Abstract
Small non-protein coding RNAs are involved in pathways that control the genome at the level of chromatin. In Schizosaccharomyces pombe, small interfering RNAs (siRNAs) are required for the faithful propagation of heterochromatin that is found at peri-centromeric repeats. In contrast to repetitive DNA, protein-coding genes are refractory to siRNA-mediated heterochromatin formation, unless siRNAs are expressed in mutant cells. Here we report the identification of 20 novel mutant alleles that enable de novo formation of heterochromatin at a euchromatic protein-coding gene by using trans-acting siRNAs as triggers. For example, a single amino acid substitution in the pre-mRNA cleavage factor Yth1 enables siRNAs to trigger silent chromatin formation with unparalleled efficiency. Our results are consistent with a kinetic nascent transcript processing model for the inhibition of small-RNA-directed de novo formation of heterochromatin and lay a foundation for further mechanistic dissection of cellular activities that counteract epigenetic gene silencing.
Highlights
Small RNAs are the common denominator of various RNA silencing pathways that regulate gene expression and protect the genome against mobile repetitive DNA sequences, retroelements, and transposons [1,2,3]
Besides silencing gene expression at the post-transcriptional level, small RNAs mediate the formation of silent chromatin that is heritable across generations
Over the last two decades, fission yeast has been serving as an excellent model organism to elucidate the mechanism of small-RNA-mediated heterochromatin formation at repetitive DNA
Summary
Small RNAs are the common denominator of various RNA silencing pathways that regulate gene expression and protect the genome against mobile repetitive DNA sequences, retroelements, and transposons [1,2,3] They function as specificity factors by guiding Argonaute protein-containing silencing complexes to their respective targets via base-pairing interactions [4, 5]. In the fission yeast Schizosaccharomyces pombe, endogenous small interfering RNAs (siRNAs) are indispensable for the maintenance of centromeric heterochromatin [6] They originate from within centromeric heterochromatin and target the Argonaute-containing (Ago1) RNA-Induced Silencing Complex (RITS) in cis to nascent heterochromatic transcripts that are emanating from RNA polymerase II (RNA Pol II) transcribing the underlying repetitive DNA [7, 8]. Dicer-mediated (Dcr1) processing of the resulting double-stranded RNAs leads to amplification of the siRNA pool and thereby reinforcement of the positive feedback loop [14]
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