Deep Sequencing Discovery and Profiling of Known and Novel miRNAs Produced in Response to DNA Damage in Rice.

Jianxiang Zhang,Cheng Xu,Lian Tao,Yaoqinq Li,Hengxiu Yu,Mengna Wang,Kangwei Liu,Chao Zhang

doi:10.3390/ijms22189958

Jianxiang Zhang, Cheng Xu + Show 6 more

Open Access

https://doi.org/10.3390/ijms22189958

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Abstract

Under extreme environmental conditions such as ultraviolet and ionizing radiation, plants may suffer DNA damage. If these damages are not repaired accurately and rapidly, they may lead to chromosomal abnormalities or even cell death. Therefore, organisms have evolved various DNA repair mechanisms to cope with DNA damage which include gene transcription and post-translational regulation. MicroRNA (miRNA) is a type of non-coding single-stranded RNA molecule encoded by endogenous genes. They can promote DNA damage repair by regulating target gene transcription. Here, roots from seedlings of the japonica rice cultivar ‘Yandao 8’ that were treated with bleomycin were collected for transcriptome-level sequencing, using non-treated roots as controls. A total of 14,716,232 and 17,369,981 reads mapping to miRNAs were identified in bleomycin-treated and control groups, respectively, including 513 known and 72 novel miRNAs. Compared with the control group, 150 miRNAs showed differential expression levels. Target predictions of these differentially expressed miRNAs yielded 8731 potential gene targets. KEGG annotation and a gene ontology analysis indicated that the highest-ranked target genes were classified into metabolic processes, RNA degradation, DNA repair, and so on. Notably, the DNA repair process was significantly enriched in both analyses. Among these differentially expressed miRNAs, 58 miRNAs and 41 corresponding potential target genes were predicted to be related to DNA repair. RT-qPCR results confirmed that the expression patterns of 20 selected miRNAs were similar to those from the sequencing results, whereas four miRNAs gave opposite results. The opposing expression patterns of several miRNAs with regards to their target genes relating to the DNA repair process were also validated by RT-qPCR. These findings provide valuable information for further functional studies of miRNA involvement in DNA damage repair in rice.

Highlights

IntroductionThere are many environmental factors that can cause DNA damage in living organisms, such as ultraviolet, ionizing radiation, alkylating agents, base analogs, and many more
Our study suggests that Micro RNAs (miRNAs) may be widely involved in regulating DNA damage repair in rice and provides novel insights into the molecular mechanisms of DNA damage repair
Double-strand breaks (DSBs) were induced in rice seedling roots via treatment with the DNA damage inducer bleomycin for 3 h, after which the DNA damage response (DDR)

Summary

Introduction

There are many environmental factors that can cause DNA damage in living organisms, such as ultraviolet, ionizing radiation, alkylating agents, base analogs, and many more. Extensive DNA damage can even cause chromosomal instabilities resulting in the death of cells and/or the whole organism [3]. Hundreds of genes related to DNA damage repair have been identified. They are primarily involved in five different, but functionally related, pathways: base excision repair (BER), nucleotide excision repair (nucleotide excision repair, NER), mismatch repair (MMR), non-homologous end joining (NHEJ), and homologous recombination (HR) [4]. DNA double-strand breaks (DSBs) are one type of DNA damage that can cause deleterious genetic lesions that drive genetic instability. NHEJ promotes direct ligation of the DSB ends and is an efficient but error-prone manner, while HR is largely error free, but it requires homologous DNA sequences as a template for repair by DNA synthesis [6,7]

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