Abstract
Recently, a new type of small interfering RNAs (qiRNAs) of typically 20~21 nucleotides was found in Neurospora crassa and rice and has been shown to regulate gene silencing in the DNA damage response. Identification of qiRNAs is fundamental for dissecting regulatory functions and molecular mechanisms. In contrast to other expensive and time-consuming experimental methods, the computational prediction of qiRNAs is a conveniently rapid method for gaining valuable information for a subsequent experimental verification. However, no tool existed to date for the prediction of qiRNAs. To this purpose, we developed the novel qiRNA prediction software package qiRNApredictor. This software demonstrates a promising sensitivity of 93.55% and a specificity of 71.61% from the leave-one-out validation. These studies might be beneficial for further experimental investigation. Furthermore, the local package of qiRNApredictor was implemented and made freely available to the academic community at Supplementary material.
Highlights
Small non-coding RNAs of 20~30 nucleotides have gained significant attention in recent years as they are widely involved in various biological processes such as the embryonic, neuronal, muscle, and germline development [1,2,3]
QDE-2-interacting small RNAs of typically 20~21 nt are a new class of sRNAs. qiRNAs are induced by DNA damage [4] and mediate gene silencing in the DNA damage response (DDR) pathway in Neurospora crassa by inhibiting protein translation [4]
Nucleotides at the first and last position, such as 1U, 1A, 1C, or -1A, exhibit high F-scores (Fig 4). This is consistent with the position-specific preferences of nucleotides in qiRNA sequences, which demonstrates that we have succeeded in capturing these characteristics in qiRNA sequences
Summary
Small non-coding RNAs (sRNAs) of 20~30 nucleotides (nt) have gained significant attention in recent years as they are widely involved in various biological processes such as the embryonic, neuronal, muscle, and germline development [1,2,3]. It has been demonstrated that the biogenesis of qiRNAs requires DNA-damage-induced aberrant RNAs (aRNAs) as precursors [4]. RNA-dependent RNA polymerase QDE-1, the Werner and Bloom RecQ DNA helicase homologue QDE-3, as well as dicers have been previously shown to be involved in the production of qiRNAs [4]. After DNA damage, aRNAs are highly induced and recognized by RNA-dependent polymerases to produce double-stranded RNAs (dsRNAs).
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