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Investigating the role of Dicer-dependent transfer RNA-derived small RNAs in gene expression regulation

ABSTRACT: Investigating the role of Dicer-dependent transfer RNA-derived small RNAs in gene expression regulation

PROVIDER: PRJNA523191 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8591370.fastq.gz	Fastqsanger.gz
	SRR8591380.fastq.gz	Fastqsanger.gz
	SRR8591390.fastq.gz	Fastqsanger.gz
	SRR8591371_1.fastq.gz	Fastqsanger.gz
	SRR8591371_2.fastq.gz	Fastqsanger.gz

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Investigating the role of Dicer-dependent transfer RNA-derived small RNAs in gene expression regulation

Project description:We used sequencing analyses to identify small RNAs that are generated in a Dicer-dependent manner and the genes that are dysregulated upon Dicer knockdown at the mRNA level, and upon Drosha, Dicer and Ago2 knockdown at the chromatin level in HEK293 cells. We found that levels of tRNA-derived sRNAs decreased alongside microRNAs upon Dicer knockdown. Many genes are dysregulated at the chromatin levels when Dicer and Ago2 levels are reduced, indicating that Dicer and Ago2 can regulate genes directly or indirectly at the transcriptional level. Drosha knockdown, on the other hand, has a marginal effect on RNA levels at the chromatin.

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Project description:A variety of small RNAs, including the Dicer-dependent miRNAs and the Dicer-independent Piwi-interacting RNAs, associate with Argonaute family proteins to regulate gene expression in diverse cellular processes. These two species of small RNA have not been found in fungi. Here, by analyzing small RNA associated with the Neurospora Argonaute protein QDE-2, we show that diverse pathways generate miRNA-like small RNAs (milRNAs) and Dicer-independent small interfering RNAs (disiRNAs) in this filamentous fungus. Surprisingly, milRNAs are produced by at least four different mechanisms that use a distinct combination of factors, including Dicers, QDE-2, the exonuclease QIP and an RNAse III domain-containing protein MRPL3. In contrast, disiRNAs originate from loci producing overlapping sense and antisense transcripts, and do not require the known RNAi components for their production. Taken together, these results uncover several pathways for small RNA production in filamentous fungi, shedding light on the diversity and evolutionary origins of eukaryotic small RNAs.

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Project description:Dicer-dependent small RNAs production from antisense long non-coding RNAs in N. castellii

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