Abstract
Long noncoding RNAs (lncRNAs), which form a diverse class of RNAs, remain the least understood type of noncoding RNAs in terms of their nature and identification. Emerging evidence has revealed that a small number of newly discovered lncRNAs perform important and complex biological functions such as dosage compensation, chromatin regulation, genomic imprinting, and nuclear organization. However, understanding the wide range of functions of lncRNAs related to various processes of cellular networks remains a great experimental challenge. Structural versatility is critical for RNAs to perform various functions and provides new insights into probing the functions of lncRNAs. In recent years, the computational method of RNA structure prediction has been developed to analyze the structure of lncRNAs. This novel methodology has provided basic but indispensable information for the rapid, large-scale and in-depth research of lncRNAs. This review focuses on mainstream RNA structure prediction methods at the secondary and tertiary levels to offer an additional approach to investigating the functions of lncRNAs.
Highlights
The term noncoding RNAs refers to RNA transcripts that do not encode proteins [1]
The known mechanisms involved in the function of Long noncoding RNAs (lncRNAs) are as follows (Figure 2): (a) To induce transcriptional interference, lncRNAs spanning downstream promoter regions of protein-coding genes interfere with transcription factors via binding to their activators and repress the expression of these protein-coding genes [94]; (b) To initiate chromatin remodeling, the transcription of lncRNAs may induce heterochromatin formation and DNA methylation, leading to the silencing of tumor suppressor genes [47,95]; (c) lncRNAs bind to basal transcription factors to inactivate their promoters and repress the expression of target genes [96]; (d) lncRNAs activate accessory proteins to repress gene expression [83,97]; (e) lncRNAs activate transcription factors to promote the expression of target genes
This reveals a novel mechanism involving the cooperative actions of an lncRNA and a homeodomain protein to regulate transcription [98]; (f) The formation of a trimer containing an activator protein, a translation elongation factor and an lncRNA accelerates the expression of target genes [99]; (g) lncRNAs interact with importin proteins to regulate the subcellular localization of transcription factors. [100]; (h) lncRNAs act as the precursors of small RNAs to perform functions [101]; (i) lncRNAs bind to small RNAs to modulate their activities [102]
Summary
The term noncoding RNAs (ncRNAs) refers to RNA transcripts that do not encode proteins [1]. NcRNAs can be classified as housekeeping or regulatory ncRNAs. Housekeeping ncRNAs include ribosome RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNA (snRNAs) and small nucleolar RNA (snoRNAs), while regulatory RNAs include small interfering RNA (siRNAs), microRNA (miRNAs), long noncoding RNAs (lncRNA), piRNA, natural antisense transcripts (NATs) and circular RNA (circRNAs) [4,5,6,7]. 22ooff2254 transcribed long noncoding RNAs (lncRNAs) (>200 nt) may perform more complex biological tfruanncstciorinbsed[12lo–n14g].nTohnecsoediRnNg ARsNhAasve(lnbecRenNiAmsp) l(ic>a2t0e0d nint) tmheayregpuerlafotiromn omfogreenceoemxpplreexssbioinoloagt itchael fturanncstciorinpsti[o1n2a–l14o]r. MiRNAs, siRNAs, lncRNAs and other ncRNAs have been found to play significant roles in various physiological and developmental processes in eukaryotes, furthering our knowledge of ncRNAs Recent advances in the study of ncRNAs have demonstrated the existence of ncRNAs in a wide variety of mammalian transcriptomes. miRNAs, siRNAs, lncRNAs and other ncRNAs have been found to play significant roles in various physiological and developmental processes in eukaryotes, furthering our knowledge of ncRNAs
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