Below you will find a list of our lab's significant interests. Each one is described briefly and provides a general overview of what we would like to accomplish. If you are interested in learning more about any of the projects affiliated with these research interests please feel free to contact us.
Frequently Asked Questions
- Rb/E2F Pathway: Tissue-specific Gene Expression
The Rb/E2F pathway regulates gene expression in many cell types to mediate the transition from a progenitor state to a stably differentiated fate. Underscoring its importance in tissue homeostasis, this pathway is frequently mutated and inactivated in human tumors. In C. elegans, Rb/E2F represses the progenitor-like germ line fate in terminally differentiated somatic cells, yet also promotes the germline fate within germ cells. However, the mechanisms by which Rb/E2F regulates the correct target genes within the tissue-specific restrictions imposed in vivo are still unknown.
To gain a deeper understanding of how Rb/E2F regulates gene expression in vivo, we developed a system to define DNA binding sites in individual cell types for C. elegans transcription factors in vivo using chromatin immunoprecipitation (ChIP). These data reveal strikingly different behaviors, relationships, and target genes for Rb/E2F in progenitor germline tissue relative to differentiated somatic tissues. We are now endeavoring to understand how histone modifications contribute to differential gene expression in germ line and somatic tissues, and how Rb/E2F interacts with these modifications.
Tissue-Specific Direct Targets of C. Elegans Rb/E2F Dictate Distinct Somatic and Germline Programs
- piRNA Biogenesis
- piRNAs are small noncoding RNAs primarily expressed in the gonad that play an essential role in germ line development and function in maintaining genome integrity in many species. The mechanisms of piRNA biogenesis are distinct from other small RNAs such as miRNAs or siRNAs, and are poorly understood. piRNA loci are clustered in discrete regions of the genome and produce thousands of distinct piRNAs, but a basic understanding of the mechanisms that determine germline-specific expression of piRNAs is lacking. We have identified a transcription factor that preferentially binds to piRNA loci only in the germ line, and promotes piRNA expression. We are now working to identify and characterize other transcriptional regulators that are required for piRNA processing. Ultimately, knowledge of how piRNAs are generated will facilitate our understanding of how piRNAs function in gametogenesis to protect genome integrity and ensure fertility and successful fetal development.
- Fertilization & Early Embryogenesis
An important property of germ cells is to contribute key proteins and RNAs that function during fertilization and early embryogenesis. These complex cell biological events must be precisely coordinated to set the stage for successful development. We conducted a chemical screen to identify agents that disrupt fertilization and/or early embryogenesis in C. elegans, and identified a novel small molecule that causes a diverse array of defects in meiosis and mitosis in just-fertilized oocytes, leading to early embryonic lethality. Notably, this small molecule acts specifically in the germ line and has no effect on somatic tissues.
To better understand its mechanism of action, we conducted a genetic screen for mutants resistant to the small molecule, and isolated several suppressors. We are currently determining the molecular identity of these suppressor genes and investigating specific cellular pathways affected by the chemical.
- Germline-Specific Organelles
In C. elegans, the germ line is set aside within the first few embryonic divisions. As each cell in the embryonic P lineage divides, it produces another P cell that retains germ cell characteristics, and a somatic cell that does not. Within four divisions, the P lineage is completely segregated from all somatic lineages. One feature that distinguishes germ cells from somatic cells is the presence of unique cytoplasmic, RNA-rich, granular organelles, called P granules, whose exact function remains mysterious. P granules are provided maternally and segregate with the P lineage during the initial embryonic divisions. All germ cells born from the P lineage contain P granules (except mature sperm). Several protein components of P granules have been identified, but their contribution to P granule function and germline viability remains unclear.
We have identified two novel, related proteins, called MEG-1 and MEG-2, that localize exclusively to embyonic P granules. MEG-1 and MEG-2 (maternal-effect germ cell-defective) are not found in other cell compartments or on P granules in larvae or adults, yet are required for larval germ cell proliferation and normal P granule morphology. meg-1 has genetic interactions with core components of P granules that suggests that meg-1 and meg-2 are required to regulate certain aspects of P granule function in the early P blastomeres during the time that somatic and germ fates are intermingled. Current efforts in the lab are directed toward defining the exact function of MEG-1 and MEG-2 and dissecting how P granules affect transcript stability in the early embryo.
- Transcription Factors: Systematic Identification of Transcription Factor Binding Sites
For the past five years, we have participated in modENCODE (model organism ENCyclopedia Of DNA Elements), a consortium dedicated to systematic identification of functional elements in the worm and fly genomes. We collaborated with other labs in two projects, one to comprehensively identify transcribed regions and another to identify transcription factor binding sites in the worm genome. We used ChIP-seq to categorize binding sites for over 100 transcription factors, many at more than one stage of development.
Although the modENCODE project has been completed, many more transcription factors remain to be profiled. We are continuing our collaboration with other labs associated with the project to tackle these remaining transcription factors. Our goal is to release these large scale datasets to the research community, thereby facilitating investigation of many different aspects of gene regulation in C. elegans.