Research Interests

The growth and development of eukaryotic organisms is determined by the interactions between their genetic make-up and the environment. At the molecular level this translates into differential gene expression, giving rise to distinctly specialized cells, tissues, and/or organs. Indeed, the complex development of multicellular eukaryotes requires the silencing of many of their genes in different cell types at any given time. Cell and tissue-specific gene inactivation is a characteristic feature of many developmentally regulated genes and is associated with differentiation processes. This gene silencing involves heritable (but reversible) epigenetic mechanisms, in contrast to genetic effects that are based on stable changes at the DNA level. Epigenetic patterns of expression/repression can be altered in response to environmental or physiological signals, repressing genes under conditions where they are not needed and reactivating their expression if internal or external influences change again. Epigenetic mechanisms also play an essential role in defense responses against a variety of intracellular genomic parasites, such as viruses and transposable elements. The long-term goal of our research projects is to understand the molecular basis of these epigenetic phenomena. We are using the unicellular green alga Chlamydomonas reinhardtii and the higher plant Arabidopsis thaliana as model systems to identify and characterize molecular components that determine transcriptional or post-transcriptional gene silencing. We are concentrating on two main areas: RNA-mediated gene silencing and histone modifications associated with euchromatic transcriptional silencing. More recently we have also become interested in the gene regulatory networks that control nonpolar lipid accumulation in microalgae.

RNA-Mediated Gene Silencing

RNA-mediated processes result in suppression of gene expression in eukaryotes, a phenomenon initially termed RNA interference (RNAi) in animals. Double-stranded RNA (dsRNA) appears to be the trigger at the heart of these processes and it can induce, in different eukaryotes, a variety of outcomes such as the degradation of homologous RNAs, translation repression, or heterochromatin formation. The RNAi machinery has also been implicated in the processing and function of microRNAs, a class of endogenous small RNAs that regulate gene expression by translational repression or mRNA cleavage. Despite rapid progress in understanding key steps of these pathways, genetic screens suggest that many factors required for RNAi have not been characterized as yet. We are isolating, by a variety of genetic and functional genomic approaches, mutants defective in RNAi with the purpose of identifying new pathway components as well as characterizing their role(s) in controlling endogenous gene expression. RNA interference is also becoming a valuable tool for loss-of-function high-throughput genomic studies in eukaryotes and for practical applications in animals, plants and algae. Our lab is also involved in the development of effective technical approaches for gene inactivation. Further elucidation of the RNA silencing pathway will likely have an impact not only in basic biology but also in medicine and agriculture.

Histone Modifications Linked to Euchromatic Transcriptional Silencing

In eukaryotes, nuclear DNA is associated with histones and other proteins in a complex structure referred to as chromatin. Histones are subject to multiple post-translational modifications (PTMs), including acetylation, methylation, and phosphorylation. These histone PTMs influence chromatin organization and can regulate many DNA-templated processes such as transcription, replication, recombination, and repair. However, relatively little is known about the role of histone methylation or phosphorylation in the regulation of euchromatic genes in photosynthetic eukaryotes, both during development and in response to changing environmental conditions. Our lab is addressing the molecular mechanisms responsible for methylation and phosphorylation of core histones in Chlamydomonas and Arabidopsis. We are particularly interested in the role of histone phosphorylation in mediating rapid changes in gene expression/repression in response to abiotic stresses such as drought.

Gene Regulatory Networks Controlling Neutral Lipid Accumulation

The great potential of microalgae as feedstocks for renewable biofuel production has recently gained recognition. The environmental conditions that trigger lipid accumulation in algae are under careful investigation. However, the complexity of biological systems, including elaborate networks and mutual dependency of cellular processes, makes it difficult to develop the most efficient strategy for biotechnological improvement via traditional approaches. In particular, the gene regulatory systems of microalgae remain virtually unexplored and, yet, represent an interesting target for pathway engineering leading to improved biofuel production. These systems involve not only transcription factors but also a complex array of small RNAs/microRNAs and other post-transcriptional mechanisms. The main goal of this project is to understand the gene regulatory networks that control lipid accumulation in Chlamydomonas reinhardtii. Our specific objectives are to identify transcription factors and miRNAs involved in gene regulation of metabolic components under nitrogen deprivation (with an emphasis on the control of triacylglycerol biosynthesis and competing pathways) and to model gene regulatory networks integrating miRNAs and, to the extent possible, transcription factors.

Specialization:

• Functional Genomics; Epigenetics; RNA interference; Biotechnology; Renewable Biofuels

Links:

• Bioenergy Systems Summer REU Program

News:

• Study reveals mechanims of plants' drought response
• PNAS paper cites discovery of small RNA 'quality-control' mechanism
• UNL plant researchers publish finding on enzyme, drought connection
• Work on gene-silencing machinery could help fight viral, other diseases