RNA-Mediated Programming of Developmental Genome Rearrangements in Paramecium tetraurelia

Abstract

The germ line genome of ciliates is extensively rearranged during development of the somatic macronucleus. Numerous sequences are eliminated, while others are amplified to a high ploidy level. In the Paramecium aurelia group of species, transformation of the maternal macronucleus with transgenes at high copy numbers can induce the deletion of homologous genes in sexual progeny, when a new macronucleus develops from the wild-type germ line. We show that this trans-nuclear effect correlates with homology-dependent silencing of maternal genes before autogamy and with the accumulation of ϳ22-to 23-nucleotide (nt) RNA molecules. The same effects are induced by feeding cells before meiosis with bacteria containing double-stranded RNA, suggesting that small interfering RNA-like molecules can target deletions. Furthermore, experimentally induced macronuclear deletions are spontaneously reproduced in subsequent sexual generations, and reintroduction of the missing gene into the variant macronucleus restores developmental amplification in sexual progeny. We discuss the possible roles of the ϳ22-to 23-nt RNAs in the targeting of deletions and the implications for the RNA-mediated genome-scanning process that is thought to determine developmentally regulated rearrangements in ciliates.

RNA-mediated epigenetic regulation of DNA copy number

“…Furthermore, the effect of RNA injection on chromosome copy number is not dependent on the type of DNA rearrangement during chromosomal maturation, influencing both scrambled and nonscrambled genes. A previous observation in Paramecium noted that the presence of siRNA during conjugation leads to local DNA deletions within the targeted region (33). This is consistent with a "scan-RNA" model proposed for Paramecium and Tetrahymena (34,35) wherein injected siRNA cause degradation of homologous maternal transcripts, which subsequently are unable to sequester the germline scan RNAs, resulting in deletion of corresponding DNA in the developing nucleus.…”

On the origin and functions of RNA-mediated silencing: from protists to man

“…RNAi has also been implicated in the programmed excision of excess DNA in ciliated protozoa such as T. thermophila and P. tetraurelia (Garnier et al 2004;Mochizuki and Gorovsky 2005;Nowacki et al 2005;Yao and Chao 2005). This process requires small RNAs, termed scan RNAs, and components of the RNA machinery that direct H3K9 methylation of the chromatin associated with the sequences to be deleted (Garnier et al 2004;Liu et al 2004b;Mochizuki and Gorovsky 2005;Yao and Chao 2005).…”

“…This process requires small RNAs, termed scan RNAs, and components of the RNA machinery that direct H3K9 methylation of the chromatin associated with the sequences to be deleted (Garnier et al 2004;Liu et al 2004b;Mochizuki and Gorovsky 2005;Yao and Chao 2005). Many of the eliminated sequences appear to be derived from transposons (Lee and Collins 2006;Yao and Chao 2005) and RNA-mediated DNA elimination may have evolved as an extension of the role of the RNAi machinery in the transcriptional silencing of transposon/repetitive sequences.…”

RNA meets chromatin

“…Recently, important molecular insights have been gained into the process of DNA elimination in ciliates by demonstrating that this remarkable genomic-downsizing process is also mediated by an RNAi-like mechanism (Mochizuki et al 2002;Yao et al 2003;Garnier et al 2004). Pivotal to these findings was the discovery of a remarkably abundant population of small (28-nt) RNAs specifically expressed during the conjugation pathway prior to the timing of large-scale DNA elimination (Mochizuki et al 2002).…”