QIP, a putative exonuclease, interacts with the <i>Neurospora</i> Argonaute protein and facilitates conversion of duplex siRNA into single strands

Maiti, Mekhala; Lee, Heng-Chi; Liu, Yi

doi:10.1101/gad.1497607

Cited by 114 publications

(155 citation statements)

References 48 publications

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“…Since the initial discovery of MSUD in the laboratory of R. L. Metzenberg, much has been learned about the latter process. Essentially, it appears to be mediated by an elaborate silencing complex that stations itself around the perimeter of the nucleus, (Catalanotto et al 2004;Maiti et al 2007;Alexander et al 2008;Lee et al 2010;Xiao et al 2010). …”

Section: Discussionmentioning

confidence: 99%

Efficient Detection of Unpaired DNA Requires a Member of the Rad54-Like Family of Homologous Recombination Proteins

et al. 2014

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Meiotic silencing by unpaired DNA (MSUD) is a process that detects unpaired regions between homologous chromosomes and silences them for the duration of sexual development. While the phenomenon of MSUD is well recognized, the process that detects unpaired DNA is poorly understood. In this report, we provide two lines of evidence linking unpaired DNA detection to a physical search for DNA homology. First, we have found that a putative SNF2-family protein (SAD-6) is required for efficient MSUD in Neurospora crassa. SAD-6 is closely related to Rad54, a protein known to facilitate key steps in the repair of double-strand breaks by homologous recombination. Second, we have successfully masked unpaired DNA by placing identical transgenes at slightly different locations on homologous chromosomes. This masking falls apart when the distance between the transgenes is increased. We propose a model where unpaired DNA detection during MSUD is achieved through a spatially constrained search for DNA homology. The identity of SAD-6 as a Rad54 paralog suggests that this process may be similar to the searching mechanism used during homologous recombination. MEIOSIS is fundamental to sexual reproduction. During meiosis, chromosomes are replicated, aligned, recombined, and segregated to nuclei that will develop into gametes. Two of these key processes, alignment and recombination, likely require a search for DNA homology between chromosomes (Barzel and Kupiec 2008;Moore and Shaw 2009). Such homology searching is necessary because sexual organisms inherit a copy of each chromosome from each of its parents. These chromosomes, referred to as homologs, must somehow find each other so that alignment, recombination, and segregation can occur.Although recent research has improved our understanding of homology search mechanisms (Forget and Kowalczykowski 2012;Renkawitz et al. 2013), there are many questions that remain unanswered. The filamentous fungus Neurospora crassa may be useful for investigating the unknowns of homology searching because it possesses a genetically tractable phenomenon called meiotic silencing by unpaired DNA (MSUD) (Aramayo and Selker 2013;Billmyre et al. 2013). MSUD scans pairs of homologs for segments of DNA that are not accurately paired between them. If improper pairing (i.e., unpairing) is identified, the offending sequences are silenced for the duration of sexual development. For example, if a hypothetical gene called "gene A" is on the left arm of one chromosome but on the right arm of its homolog, it will be silenced. The same holds true if gene A has been lost from one of the homologs.A functional MSUD response can be easily detected with alleles that affect ascospore (sexual spore) color or shape. Indeed, MSUD was discovered during studies of ascospore maturation-1 (asm-1), a gene required for the production of pigmented (black) ascospores . A cross between an asm-1 + strain and an asm-1 D strain produces mostly unpigmented (white) ascospores. This is because MSUD silences the unpaired asm-1 + all...

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Section: Discussionmentioning

confidence: 99%

Efficient Detection of Unpaired DNA Requires a Member of the Rad54-Like Family of Homologous Recombination Proteins

et al. 2014

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“…Total RNA extraction, enrichment of small sized RNA, and Northern blots were performed as described previously (17). RNA probes were made using the MAXIscript T7 kit (Ambion) from a T7 promoter on a PCR product template.…”

Section: Methodsmentioning

confidence: 99%

“…RecQ DNA helicase QDE-3 and the single-stranded DNA binding complex replication protein A are also involved in this process (14 -16). dsRNA is cleaved by Dicer proteins to produce siRNA, which is then loaded onto QDE-2 to mediate gene silencing (17). Although how siRNA is produced from dsRNA and acts are well understood, little is known about how aRNA and siRNA is specifically transcribed from repetitive loci.…”

mentioning

confidence: 99%

Histone H3K56 Acetylation Is Required for Quelling-induced Small RNA Production through Its Role in Homologous Recombination

Zhang

Yang

Sun

et al. 2014

Journal of Biological Chemistry

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Background: Quelling and DNA damage induce small RNA from repetitive DNA regions. Results: Genetic Screen identified RTT109 as a critical component of the siRNA production pathway in Neurospora. Conclusion: RTT109 acts as a histone H3K56 acetyltransferase to mediate siRNA biogenesis through its role in homologous recombination. Significance: This study identifies a new link between DNA damage response and small RNA production at the chromatin level.

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“…Recent evidence suggests that a siRNA duplex is first loaded into RISC and AGO cleaves one of the siRNA strands (the passenger strand) (1,2). Ribonucleases, such as Trax or QIP, then promote RISC activation by removing the passenger strand cleavage products (8,9). Activated RISC uses the remaining single-stranded siRNA as a guide to identify homologous RNAs, ultimately triggering transcript degradation and/or translation repression (1)(2)(3).…”

mentioning

confidence: 99%

Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in Chlamydomonas

Ibrahim

Rymarquis

Kim

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

126

185

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Regulation of gene expression by small RNAs (∼20-30 nucleotides in length) plays an essential role in developmental pathways and defense responses against genomic parasites in eukaryotes. MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) commonly direct the inactivation of cognate sequences through a variety of mechanisms, including RNA degradation, translation inhibition, and transcriptional repression. Recent studies have provided considerable insight into the biogenesis and the mode of action of miRNAs and siRNAs. However, relatively little is known about mechanisms of quality control and small RNA decay in RNA interference (RNAi) pathways. Here we show that deletion of MUT68, encoding a terminal nucleotidyltransferase in the alga Chlamydomonas reinhardtii, results in elevated miRNA and siRNA levels. We found that MUT68 plays a role in the untemplated uridylation of the 3′ ends of small RNAs in vivo and stimulates their degradation by the RRP6 exosome subunit in vitro. Moreover, RRP6 depletion also leads to accumulation of small RNAs in vivo. We propose that MUT68 and RRP6 cooperate in the degradation of mature miRNAs and siRNAs, as a quality control mechanism to eliminate dysfunctional or damaged small RNA molecules.exosome | RNA interference | miRNA quality control

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QIP, a putative exonuclease, interacts with the Neurospora Argonaute protein and facilitates conversion of duplex siRNA into single strands

Cited by 114 publications

References 48 publications

Efficient Detection of Unpaired DNA Requires a Member of the Rad54-Like Family of Homologous Recombination Proteins

Efficient Detection of Unpaired DNA Requires a Member of the Rad54-Like Family of Homologous Recombination Proteins

Histone H3K56 Acetylation Is Required for Quelling-induced Small RNA Production through Its Role in Homologous Recombination

Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in Chlamydomonas

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