Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R. 999078, China.
Department of Computer Science, School of Engineering, Shantou University, Shantou, China.
Brief Bioinform. 2022 Jul 18;23(4). doi: 10.1093/bib/bbac217.
PIWI-interacting RNAs (piRNAs) are short 21-35 nucleotide molecules that comprise the largest class of non-coding RNAs and found in a large diversity of species including yeast, worms, flies, plants and mammals including humans. The most well-understood function of piRNAs is to monitor and protect the genome from transposons particularly in germline cells. Recent data suggest that piRNAs may have additional functions in somatic cells although they are expressed there in far lower abundance. Compared with microRNAs (miRNAs), piRNAs have more limited bioinformatics resources available. This review collates 39 piRNA specific and non-specific databases and bioinformatics resources, describes and compares their utility and attributes and provides an overview of their place in the field. In addition, we review 33 computational models based upon function: piRNA prediction, transposon element and mRNA-related piRNA prediction, cluster prediction, signature detection, target prediction and disease association. Based on the collection of databases and computational models, we identify trends and potential gaps in tool development. We further analyze the breadth and depth of piRNA data available in public sources, their contribution to specific human diseases, particularly in cancer and neurodegenerative conditions, and highlight a few specific piRNAs that appear to be associated with these diseases. This briefing presents the most recent and comprehensive mapping of piRNA bioinformatics resources including databases, models and tools for disease associations to date. Such a mapping should facilitate and stimulate further research on piRNAs.
PIWI 相互作用 RNA（piRNA）是短的 21-35 个核苷酸分子，构成了最大的非编码 RNA 类别，存在于包括酵母、蠕虫、苍蝇、植物和哺乳动物（包括人类）在内的多种物种中。piRNA 最被理解的功能是监测和保护基因组免受转座子的影响，特别是在生殖细胞中。最近的数据表明，piRNA 可能在体细胞中具有额外的功能，尽管它们在那里的表达量要低得多。与 microRNAs（miRNAs）相比，piRNA 可用的生物信息学资源有限。本综述汇集了 39 个 piRNA 特异性和非特异性数据库和生物信息学资源，描述并比较了它们的用途和属性，并概述了它们在该领域的地位。此外，我们还综述了 33 种基于功能的计算模型：piRNA 预测、转座子元件和 mRNA 相关 piRNA 预测、簇预测、特征检测、靶标预测和疾病关联。基于数据库和计算模型的收集，我们确定了工具开发中的趋势和潜在差距。我们进一步分析了公共资源中可用的 piRNA 数据的广度和深度，它们对特定人类疾病（特别是癌症和神经退行性疾病）的贡献，并突出了一些似乎与这些疾病相关的特定 piRNA。本简报介绍了迄今为止最新和最全面的 piRNA 生物信息学资源图谱，包括数据库、模型和与疾病关联的工具。这种映射应该有助于并激发对 piRNA 的进一步研究。
