Chapter 7 - From Micronucleus to Macronucleus: Programmed DNA Rearrangement Processes in Ciliates Are Regulated Epigenetically by Small and Long Noncoding RNA Molecules

Abstract

During the last decade, more and more developmental processes regulated by diverse noncoding RNA (ncRNA) molecules have been described. During development of a new macronucleus in ciliates, unicellular eukaryotes, extensive genome rearrangement processes (including amplification, elimination, and fragmentation, as well as reordering of DNA sequences) have been shown to be regulated by processes involving different ncRNA molecules. Small RNAs target sequences for specific developmental fates (eg, elimination, a process strongly resembling RNA-induced gene silencing), while long ncRNA molecules in some ciliate species guide reorganization of DNA sequences into new orders and act as templates correcting mistakes arising during the process of DNA reorganization. The nuclear organization of different ciliate classes reflects different adaptations of these regulation mechanisms showing the power of ncRNAs in genome evolution. In this chapter, macronuclear development of two distantly related ciliate classes is discussed with focus on similarities and differences in the regulating mechanisms involved in differentiating new macronuclei in these ciliate classes.