van Nocker lab

390 Plant and Soil Sciences

Michigan State University




Research Interests - Plant Developmental Genetics

What are the underlying genetic mechanisms that determine plant form, and how are these controlled? What are the key genes that influence agriculturally important traits such as flowering?  What parallels exist between plant and human development, and can studies in plants shed light on issues such as cancer and stem cell biology?

Current Projects:

Exploiting chromatin landmarks to characterize complex plant genomes. Progress is the science of genomics is no longer limited by the technologies that obtain genomic DNA sequence, but rather by the ability to interpret this information and uncover biologically relevant features of the genome.  In addition, DNA sequence is only one component of the information content of the genome.  Additional information - called epigenetic information - is encoded partly by the proteinaceous matrix called chromatin in which the DNA is packaged.  Specific modifications to the histone proteins, which make up the bulk of chromatin, are closely associated with the characteristics of the genes to which they are affixed.  The objective of this project is to evaluate novel approaches to facilitate sequence analysis of gene-rich regions in plants with complex genomes, identify chromatin landmarks useful for genome annotation, and identify polymorphic sequences most useful for genetic map construction, utilizing a wild apple species as a reference.  The project is expected to help uncover how epigenetic information is linked to gene activity, add accuracy to annotation efforts, and uncover cryptic and previously unanticipated features of the genome. (MORE INFO)

Transcriptional memory and epigenetic mechanisms. As an organism develops, cells may proliferate to maintain a pool of stem cells, or differentiate to form specialized tissues. We are studying the mechanisms by which states of gene activity are propagated within and across mitotic boundaries, specifically in relation to chromatin-associated proteins and modifications of DNA and histones at specific genetic sites. In Arabidopsis, we identified a class of protein required for maintaining transcriptional activity of a subset of developmental regulatory genes by counteracting the repressive activity of the so-called Polycomb-group proteins. As part of this project, we recently published the first genome-wide map of transcriptional-activating chromatin modifications in a plant genome (Oh et al 2008). This project also involves gene mapping and cloning, identification of unknown, related proteins through purification and mass spectrometry.

Flowering. Plants have evolved an enormous diversity of strategies to flower at the time of year best suited to their reproduction. Most have intricate mechanisms to perceive daylength and temperature, which are superimposed onto an endogenous flowering program. We are using genetic and molecular techniques to elucidate the networks of gene expression involved in triggering flowering in plants, using Arabidopsis as a model. We are focusing on vernalization (acceleration of flowering by cold) which, in Arabidopsis, results in the downregulation of the FLC/MAF family of MADS-box flowering-inhibitor genes. This project involves genetic screens, mapping, gene cloning, and analyses of genetic interactions. For more information on the genetic mechanisms of flowering, see our review (van Nocker and Ek-Ramos 2004).

Juvenility. Higher plants, like people, transition through a juvenile phase before attaining adulthood. Juvenility is possibly the single most important factor limiting rapid development of new and superior cultivars of woody plants including tree fruits and nuts, and the general nature of phase change is also among the most intriguing and longstanding questions in plant biology. Through exhaustive genome-wide ChIP-seq and RNA-seq experiments, we have linked phase-dependent transcriptional switches with locus-specific chromatin transitions. This knowledge may be employed for the engineering of rapid-cycling genotypes for more efficient breeding.

Selected Recent Publications:

Assistantships may be available for PhD graduate students for the projects below through the Program in Genetics, Cell and Molecular Biology, Plant Breeding/Genetics/Biotechnology, or Horticulture

To facilitate application, first send an email describing interests, goals and background to Steve van Nocker (