Small RNA in the nucleus: The RNA-chromatin ping-pong

California Institute of Technology, Division of Biology, Pasadena, CA 91125, USA.
Current opinion in genetics & development (Impact Factor: 7.57). 02/2012; 22(2):164-71. DOI: 10.1016/j.gde.2012.01.002
Source: PubMed


Eukaryotes use several classes of small RNA molecules to guide diverse protein machineries to target messenger RNA. The role of small RNA in post-transcriptional regulation of mRNA stability and translation is now well established. Small RNAs can also guide sequence-specific modification of chromatin structure and thus contribute to establishment and maintenance of distinct chromatin domains. In this review we summarize the model for the inter-dependent interaction between small RNA and chromatin that has emerged from studies on fission yeast and plants. We focus on recent results that link a distinct class of small RNAs, the piRNAs, to chromatin regulation in animals.

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    • "Piwi proteins and piRNAs are involved in the degradation of transposon RNAs in the germ cells of many animals (Brennecke et al., 2007; Gunawardane et al., 2007; Reuter et al., 2011; Saito et al., 2006). In addition, they regulate transposon expression at the transcriptional level by inducing repressive epigenetic marks such as histone H3K9me3 and DNA methylation, which has been well summarized by several reviews and thus will not be the focus of this review (Castel and Martienssen, 2013; Luteijn and Ketting, 2013; Olovnikov et al., 2012; Peng and Lin, 2013; Ross et al., 2014). Beyond transcriptional regulation, a growing number of studies have suggested that piRNAs are involved in the posttranscriptional regulation of not only transposon RNAs but also other types of RNAs including mRNAs and RNA viruses (Gou et al., 2014; Kiuchi et al., 2014; Kotelnikov et al., 2009; Lim et al., 2013; Morazzani et al., 2012; Rouget et al., 2010). "
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    ABSTRACT: Piwi proteins and Piwi-interacting RNAs (piRNAs) are essential for gametogenesis, embryogenesis, and stem cell maintenance in animals. Piwi proteins act on transposon RNAs by cleaving the RNAs and by interacting with factors involved in RNA regulation. Additionally, piRNAs generated from transposons and psuedogenes can be used by Piwi proteins to regulate mRNAs at the posttranscriptional level. Here we discuss piRNA biogenesis, recent findings on posttranscriptional regulation of mRNAs by the piRNA pathway, and the potential importance of this posttranscriptional regulation for a variety of biological processes such as gametogenesis, developmental transitions, and sex determination.
    Molecular Cell 10/2014; 56(1):18–27. DOI:10.1016/j.molcel.2014.09.012 · 14.02 Impact Factor
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    • "The demethylation of this region can drive transcription of LINE1s and induce functional chromatin domains that may inhibit the influence of repressive chromatin modifications, a mechanism already described for the mouse growth hormone locus (Lunyak et al., 2007). In addition, small non-coding RNAs transcribed from LINE1s and other retrotransposons may also be involved in the regulation of local chromatin structure (Olovnikov et al., 2012). "
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    Frontiers in Cellular Neuroscience 02/2014; 8:41. DOI:10.3389/fncel.2014.00041 · 4.29 Impact Factor
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    • "Heterochromatic loci in this pathway are thus paradoxically first transcribed by specific RNA polymerases to be silenced by the deposition of repressive epigenetic marks (Furner and Matzke, 2011). Although RNA Pol IV and V have only been found in plants, de novo methylation driven by sRNAs has also been described in mammals (for a review, see Olovnikov et al., 2012). "
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    ABSTRACT: In the past years a plethora of roles for small RNAs (sRNAs) have been revealed in developmental biology, physiology, pathogen interactions, and more recently in genome stability and transposon control. sRNAs have a repressive impact on gene expression by directly interfering with endogenous mRNAs or virus RNA, or by maintaining heterochromatin. In plants, the most abundant sRNAs are by far the ones produced from heterochromatic loci and playing a role in epigenetic regulation. Here, I review some specific examples of the roles of these sRNAs belonging to the class of small interfering RNAs (siRNAs) in controlling the epigenetic regulation of the genome. I will highlight their role as mediators of epigenetic information at various organization levels: between two alleles within a single cell, two tissues within an organism, two individuals or two generations within a species, and even two species within a kingdom.
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