RNA-mediated epigenetic programming of a genome-rearrangement pathway

Abstract

Genome-wide DNA rearrangements occur in many eukaryotes but are most exaggerated in ciliates, making them ideal model systems for epigenetic phenomena. During development of the somatic macronucleus, Oxytricha trifallax destroys 95% of its germ line, severely fragmenting its chromosomes, and then unscrambles hundreds of thousands of remaining fragments by permutation or inversion. Here we demonstrate that DNA or RNA templates can orchestrate these genome rearrangements in Oxytricha, supporting an epigenetic model for sequence-dependent comparison between germline and somatic genomes. A complete RNA cache of the maternal somatic genome may be available at a specific stage during development to provide a template for correct and precise DNA rearrangement. We show the existence of maternal RNA templates that could guide DNA assembly, and that disruption of specific RNA molecules disables rearrangement of the corresponding gene. Injection of artificial templates reprogrammes the DNA rearrangement pathway, suggesting that RNA molecules guide genome rearrangement.Parental RNA transcripts and microRNAs are critical for programming development in metazoa 1-4 , raising the possibility that altered RNA molecules can reprogramme patterning on a developmental or evolutionary timescale 5 . Despite the suggestion of template-directed events involving "an ancestral RNA-sequence cache" 6 there has been limited evidence for a direct role of RNA as a template of information across generations 7,8 . Information transfer from RNA to DNA usually involves polymerization 9 . Here we show that RNA molecules can also organize DNA rearrangements, expanding the epigenetic influence of RNA beyond gene expression and priming or directing DNA and RNA synthesis, editing, modification or repair 9-11 .O. trifallax is a unicellular eukaryote harbouring two kinds of nuclei: germline micronuclei and somatic macronuclei. Diploid micronuclei are transcriptionally inert during vegetative growth but they transmit the germline genome through subsequent generations. Effectively polyploid macronuclei provide all vegetative gene expression, but degrade after fertilization, when new micronuclei and macronuclei develop. DNA differentiation in ciliates such as Oxytricha (also called Sterkiella) involves massive chromosome fragmentation and deletion of transposons and internally eliminated sequences (IESs), accomplishing 95% genome Author Information TEBPα and TEBPβ macronucleus and micronucleus sequences have been submitted to GenBank under accession numbers EU047938-EU047941. Reprints and permissions information is available at www.nature.com/reprints. Correspondence and requests for materials should be addressed to L. RNAi against putative templates disrupts rearrangementTo test the hypothesis that putative maternal RNA templates influence rearrangement, we induced RNA interference (RNAi) to target homologous RNA degradation. Oxytricha cells, before and during conjugation, were fed Escherichia coli producing double stranded RNA fragments of two m...

Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution

“…The second way in which RNAs can affect cell heredity is by guiding, targeting, and assisting in transmitting variations in chromatin structure that are reconstructed and reproduced in daughter cells through the chromatin-marking EIS (Matzke and Birchler 2005;Ekwall 2007;Huettel et al 2007). The third way is by targeting DNA base sequences and guiding changes in them that are then replicated by DNA polymerases (Meyer and Chalker 2007;Nowacki et al 2008). Heritable variations can be generated and perpetuated through all three routes of RNA-mediated heredity, and the formation of a particular dsRNA may be affected by local conditions and may be developmentally regulated.…”

“…Silencing may occur through any of the following mechanisms: (i) the siRNA is loaded onto an enzyme complex that interferes with the transcription or translation of mRNAs with a homologous se-quence (Cullen 2004;Meister and Tuschl 2004); (ii) the siRNA is loaded onto an enzyme complex that targets chromatin regions with DNA that is homologous to the siRNA, and alters chromatin into a silent state (Matzke and Birchler 2005;Ekwall 2007;Huettel et al 2007); or (iii) the siRNA is loaded onto an enzymatic complex that degrades and/or excises the DNA sequences complementary to the siRNAs. The latter processes of RNA-regulated DNA rearrangement are being intensely studied in ciliates (Meyer and Chalker 2007;Nowacki et al 2008).…”

A Chimeric RNA Characteristic of Rhabdomyosarcoma in Normal Myogenesis Process

“…Nevertheless, such a connection is not unprecedented. At least in some lower organisms, such as various species of ciliates, RNA has been demonstrated to serve as a guide or template for DNA rearrangement ( 23,24 ).…”

RNA-mediated epigenetic regulation of DNA copy number

“…Our previous work revealed that noncoding template RNAs that originate from the parental macronucleus guide a highly elaborate process of DNA deletion, unscrambling, and assembly to form the macronuclear genome (32). Disruption of specific RNA templates disables rearrangement of the corresponding gene, and injection of artificial templates reprograms the DNA rearrangement pathway.…”