Identification of intermediate-size non-coding RNAs involved in the UV-induced DNA damage response in C. elegans.

Aqian Li,Xian-En Zhang,Runsheng Chen,Ying Zhou,Lijun Bi,Yunfei Wang,Guifeng Wei,Denis Dupuy

doi:10.1371/journal.pone.0048066

Aqian Li, Xian-En Zhang + Show 6 more

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https://doi.org/10.1371/journal.pone.0048066

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Abstract

BackgroundA network of DNA damage response (DDR) mechanisms functions coordinately to maintain genome integrity and prevent disease. The Nucleotide Excision Repair (NER) pathway is known to function in the response to UV-induced DNA damage. Although numbers of coding genes and miRNAs have been identified and reported to participate in UV-induced DNA damage response (UV-DDR), the precise role of non-coding RNAs (ncRNAs) in UV-DDR remains largely unknown.Methodology/Principal FindingsWe used high-throughput RNA-sequencing (RNA-Seq) to discover intermediate-size (70–500 nt) ncRNAs (is-ncRNAs) in C. elegans, using the strains of L4 larvae of wild-type (N2), UV-irradiated (N2/UV100) and NER-deficient mutant (xpa-1), and 450 novel non-coding transcripts were initially identified. A customized microarray assay was then applied to examine the expression profiles of both novel transcripts and known is-ncRNAs, and 57 UV-DDR-related is-ncRNA candidates showed expression variations at different levels between UV irradiated strains and non- irradiated strains. The top ranked is-ncRNA candidates with expression differences were further validated by qRT-PCR analysis, of them, 8 novel is-ncRNAs were significantly up-regulated after UV irradiation. Knockdown of two novel is-ncRNAs, ncRNA317 and ncRNA415, by RNA interference, resulted in higher UV sensitivity and significantly decreased expression of NER-related genes in C. elegans.Conclusions/SignificanceThe discovery of above two novel is-ncRNAs in this study indicated the functional roles of is-ncRNAs in the regulation of UV-DDR network, and aided our understanding of the significance of ncRNA involvement in the UV-induced DNA damage response.

Highlights

Genomic integrity is essential for the survival of the individual and the reproductive success of the species
We have previously investigated the functions of the is-non-coding RNAs (ncRNAs), showing that they have a high degree of developmentally-specific expression in C. elegans [22] and may play important tissue-specific roles in the development and tumorigenesis of the human brain [23]
Since it has been reported that Nucleotide Excision Repair (NER) is a main pathway to repair UV-induced DNA damage [3], NER deficient mutant was analyzed to reveal more is-ncRNA candidates in UV-DNA damage response (DDR) that potentially being modulated by the NER pathway

Summary

Introduction

Genomic integrity is essential for the survival of the individual and the reproductive success of the species. Nucleotide Excision Repair (NER) is one of the main repair mechanisms involved in the response to UV-induced DNA damage [3]. The importance of this repair mechanism is illustrated clinically by three severe NER-defective syndromes: xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD) [4]. Sufferers of these three syndromes exhibit hypersensitivity to sunlight and a predisposition to skin cancer, indicating that the molecular response to UV light is critical for protecting organisms. A network of DNA damage response (DDR) mechanisms functions coordinately to maintain genome integrity and prevent disease. Numbers of coding genes and miRNAs have been identified and reported to participate in UVinduced DNA damage response (UV-DDR), the precise role of non-coding RNAs (ncRNAs) in UV-DDR remains largely unknown

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