, Schimke KD, Corbett-Detig R, Russell SL, Zhang X, Schmitz RJ, Vollmers C: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2. Genome Res 2022. Tu X, Marand AP, Schmitz RJ, Zhong S: A combinatorial indexing strategy for low-cost epigenomic profiling of plant single cells. Plant Commun 2022, 3:100308. Schmitz RJ, Mittelsten Scheid O: Editorial overview: COPB issue 2022 on "epigenetics and gene regulation". Curr Opin Plant Biol 2022, 70:102305. Murray A, Mendieta JP, Vollmers C, Schmitz RJ: Simple and Accurate Transcriptional Start Site Identification Using Smar2C2 and Examination of Conserved Promoter Features. Plant J 2022. Marchant DB, Chen G, Cai S, Chen F, Schafran P, Jenkins J, Shu S, Plott C, Webber J, Lovell JT, He G, Sandor L, Williams M, Rajasekar S, Healey A, Barry K, Zhang Y, Sessa E, Dhakal RR, Wolf PG, Harkess A, Li FW, Rossner C, Becker A, Gramzow L, Xue D, Wu Y, Tong T, Wang Y, Dai F, Hua S, Wang H, Xu S, Xu F, Duan H, Theissen G, McKain MR, Li Z, McKibben MTW, Barker MS, Schmitz RJ, Stevenson DW, Zumajo-Cardona C, Ambrose BA, Leebens-Mack JH, Grimwood J, Schmutz J, Soltis PS, Soltis DE, Chen ZH: Dynamic genome evolution in a model fern. Nat Plants 2022. Hazarika RR, Serra M, Zhang Z, Zhang Y, Schmitz RJ‡, Johannes F‡: Molecular properties of epimutation hotspots. Nat Plants 2022, 8:146-156. Bewg WP, Harding SA, Engle NL, Vaidya BN, Zhou R, Reeves J, Horn TW, Joshee N, Jenkins JW, Shu S, Barry KW, Yoshinaga Y, Grimwood J, Schmitz RJ, Schmutz J, Tschaplinski TJ, Tsai CJ: Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA. Plant Physiol 2022, 189:516-526. Bang S, Galli M, Crisp PA, Gallavotti A, Schmitz RJ: Identifying transcription factor–DNA interactions using machine learning. in silico Plants 2022, 4. Zhang Y, Jang H, Xiao R, Kakoulidou I, Piecyk RS, Johannes F‡, Schmitz RJ‡: Heterochromatin is a quantitative trait associated with spontaneous epiallele formation. Nat Commun 2021, 12:6958. Yocca AE, Lu Z, Schmitz RJ, Freeling M, Edger PP: Evolution of Conserved Noncoding Sequences in Arabidopsis thaliana. Mol Biol Evol 2021, 38:2692-2703. Yao N, Schmitz RJ, Johannes F: Epimutations Define a Fast-Ticking Molecular Clock in Plants. Trends Genet 2021, 37:699-710. Xu X, Crow M, Rice BR, Li F, Harris B, Liu L, Demesa-Arevalo E, Lu Z, Wang L, Fox N, Wang X, Drenkow J, Luo A, Char SN, Yang B, Sylvester AW, Gingeras TR, Schmitz RJ, Ware D, Lipka AE, Gillis J, Jackson D: Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery. Dev Cell 2021, 56:557-568 e556. Washington JT, Cavender KR, Amukamara AU, McKinney EC, Schmitz RJ, Moore PJ: The essential role of Dnmt1 in gametogenesis in the large milkweed bug Oncopeltus fasciatus. Elife 2021, 10. Schmitz RJ, Marand AP, Zhang X, Mosher RA, Turck F, Chen X, Axtell MJ, Zhong X, Brady SM, Megraw M, Meyers BC: Quality control and evaluation of plant epigenomics data. Plant Cell 2021. Schmitz RJ, Grotewold E, Stam M: Cis-regulatory sequences in plants: their importance, discovery, and future challenges. Plant Cell 2021. Provart NJ, Brady SM, Parry G, Schmitz RJ, Queitsch C, Bonetta D, Waese J, Schneeberger K, Loraine AE: Anno genominis XX: 20 years of Arabidopsis genomics. Plant Cell 2021, 33:832-845. Noshay JM, Marand AP, Anderson SN, Zhou P, Mejia Guerra MK, Lu Z, O'Connor CH, Crisp PA, Hirsch CN, Schmitz RJ, Springer NM: Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons. Genetics 2021, 217:1-13. Noshay JM, Liang Z, Zhou P, Crisp PA, Marand AP, Hirsch CN, Schmitz RJ, Springer NM: Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. G3 (Bethesda) 2021, 11. Minnoye L, Marinov GK, Krausgruber T, Pan L, Marand AP, Secchia S, Greenleaf WJ, Furlong EEM, Zhao K, Schmitz RJ, Bock C, Aerts S: Chromatin accessibility profiling methods. Nature Reviews Methods Primers 2021, 1. Mendieta JP, Marand AP, Ricci WA, Zhang X, Schmitz RJ: Leveraging