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Phone: (612) 625-1234
Fax: (612) 625-1738

Department of Plant Biology
University of Minnesota
250 Biological Science Center
1445 Gortner Ave.
St. Paul, MN 55108

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Nathan M. Springer

Associate Professor, Department of Plant Biology
Ph.D. University of Minnesota, 2000

Epigenetic mechanisms of gene expression, interspecific variation in genome structure and gene expression

Contact Information

Mailing Address:

Dr. Nathan M. Springer
Department of Plant Biology
University of Minnesota
250 Biological Science Center
1445 Gortner Ave.
St. Paul, MN 55108

Office: 306 Biological Sciences Center
Phone: (612) 624-6241
Fax: (612) 625-1738
E-mail: springer@umn.edu
Web Site: Springer Lab

Research Interests

I am very interested in understanding the sources of heritable phenotypic variation within a species. Phenotypic variation within a species can be harnessed by plant breeding efforts and also plays a role in heterosis. My lab focuses on studying the genetic and epigenetic mechanisms that lead to variation in gene expression levels. Genetic changes can lead to altered gene expression through variation in cis-acting or trans-acting factors. Epigenetic mechanisms of gene regulation are not based on sequence specific regulation. The molecular basis of epigenetic regulation occurs through the modification of chromatin states, such as DNA methylation or histone modifications. One project in my lab involves the use of microarrays and allele-specific expression analysis to study the prevalence and causes of differential expression in different maize inbreds. By studying gene expression levels in different maize inbreds we have identified genes that have altered expression. Comparisons of the expression patterns of the two alleles in heterozygous individuals reveals whether the altered expression is likely due to altered cis-regulatory factors or trans-acting factors. We are currently extending this work to additional tissues and genotypes to characterize the expression diversity of maize. In addition, experiments are underway to characterize the actual sequence changes responsible for altered expression levels. Another project focuses on understanding imprinted gene expression. Imprinting is an example of epigenetic regulation in which the expression of a gene is dependant upon the parent of origin. In maize, several genes are imprinted such that only the maternal allele of the gene is expressed. We are studying the molecular basis of this process in an attempt to define the cis- and trans-acting factors that are required to establish, maintain and interpret imprinting. As a member of the Functional Genomics of Maize Chromatin project we are using RNAi lines to identify chromatin genes that are required to maintain imprinted gene expression patterns. Recent work has focused on characterizing differential DNA and histone methylation near the promoter of the imprinted gene Mez1. DNA methylation is commonly associated with epigenetic changes. Several other studies in the lab have focused on characterizing the genes involved in maintaining DNA methylation in maize. Microarray profiling has been utilized to identify the functional targets of CpNpG methylation in maize. We have found evidence that the presence of certain "epialleles" often varies within a species such that the targets of methylation vary from one inbred line to another. Future work in my lab will continue to study the sources of expression variation in maize. Specifically, I would like to know the contribution of epigenetics to expression variation and semi-heritable phenotypic diversity. In addition, I am interested in understanding how the complex arrangement of genes and transposons in the maize genome affects the expression level of genes.

Selected Publications

Stupar RM, Hermanson PJ, Springer NM. (2007) Non-additive expression and parent-of-origin effects in maize endosperm. Plant Physiology. In press.

Springer NM, Stupar RM. (2007) Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize. Plant Cell. In press.

Makarevitch I, Stupar RM, Iniguez AL, Haun WJ, Barbazuk WB, Kaeppler SM, Springer NM. (2007) Natural Variation for Alleles Under Epigenetic Control by the Maize Chromomethylase Zmet2. Genetics.

McGinnis K, Murphy N, Carlson AR, Akula A, Akula C, Basinger H, Carlson M, Hermanson P, Kovacevic N, McGill MA, Seshadri V, Yoyokie J, Cone K, Kaeppler HF, Kaeppler SM, Springer NM. (2007) Assessing the efficiency of RNA interference for maize functional genomics. Plant Physiol. 143: 1441-1451.

Springer NM, Stupar RM. (2007) Allelic variation and heterosis in maize: how do two halves make more than a whole? Genome Res. 17: 264-275.

Haun WJ, Laoueille-Duprat S, O'connell MJ, Spillane C, Grossniklaus U, Phillips AR, Kaeppler SM, Springer NM. (2007) Genomic imprinting, methylation and molecular evolution of maize Enhancer of zeste (Mez) homologs. Plant J. 49: 325-337.

Stupar RM, Springer NM (2006) Cis-transcriptional variation in maize inbred lines B73 and Mo17 lead to additive expression patterns in the F1 hybrid.   Genetics 2006 May 15.

Springer N.M., Kaeppler SM. (2005) Evolutionary Divergence of Monocot and Dicot Methyl-CpG-Binding Domain Proteins. Plant Physiol. 138(1):92-104.

Till B.J., S.H. Reynolds, C. Weil, N.M. Springer, C. Burtner, C.A. Codomo, L.C. Enns, A.R. Odden, K. Young, E. Bowers, E.A. Greene, L. Comai, S. Henikoff. (2004). Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol. 4(1):12.

McGinnis K, Chandler VL, Cone K, Kaeppler HF, Kaeppler SM, Kerschen A, Pikaard C, Richards E, Sidorenko L, Smith T, Springer NM, Wulan T (2005) Transgene-induced RNA interference as a Tool for Plant Functional Genomics. In RNA Interference Methods in Enzymology eds. John Rossi and David Engelke. Methods Enzymol. 392:1-24.

Springer N.M.,Xu, X., B. Barbuzuk. (2004). Utility of different gene-enrichment approaches towards identifying and sequencing the maize gene space. Plant Physiol. 136(2):3023-3033.

Springer N.M., C.A. Napoli, D.A. Selinger, R. Pandey, K.C. Cone, V.L. Chandler, H.F. Kaeppler, S.M. Kaeppler. (2003). Comparative Analysis of SET Domain Proteins in Maize and Arabidopsis Reveals Multiple Duplications Preceding the Divergence of Monocots and Dicots. Plant Physiol. 132:907-925.

Springer, N.M., O. Danilevskaya, P. Hermon, T. Helentjaris, R.L. Phillips, H.F. Kaeppler, S.M. Kaeppler. (2002). Sequence Relationships, Conserved Domains, and Expression Patterns for Zea mays Homologs of the Drosophila Polycomb Group Genes E(z), esc, and E(Pc). Plant Phys. 128:1332-1345.

Papa, C.M., N.M. Springer, M.G. Muszynski, R. Meeley, and S.M. Kaeppler. (2001). Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation. Plant Cell 13: 1919-1928.

Cao, X, N.M. Springer, M.G. Muszynski, R.L. Phillips, S. Kaeppler, and S.E. Jacobsen. (2000). Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc. Natl. Acad. Sci. 9:4979-4984.