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.
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 U S A. 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(8):2783-97
Eichten SR, Ellis NA, Makarevitch I, Yeh CT, 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.
Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh CT, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM. 2011. Heritable epigenetic variation among maize inbreds. PLoS Genet. 7:e1002372.
Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM. 2010. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Res. 20:1689-99.
Springer NM, Ying K, Fu Y, Ji T, Yeh C-T, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, Iniguez AL, Barbazuk WB, Jeddeloh JA, Nettleton D, Schnable PS. 2009. Maize Inbreds Exhibit High Levels of CNV and Presence/Absence Differences in Genome Content. PLoS Genetics 5(11): e1000734.
Stupar RM, Springer NM. 2006. Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid. Genetics 173:2199-2210.