Abstract
Noncoding RNAs (ncRNAs) play prominent roles in the regulation of gene expression via their interactions with other biological molecules such as proteins and nucleic acids. Although much of our knowledge about how these ncRNAs operate in different biological processes has been obtained from experimental findings, computational biology can also clearly substantially boost this knowledge by suggesting possible novel interactions of these ncRNAs with other molecules. Computational predictions are thus used as an alternative source of new insights through a process of mutual enrichment because the information obtained through experiments continuously feeds through into computational methods. The results of these predictions in turn shed light on possible interactions that are subsequently validated experimentally. This review describes the latest advances in databases, bioinformatic tools, and new in silico strategies that allow the establishment or prediction of biological interactions of ncRNAs, particularly miRNAs and lncRNAs. The ncRNA species described in this work have a special emphasis on those found in humans, but information on ncRNA of other species is also included.
Highlights
Published: 22 October 2021The set of RNA molecules expressed in a cell or tissue is known as a transcriptome [1].More than 90% of the human genome is transcribed, and less than 2% are protein-coding genes
Many different mechanisms that regulate gene expression (Figure 2), such as transcription factors accessing DNA, and variations in the rates of mRNA synthesis, processing, stability, and translation, are influenced by ncRNAs [58,64]. This is achieved by ncRNAs’ ability to interact with various biological molecules (Figure 3) within different cells and tissues. Among these ncRNAs with regulatory functions, this review focuses on miRNAs and long noncoding RNAs (lncRNAs), which have attracted great interest given their roles in various biological functions [51,65,66,67]
We review the latest advances in databases, bioinformatic tools, and new strategies in silico that allow the establishment or prediction of biological interactions between ncRNAs, miRNAs and lncRNAs
Summary
The set of RNA molecules expressed in a cell or tissue is known as a transcriptome [1]. This can lead to a change in the accessibility of genes to DNA-binding proteins, such as transcription factors and even RNA Pol II (Figure 3D), resulting in the activation or suppression of transcription [79,80,81,82] Another of the most widely studied regulatory mechanisms of lncRNAs involves them acting like enhancers, in which they function either by directly interacting with promoter regions of the genes they regulate or by binding to proteins that participate as mediators [11,83,84,85,86].
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