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Review
. 2019 Jul 13;16(3):20190027.
doi: 10.1515/jib-2019-0027.

Non-Coding RNAs and their Integrated Networks

Peijing Zhang  1 , Wenyi Wu  1 , Qi Chen  1 , Ming Chen  1   2
Affiliations
Review

Non-Coding RNAs and their Integrated Networks

Peijing Zhang et al. J Integr Bioinform. .

Abstract

Eukaryotic genomes are pervasively transcribed. Besides protein-coding RNAs, there are different types of non-coding RNAs that modulate complex molecular and cellular processes. RNA sequencing technologies and bioinformatics methods greatly promoted the study of ncRNAs, which revealed ncRNAs' essential roles in diverse aspects of biological functions. As important key players in gene regulatory networks, ncRNAs work with other biomolecules, including coding and non-coding RNAs, DNAs and proteins. In this review, we discuss the distinct types of ncRNAs, including housekeeping ncRNAs and regulatory ncRNAs, their versatile functions and interactions, transcription, translation, and modification. Moreover, we summarize the integrated networks of ncRNA interactions, providing a comprehensive landscape of ncRNAs regulatory roles.

Keywords: ceRNA network; integrated network; ncRNA interaction; non-coding RNA; regulatory ncRNA.

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Conflict of interest statement

Authors state no conflict of interest. All authors have read the journal’s publication ethics and publication malpractice statement available at the journal’s website and hereby confirm that they comply with all its parts applicable to the present scientific work.

Figures

Figure 1:
Figure 1:
Distinct type of ncRNAs are transcribed from eukaryotic genomes. (A) Exons in protein-coding genes can be transcribed into pseudogenes, lncRNAs, and circRNAs, most of which have introns discarded. Y RNAs transcribed from individual genes. (B) Enhancer regions can be transcribed into divergent transcripts, known as eRNAs. (C) Intronic sequences can encode for snoRNAs or miRNAs. TEs can be transcribed into siRNA. Genes for rRNAs, tRNAs, or snRNAs are transcribed from separate genes. piRNAs and miRNAs can also be derived from various intergenic regions.
Figure 2:
Figure 2:
Network of miRNAs biogenesis and ceRNAs. miRNAs may be generated from lncRNAs, snRNAs, piRNAs or tRNAs, that repress protein-coding mRNAs by binding to MREs. Different classes of ceRNAs, such as circRNAs, lncRNAs, and pseudogenes, also contain MREs and compete for miRNA binding.
Figure 3:
Figure 3:
ncRNA-mediated networks are an integral part of genomics and proteomics. (A) ncRNAs regulate the organization of genome in the nucleus by interacting with nuclear-matrix factors. (B) ncRNAs mediate promoter-enhancer interactions to regulate the expression of protein-coding genes. (C) ncRNAs are extensively involved in protein interaction networks.
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Grants and funding

This work has been supported by the National Key Research and Development Program of China (Grant Nos. 2018YFC0310602 and 2016YFA0501704), National Natural Science Foundation of China (Funder Id: Funder Id: http://dx.doi.org/10.13039/501100001809, Grant Nos. 31771477 and 31571366), the Fundamental Research Funds for the Central Universities, Jiangsu Collaborative Innovation Center for Modern Crop Production and 2018 Zhejiang University Academic Award for Outstanding Doctoral Candidates.

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