Robert J. Schmitz

Robert J. Schmitz is plant biologist and epigenomicist at the University of Georgia where he studies the generation and phenotypic consequences of plant epialleles as well as developing new techniques to identify and study cis-regulatory sequences. He is an associate professor in the department of genetics and the UGA Foundation Endowed Pant Sciences Professor.[1]

Prof.

Robert J. Schmitz

PhD
Born1980
CitizenshipUnited States
EducationSalk Institute
Alma materUniversity of Arizona, University of Wisconsin, Madison
Known forCreating epigenetic recombinant inbred lines.
Scientific career
FieldsGenomics, Epigenetics, Plant Biology
InstitutionsUniversity of Georgia
ThesisVernalization : a model for investigating epigenetics and eukaryotic gene regulation in Arabidopsis thaliana (2007)
Doctoral advisorRichard Amasino
Other academic advisorsJoseph R. Ecker
Websiteschmitzlab.genetics.uga.edu

Education and Career

Schmitz attended the University of Arizona for his bachelors and the University of Wisconsin for his PhD.[2] As a PhD student he worked in the lab of Richard Amasino studying the role of epigenetic modifications on vernalization in Arabidopsis thaliana. He graduated from Wisconsin in 2007.[1] From 2007 to 2013 he was a postdoctoral scholar with Joe Ecker at the Salk Institute. In 2013 he was hired as an assistant professor in the Department of Genetics at the University of Georgia-Athens where he continues to work as an associate professor and director of the Georgia Genomics & Bioinformatics Core.[1]

Research

Postdoctoral Research

As a postdoc Schmitz developed technologies for determining the methylation status of individual cytosines in plant genomes using sequencing technologies, and used them to quantify how methylation patterned varied across different individuals of the same species.[3][4] He used the same technology to map segregating differentially methylated regions in recombinant inbred populations of soybean, finding underlying genetic haplotype did not consistently predict which parent's methylation state would be observed in a given genotype.[5] He demonstrated that the loss of Chromomethylase 3, a plant methyltransferase abolishes gene body methylation and that this loss has occurred repeatedly in wild plant species. [6]

Linking Epigenetics to Phenotype

His research group is working to use epigenetic variation to modify the phenotype of plants. They work with naturally occurring epimutations but have also developed sets of epi-RILs which have identical DNA but different DNA methylation.[1][7] By using an enzyme from humans, they can remove the methylation from specifically targeted genes in plants, waking up genes which have been long dormant in the genome.[8][9]

Discovering Cisregulatory Sequences

He is also working to apply epigenome profiling to the discovery of noncoding regulatory sequences in different plant species.[1] His lab identified cis-regulatory elements in maize that control the expression of genes that are located long distances away in the genome.[10] They combine ATAC-seq with fluorescence-activated nuclei sorting to identify the locations of open chromatin regions and transcription factor binding sites in plant genomes.[11]

Recognition
  • Pew Biomedical Scholar (2015)[3]
  • Hans Fischer Fellow, Technical University of Munich (2018)[12]
gollark: ```haskellshare [mkPersist sqlSettings, mkMigrate "migrateAll"] [persistLowerCase|User json username Text password Text Username username deriving Show Generic EqPaste json poster UserId name Text content Text type PasteType PasteNamePoster name poster deriving Show Generic Eq|]```This is nice though.
gollark: Main file is 176 lines (API.hs).
gollark: https://osmarks.tk/git/osmarks/pastecanPastebin clone, quite long.
gollark: Though Persistent *is* very terse.
gollark: I doubt you'd also get actual DB access.

References
  1. https://www.genetics.uga.edu/directory/bob-schmitz
  2. https://news.uga.edu/bob-schmitz/
  3. https://www.pewtrusts.org/es/projects/pew-biomedical-scholars/directory-of-pew-scholars/2015/robert-schmitz
  4. Schmitz, Robert J.; Schultz, Matthew D.; Urich, Mark A.; Nery, Joseph R.; Pelizzola, Mattia; Libiger, Ondrej; Alix, Andrew; McCosh, Richard B.; Chen, Huaming; Schork, Nicholas J.; Ecker, Joseph R. (2013). "Patterns of population epigenomic diversity". Nature. 495 (7440): 193–198. Bibcode:2013Natur.495..193S. doi:10.1038/nature11968. PMC 3798000. PMID 23467092.
  5. Schmitz, R. J.; He, Y.; Valdes-Lopez, O.; Khan, S. M.; Joshi, T.; Urich, M. A.; Nery, J. R.; Diers, B.; Xu, D.; Stacey, G.; Ecker, J. R. (2013). "Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population". Genome Research. 23 (10): 1663–1674. doi:10.1101/gr.152538.112. PMC 3787263. PMID 23739894.
  6. Bewick, Adam J.; Ji, Lexiang; Niederhuth, Chad E.; Willing, Eva-Maria; Hofmeister, Brigitte T.; Shi, Xiuling; Wang, Li; Lu, Zefu; Rohr, Nicholas A.; Hartwig, Benjamin; Kiefer, Christiane; Deal, Roger B.; Schmutz, Jeremy; Grimwood, Jane; Stroud, Hume; Jacobsen, Steven E.; Schneeberger, Korbinian; Zhang, Xiaoyu; Schmitz, Robert J. (2016). "On the origin and evolutionary consequences of gene body DNA methylation". Proceedings of the National Academy of Sciences. 113 (32): 9111–9116. doi:10.1073/pnas.1604666113. PMC 4987809. PMID 27457936.
  7. Hofmeister, Brigitte T.; Lee, Kevin; Rohr, Nicholas A.; Hall, David W.; Schmitz, Robert J. (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. 18 (1): 155. doi:10.1186/s13059-017-1288-x. PMC 5559844. PMID 28814343.
  8. https://news.uga.edu/uga-researchers-develop-new-method-improve-crops/
  9. Ji, Lexiang; Jordan, William T.; Shi, Xiuling; Hu, Lulu; He, Chuan; Schmitz, Robert J. (2018). "TET-mediated epimutagenesis of the Arabidopsis thaliana methylome". Nature Communications. 9 (1): 895. Bibcode:2018NatCo...9..895J. doi:10.1038/s41467-018-03289-7. PMC 5832761. PMID 29497035.
  10. Ricci, William A.; Lu, Zefu; Ji, Lexiang; Marand, Alexandre P.; Ethridge, Christina L.; Murphy, Nathalie G.; Noshay, Jaclyn M.; Galli, Mary; Mejía-Guerra, María Katherine; Colomé-Tatché, Maria; Johannes, Frank; Rowley, M. Jordan; Corces, Victor G.; Zhai, Jixian; Scanlon, Michael J.; Buckler, Edward S.; Gallavotti, Andrea; Springer, Nathan M.; Schmitz, Robert J.; Zhang, Xiaoyu (2019). "Widespread long-range cis-regulatory elements in the maize genome". Nature Plants. 5 (12): 1237–1249. doi:10.1038/s41477-019-0547-0. PMC 6904520. PMID 31740773.
  11. Lu, Zefu; Hofmeister, Brigitte T.; Vollmers, Christopher; Dubois, Rebecca M.; Schmitz, Robert J. (2017). "Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes". Nucleic Acids Research. 45 (6): e41. doi:10.1093/nar/gkw1179. PMC 5389718. PMID 27903897.
  12. https://www.ias.tum.de/active-fellows/schmitz-robert-j/
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