histone modifications to improve genome annotations. G3 (Bethesda) 2021, 11. Marand AP, Zhang X, Nelson J, Braga Dos Reis PA, Schmitz RJ: Profiling single-cell chromatin accessibility in plants. STAR Protoc 2021, 2:100737. Marand AP, Schmitz RJ: Single-cell analysis of cis-regulatory elements. Curr Opin Plant Biol 2021, 65:102094. Marand AP‡, Chen Z, Gallavotti A, Schmitz RJ‡: A cis-regulatory atlas in maize at single-cell resolution. Cell 2021, 184:3041-3055 e3021. Kamei M, Ameri AJ, Ferraro AR, Bar-Peled Y, Zhao F, Ethridge CL, Lail K, Amirebrahimi M, Lipzen A, Ng V, Grigoriev IV, Schmitz RJ, Liu Y, Lewis ZA: IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains. Proc Natl Acad Sci U S A 2021, 118. Jordan WT, Currie S, Schmitz RJ: Multiplex genome editing in Arabidopsis thaliana using Mb3Cas12a. Plant Direct 2021, 5:e344. Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Della Coletta R, Tittes S, Hudson AI, Marand AP, Wei S, Lu Z, Wang B, Tello-Ruiz MK, Piri RD, Wang N, Kim DW, Zeng Y, O'Connor CH, Li X, Gilbert AM, Baggs E, Krasileva KV, Portwood JL, 2nd, Cannon EKS, Andorf CM, Manchanda N, Snodgrass SJ, Hufnagel DE, Jiang Q, Pedersen S, Syring ML, Kudrna DA, Llaca V, Fengler K, Schmitz RJ, Ross-Ibarra J, Yu J, Gent JI, Hirsch CN, Ware D, Dawe RK: De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 2021, 373:655-662. Ferraro AR, Ameri AJ, Lu Z, Kamei M, Schmitz RJ, Lewis ZA: Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin. BMC Genomics 2021, 22:459. Zhang Y, Wendte JM, Ji L, Schmitz RJ: Natural variation in DNA methylation homeostasis and the emergence of epialleles. Proc Natl Acad Sci U S A 2020, 117:4874-4884. Wang T, Kwon SH, Peng X, Urdy S, Lu Z, Schmitz RJ, Dalton S, Mostov KE, Zhao S: A Qualitative Change in the Transcriptome Occurs after the First Cell Cycle and Coincides with Lumen Establishment during MDCKII Cystogenesis. iScience 2020, 23:101629. Shahryary Y, Symeonidi A, Hazarika RR, Denkena J, Mubeen T, Hofmeister B, van Gurp T, Colome-Tatche M, Verhoeven KJF, Tuskan G, Schmitz RJ, Johannes F: AlphaBeta: computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants. Genome Biol 2020, 21:260. Kieft R, Zhang Y, Marand AP, Moran JD, Bridger R, Wells L, Schmitz RJ, Sabatini R: Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes. PLoS Genet 2020, 16:e1008390. Hofmeister BT, Denkena J, Colome-Tatche M, Shahryary Y, Hazarika R, Grimwood J, Mamidi S, Jenkins J, Grabowski PP, Sreedasyam A, Shu S, Barry K, Lail K, Adam C, Lipzen A, Sorek R, Kudrna D, Talag J, Wing R, Hall DW, Jacobsen D, Tuskan GA, Schmutz J, Johannes F, Schmitz RJ: A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. Genome Biol 2020, 21:259. Grover CE, Pan M, Yuan D, Arick MA, Hu G, Brase L, Stelly DM, Lu Z, Schmitz RJ, Peterson DG, Wendel JF, Udall JA: The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution. G3 (Bethesda) 2020, 10:1457-1467. Crisp PA, Marand AP, Noshay JM, Zhou P, Lu Z, Schmitz RJ, Springer NM: Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes. Proc Natl Acad Sci U S A 2020, 117:23991-24000. Lu Z, Marand AP, Ricci WA, Ethridge CL, Zhang X‡, Schmitz RJ‡. (2019) The prevalence, evolution and chromatin signatures of plant regulatory elements. Nature Plants Ricci WA*, Lu Z*, Ji L*, Marand AP, Ethridge CL, Murphy NG, Noshay JM, Galli M, Mejía-Guerra MK, Colomé-Tatché M, Johannes F, Rowley MJ, Corces VG, Zhai J, Scanlon MJ, Buckler ES, Gallavotti A, Springer NM, Schmitz RJ‡, Zhang X‡. (2019) Widespread long-range cis-regulatory elements in the maize genome. Nature Plants Dekker JD*, Baracho GV*, Zhu Z, Ippolito GC, Schmitz RJ, Rickert RC, Tucker HO. (2019) Loss of the FOXP1 Transcription Factor Leads to Deregulation of B Lymphocyte Development and Function at Multiple Stages. Immuno Horizons Drinnenberg IA‡, Berger F‡, Elsässer SJ, Andersen PR, Ausió J, Bickmore WA, Blackwell