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Nathan M. Springer

McKnight Presidential Endowed Professor


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Research Interests

As a geneticist, I seek to understand the basis for heritable variation within a species. My group uses a combination of classical genetics, molecular genetics and genomics approaches to study molecular variation and inheritance in maize. Maize is one of the most important crop plants and also provides a strong model system for studying genetic variation. The maize genome is has a complex organization of genes and transposons and has high levels of variation among different individuals.

Heritable variation within a species can include DNA sequence changes that affect the quality of gene products, DNA sequence changes that influence expression levels of genes or epigenetic variation that can influence expression levels without requiring DNA sequence changes. My lab focuses on studying the genetic and epigenetic mechanisms that lead to variation in gene expression levels. Many of our current studies are focused on how genetic variation, such as transposon insertions, and epigenetic variation influences chromatin modifications such as DNA methylation. We utilize genomic technologies to profile the epigenome of maize in different genotypes, tissue or environmental conditions to understand the factors that influence variation in chromatin modifications.

The members of my lab have active research projects studying the epigenome, transcriptome or genome of maize. We are interested in understanding how variation in chromatin, gene expression or genetic content leads to changes in phenotype. By improving our understanding of how the heritable information in the genome leads to altered phenotype we hope to enable crop improvement. My group also studies how transposons contribute to regulatory variation in maize, the prevalence and consequences of structural variation including copy number variation (CNV) and presence-absence variation (PAV) and how heritable variation contributes to heterosis in maize.

Selected Publications

Han Z, Crisp PA, Stelpflug SA, Kaeppler SM, Li Q, Springer NM. (2018) Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture. Genetics, doi: 10.1534/genetics.118.300987 

Anderson SN, Zynda G, Song J, Han Z, Vaughn M, Li Q, Springer NM. (2018) Subtle perturbations of the maize methylome reveal genes and transposons silenced by DNA methylation. G3 (Bethesda). 8(6):1921-1932 

Springer NM, Schmitz RJ. (2017) Exploiting induced and natural epigenetic variation for crop improvement. Nat Rev Genet. 18(9):563-575. 

Waters AJ, Makarevitch I, Noshay J, Burghardt LT, Hirsch CN, Hirsch CD, Springer NM. (2017) Natural variation for gene expression responses to abiotic stress in maize. Plant J. 89(4):706-717

Springer NM, Lisch D, Li Q (2016) Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes. Plant Cell 28:314-325. 

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 USA. 112(47):14728-33. 

Makarevitch I, Waters AJ, West PT, Stitzer M, Ross-Ibarra J, Springer NM. 2015. Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genetics 11:e1004915. 

Li Q, Eichten SR, Hermanson PJ, Zaunbrecher V, Song J, Wendt J, Rosenbaum H, Madzima TF, Sloan AE, Huang J, Burgess D, Richman TA, Kaeppler SM, McGinnis KM, Meeley RB, Danilevskaya ON, Vaughn MW, Jeddeloh JA, Springer NM. 2014. Genetic perturbation of the maize methylome. Plant Cell 26:4602-4616. 

Waters AJ, Bilinski P, Eichten SR, Vaughn MW, Ross-Ibarra J, Gehring M, Springer NM. 2013. Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species. Proc Natl Acad Sci USA 110(48):19639-44. 

Eichten SR, Briskine R, Song J, Li Q, Swanson-Wagner R, Hermanson PJ, Waters AJ, Starr E, West PT, Tiffin P, Myers CL, Vaughn MW, Springer NM. 2013. Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell 25:2783-2797. 

Swanson-Wagner RA, Briskine R, Schaefer R, Hufford MB, Ross-Ibarra J, Myers CL, Tiffin P, Springer NM. 2012. Reshaping of the maize transcriptome by domestication. Proc Natl Acad Sci USA, 109(29):11878-11883. 

Eichten SR, Ellis NA, Makarevtich I, Yeh C-T, Gent JI, Guo L, McGinnis KM, Zhang X, Schnable PS, Vaughn MW, Dawe RK, Springer NM. 2012. Spreading of heterochromatin is limited to specific families of maize retrotransposons. PLoS Genet 8(12): e1003127. 

  • BS 1997; Biology Major, Southeast Missouri State University 
  • PhD 2000; Plant Biology, University of Minnesota 
  • Post-doc 2000-2004; University of Wisconsin-Madison 
Office: 612-624-6241 Lab: 612-624-6163

Office: 306 Biological Sciences Lab: 313 Biological Sciences
1445 Gortner Avenue
St. Paul, MN 55108