EAGER: Developing Oxytricha Trifallax as a Model System for Small RNA Biogenesis and Function

University Of California-Santa Cruz, Santa Cruz CA

Investigators

Abstract

Intellectual Merit: This project addresses how the organization of genes is inherited from generation to generation through the action of small RNAs. It involves the study of the genetic organization of an unusual single-celled pond organism, Oxytricha trifallax, which contains two kinds of nuclei where genetic information is held. All gene transcription and activity occurs in the macronucleus. This highly unusual nucleus contains 16,000 different gene-sized chromosomes called nanochromosomes. By contrast, the micronucleus is the nucleus that stores genetic information for the next generation. It has long chromosomes each with thousands of genes. During sexual mating, micronuclei are exchanged between cells (similar to fusion of egg and sperm nuclei in animals), and a new diploid micronucleus is formed. The new micronucleus divides once, and one of its daughters develops into the new macronucleus. The process of macronuclear development involves elimination of 95% of the unique sequences in the micronucleus. Sequences that are eliminated are not only found between genes, but also within the regions destined to become individual nanochromosomes. One fascinating twist in Oxytricha macronuclear development is that for many genes, the pieces that need to be joined to form a nanochromosome occur in a scrambled order. Complex DNA rearrangements are required to unscramble the micronuclear genome, eliminate the unwanted sequences, and paste together what is left into the individual nanochromosomes. This project explores the hypothesis that small RNAs called 27macRNAs, that are derived from sequences in the parental macronucleus and are made only during mating in Oxytricha, play a role in guiding macronuclear development in the next generation. In essence the idea is that the parental macronucleus is providing epigenetic information in the form of these small RNAs to guide which sequences will be present in the macronucleus in the next generation. The goal of the project is to develop the Oxytricha system as a model for understanding how small RNAs are produced and how they affect DNA structure. One unusual aspect of Oxytricha 27macRNA production is that, unlike known small RNA classes in animals, the production of these small RNAs is dramatically induced. Understanding the details of this induction could provide transformative insights to a new aspect of small RNA-mediated regulation. Broader Impacts. The project will support training of both graduate and undergraduate students, in part through collaboration with the NIH-funded UCSC Minority Access to Research Careers (MARC) program for which the PI is director. This project is perfect for introducing undergraduates to the excitement of biochemical and bioinformatics research science.