AR, Erwin DH, Gahan JM, Gaut BS, Harvey ZH, Henikoff S, Kao JY, Kurdistani SK, Lemos B, Levine MT, Luger K, Malik HS, Martín-Durán JM, Peichel CL, Renfree MB, Rutowicz K, Sarkies P, Schmitz RJ, Technau U, Thornton JW, Warnecke T, Wolfe KH. (2019) EvoChromo: towards a synthesis of chromatin biology and evolution. Development Ding Y, Murphy KM, Poretsky E, Mafu S, Yang B, Char SN, Christensen SA, Saldivar E, Wu M, Wang Q, Ji L, Schmitz RJ, Kremling KA, Buckler ES, Shen Z, Briggs SP, Bohlmann J, Sher A, Castro-Falcon G, Hughes CC, Huffaker A, Zerbe P, Schmelz EA. (2019) Multiple genes recruited from hormone pathways partition maize diterpenoid defences. Nature Plants Noshay JM, Anderson SN, Zhou P, Ji L, Ricci W, Lu Z, Stitzer MC, Crisp PA, Hirsch CN, Zhang X, Schmitz RJ, Springer NM. (2019) Monitoring the interplay between transposable element families and DNA methylation in maize. PLoS Genetics Ji L, Mathioni SM, Johnson S, Tucker D, Bewick AJ, Kim KD, Daron J, Slotkin KR, Jackson SA, Parrott WA, Meyers BC‡, Schmitz RJ‡. (2019) Genome-wide reinforcement of DNA methylation occurs during somatic embryogenesis in soybean. Plant Cell Zander M, Willige BC, He Y, Nguyen TA, Langford AE, Nehring R, Howell E, McGrath R, Bartlett A, Castanon R, Nerd JR, Chen H, Zhang Z, Jupe F, Stepanowa A, Schmitz RJ, Lewsey M, Chory J, Ecker JR. (2019) Epigenetic silencing of a multifunctional plant stress regulator. eLIFE Wendte JM*, Zhang Y*, Ji L*, Shi X, Hazarika RR, Shahryary Y, Johannes F, Schmitz RJ. (2019) Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation. eLIFE Schmitz RJ, Lewis ZA, Goll MG. (2019) DNA Methylation: Shared and Divergent Features across Eukaryotes. Trends in Genetics Riley LA, Ji L, Schmitz RJ, Westpheling J, Guss AM. (2019) Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction-modification systems. Journal of Industrial Microbiology & Biotechnology Bewick AJ‡, Zhang Y, Wendte JM, Zhang X, Schmitz RJ‡. (2019) Evolutionary and Experimental Loss of Gene Body Methylation and Its Consequence to Gene Expression. G3 - Genes Genomes Genetics Argueso CT, Assman SM, Birnbaum K, Chen S, Dinneny J, Doherty CJ, Eveland AL, Friesner J, Greenlee VR, Law JA, Marshall-Colon A, Alex Mason G, O’Lexy R, Peck S, Schmitz RJ, Song L, Stern D, Varagona MJ, Walley JW, Williams CM. (2019) Directions for research and training in plant omics: Big questions and big data. Plant Direct Bewick AJ‡, Hofmeister BT, Powers R, Mondo S, James TY, Stajich JE, Schmitz RJ‡. (2019) Diversity of cytosine methylation across the fungi tree of life. Nature Ecology & Evolution Johannes F and Schmitz RJ (2019) Spontaneous epimutations in plants. New Phytologist Bewick AJ, Sanchez Z, McKinney EC, Moore AJ, Moore PJ‡, Schmitz RJ‡ (2019) Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus. Epigenetics & Chromatin Cunningham CB, Ji L, McKinney EC, Benowitz KM, Schmitz RJ, Moore AJ (2019) Changes Of Gene Expression But Not Cytosine Methylation Are Associated With Behavioural Plasticity Of Parental Care. J Exp Biol Galli M, Khakhar A, Chen Z, Lu Z, Sen S, Joshi T, Nemhauser JL, Schmitz RJ, Gallavotti A. (2018) The DNA binding landscape of the maize auxin response factor family. Nature Communications Lee BH, Weber ZT, Zourelidou M, Hofmeister BT, Schmitz RJ, Schwechheimer C, Dobrista AA (2018) Arabidopsis protein kinase D6PKL3 is involved in formation of distinct plasma-membrane aperture domains on the pollen surface. Plant Cell Rajshekar S, Yao J, Arnold PK, Payne SG, Zhang Y, Bowman TV, Schmitz RJ, Edwards JR, Goll MG (2018) Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome. eLIFE Volden R, Palmer T, Byrne A, Cole C, Schmitz RJ, Green RE, Vollmers C (2018) R2C2: Improving nanopore read accuracy enables the sequencing of highly-multiplexed full-length single-cell cDNA. Proc Natl Acad Sci Lu Z, Ricci W, Schmitz RJ, Zhang