Abstract
Cytosine methylation of DNA is an important epigenetic gene silencing mechanism in plants, fungi, and animals. In the filamentous fungus Neurospora crassa, nearly all known DNA methylations occur in transposon relics and repetitive sequences, and DNA methylation does not depend on the canonical RNAi pathway. disiRNAs are Dicer-independent small non-coding RNAs that arise from gene-rich part of the Neurospora genome. Here we describe a new type of DNA methylation that is associated with the disiRNA loci. Unlike the known DNA methylation in Neurospora, disiRNA loci DNA methylation (DLDM) is highly dynamic and is regulated by an on/off mechanism. Some disiRNA production appears to rely on pol II directed transcription. Importantly, DLDM is triggered by convergent transcription and enriched in promoter regions. Together, our results establish a new mechanism that triggers DNA methylation.
Highlights
DNA methylation at the 5th position of cytosine to form 5methylcytosine (5mC) is an important epigenetic gene silencing mechanism conserved from plants, fungi to animals [1,2]
It is tightly linked to a type of non-coding small RNA termed dicer-independent small interfering RNAs (siRNAs) and was termed disiRNA loci DNA methylation (DLDM)
We showed that DLDM is established and maintained very differently from the repeatinduced point mutation (RIP)-induced DNA methylation
Summary
DNA methylation at the 5th position of cytosine to form 5methylcytosine (5mC) is an important epigenetic gene silencing mechanism conserved from plants, fungi to animals [1,2]. DNA methylation occurs in three different nucleotide sequence contexts: CG, CHG, and CHH (where H is C, A, or T). Small non-coding RNAs have been shown to be involved in the establishment and maintenance of heterochromatin formation in different organisms. The asymmetrical CHH methylation is maintained by de novo DNA methylation mediated by 24-nt small interfering RNAs (siRNAs) [review in 7,8]. The Dicer-independent Piwi-interacting RNAs (piRNAs) are thought to be involved in DNA methylation [9,10]
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