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PIWI-interacting RNAs in human diseases: databases and computational models
Zhang, Tianjiao1; Chen, Liang2; Li, Rongzhen1; Liu, Ning1; Huang, Xiaobing1; Wong, Garry1
2022-07-18
Source PublicationBriefings in bioinformatics
Volume23Issue:4
Abstract

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.

KeywordArgonaute Protein Bioinformatics Database Pirna Transposon
DOI10.1093/bib/bbac217
URLView the original
Indexed BySCIE
Language英語English
WOS Research AreaBiochemistry & Molecular Biology ; Mathematical & Computational Biology
WOS SubjectBiochemical Research Methods ; Mathematical & Computational Biology
WOS IDWOS:000806421800001
Scopus ID2-s2.0-85134721004
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Cited Times [WOS]:0   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionUniversity of Macau
Corresponding AuthorWong, Garry
Affiliation1.Faculty of Health Sciences, University of Macau, Taipa, China
2.Department of Computer Science, School of Engineering, Shantou University, Shantou, China
First Author AffilicationFaculty of Health Sciences
Corresponding Author AffilicationFaculty of Health Sciences
Recommended Citation
GB/T 7714
Zhang, Tianjiao,Chen, Liang,Li, Rongzhen,et al. PIWI-interacting RNAs in human diseases: databases and computational models[J]. Briefings in bioinformatics,2022,23(4).
APA Zhang, Tianjiao,Chen, Liang,Li, Rongzhen,Liu, Ning,Huang, Xiaobing,&Wong, Garry.(2022).PIWI-interacting RNAs in human diseases: databases and computational models.Briefings in bioinformatics,23(4).
MLA Zhang, Tianjiao,et al."PIWI-interacting RNAs in human diseases: databases and computational models".Briefings in bioinformatics 23.4(2022).
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