Nathan Springer
Principal Investigator

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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.


Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions

Variation and Inheritance of Small RNAs in Maize Inbreds and F1 Hybrids

Monitoring the interplay between transposable element families and DNA methylation in maize

Challenges of Translating Gene Regulatory Information into Agronomic Improvements

Dynamic patterns of transcript abundance of transposable element families in maize

Opportunities to Use DNA Methylation to Distil Functional Elements in Large Crop Genomes

Transposable elements contribute to dynamic genome content in maize

Classifying coldā€stress responses of inbred maize seedlings using RGB imaging

The maize W22 genome provides a foundation for functional genomics and transposon biology

Potential roles for transposable elements in creating imprinted expression

Subtle Perturbations of the Maize Methylome Reveal Genes and Transposons Silenced by Chromomethylase or RNA-Directed DNA Methylation Pathways

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture

Natural variation for gene expression responses to abiotic stress in maize

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

Genomic limitations to RNA sequencing expression profiling

Genetic Perturbation of the Maize Methylome