X. (2018) Identification of Cis-regulatory Elements by Chromatin Structure. Current Opinions in Plant Biology Finnegan JE, Ford B, Wallace X, Pettolino F, Griffin PT, Schmitz RJ, Zhang P, Barrero JM, Hayden M, Boden S, Cavanagh C, Swain S, Trevaskis B. (2018) Zebularine treatment is associated with deletion of FT-B1 leading to an increase in spikelet number in bread wheat. Plant Cell & Environment Fallon TR, Lower SE, Chang C, Manabu BU, Martin GJ, Bewick AJ, Behringer M, Debat HJ, Wong I, Dad JC, Suvorov A, Silva CJ, Hall DW, Schmitz RJ, Nelson DR, Lewis S, Shigenobu S, Bybee SM, Larracuente AM, Oba Y, Weng JK. (2018) Firefly genomes illuminate the origin and evolution of bioluminescence. eLIFE Hofmeister BT and Schmitz RJ (2018) Enhanced JBrowse plugins for epigenomics data visualization. BMC Bioinformatics 19:159 Wendte JM and Schmitz RJ (2018) Specification of pathways targeting heterochromatin modifications in plants. Molecular Plant 11 (3), 381-387 Hofmeister BT, Lee K, Rohr NA, Hall DW, Schmitz RJ (2017) Stable inheritance of DNA methylation allows creation of epigenotype maps and the study of epiallele inheritance patterns in the absence of genetic variation. Genome Biology Jun 18:155 Stathopoulou A, Chhetri J, Esteve P, Ambrose J, Ji L, Edjument-Bromage H, Zhang G, Neubert T, Herrero J, Pradhan S, Schmitz RJ, Ooi STK (2017) A novel requirement for Drosha in maintenance of mammalian CG methylation. Nucleic Acids Research gkx695 Ji L*, Jordan WT*, Shi X, Hu L, He C, Schmitz RJ (2018) TET-mediated epimutagenesis of the Arabidopsis thaliana methylome. Nature Communications March;9(895) Springer NM and Schmitz RJ (2017) Exploiting induced and natural epigenetic variation for crop improvement. Nature Reviews in Genetics July(18):563–575 Susek K, Braszewska-Zalewska A, Bewick AJ, Hasterok R, Schmitz RJ, Naganowska B. (2017) Epigenomic diversication within the genus Lupinus. PLOS ONE June:e0179821 Mondo SJ, Dannebaum RO, Kuo RC, Louie KB, Bewick AJ, LaButti K, Haridas S, Kuo A, Salamov A, Ahrendt SR, Lau R, Bowen BP, Lipzen A, Sullivan W, Andreopoulos WB, Clum A, Lindquist E, Daum C, Northen TR, Ramamoorthy G, Schmitz RJ, Gryganskyi A, Culley D, Magnuson J, James TY, O’Malley MA, Stajich JE, Spatafora JW, Visel A, Grigoriev IV. (2017) Pervasive Adenine N6-methylation of Active Genes in Fungi. Nature Genetics 49:964-968 Bewick AJ, Niederhuth CE, Rohr NA, Griffin PT, Leebens-Mack J, Schmitz RJ (2017) The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants. Genome Biology (in press) Bewick AJ and Schmitz RJ. (2017) Gene body DNA methylation in plants. Current Opinion in Plant Biology Apr;36:103-110 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 gkw1179 Bewick AJ, Vogel KJ, Moore AJ, Schmitz RJ (2017) Sociality and DNA methylation are not evolutionary dependent. Molecular Biology and Evolution 34(3):654-665 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 214:808-819 Niederhuth CE and Schmitz RJ (2017) Putting methylation in context: from genomes to gene expression in plants. Biochemica et Biophysica Acta Jan;1860(1):149-156 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 methylation. Genome 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 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. Genome Biology 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 mutase. Front. 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 genome. PLOS ONE. Aug;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 Arabidopsis. PLoS 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 Complex. Developmental 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 genomes. Molecular 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 population. Genome 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 flowering. Plant 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.
