Long noncoding RNA in liver diseases

Abstract

The identification of the presence of large RNA transcripts that do not code for proteins but that may have biological functions has provided an important new perspective in gene regulation. These long noncoding RNAs (lncRNAs) are being increasingly recognized to contribute to many biological processes through diverse mechanisms. The roles of these emerging genes are being recognized across kingdoms. These findings are profoundly altering our understanding of disease pathobiology and leading to the emergence of new biological concepts underlying human diseases. Strategies for the discovery and characterization of lncRNAs are highlighted. Several lncRNAs have been described in liver disease, and in liver cancers in particular. Their molecular mechanisms of action, function, and contributions to disease pathophysiology are reviewed. LncRNA genes associated with liver diseases have potential roles as biomarkers of disease diagnosis, prognosis, or therapeutic response as well as direct targets for therapeutic intervention.

Conclusion: The emerging knowledge in this rapidly advancing field offers promise for new fundamental knowledge and clinical applications that will be relevant for human liver diseases.

Figure 1. Schematic of mRNA and non-coding RNA encoded within the human genome

Protein coding RNA comprises of less than 2% of the genome. Biological function is ascribed to ~ 80% of the genome. The long non-coding RNA comprise of an unknown number of genes, but are likely to exceed the total number of mRNAs.

Figure 2. Classification of non-coding RNA (ncRNA)

ncRNAs are generally divided into two groups based on transcript size, small ncRNA (< 200 nucleotides) and long ncRNA (> 200 nucleotides). Examples of each group are provided to illustrate the heterogeneity of these groups.

Figure 3. Genomic loci of lncRNA

The genomic locations for lncRNAs can be distinct from or can overlap regions that encode can encode for mRNA and proteins. LncRNAs are described in relationship to their location relative to that of nearby protein-coding genes. LncRNA can be transcribed from sense, antisense or both strands relative to the promoter of a protein-coding gene. Intronic lncRNAs initiate inside of an intron of a protein-coding gene in either direction and terminate without overlapping exons. Intergenic lncRNAs, termed lincRNAs, are lncRNAs with separate transcriptional units from protein-coding genes. Overlap may exist between categories, but is not shown. For example, some genes may be partly exonic and partly intronic. Orange arrow indicates a protein coding region. Blue arrows depict lncRNAs.

Figure 4. Expression of TUC338 in human HCC

In situ hybridization using RNAscope shows punctate expression of TUC338 in HCC tissues. Expression of dapB and PPIB are shown as negative and positive controls respectively. Original magnification, x 20.

Figure 5. Functions of long non-coding RNAs

Overview and examples of mechanisms by which lncRNAs are involved in diverse gene regulations. lncRNAs can regulate gene expression through diverse mechanisms such as chromatin remodeling, transcriptional control, post-transcriptional processing, protein functioning and localization and through intercellular signaling.

Figure 6. Mechanisms of action of selected lncRNA

lncRNA can be regulated or act through a variety of mechanisms that involve diverse processes such as transcriptional and epigenetic regulation of gene expression, regulation of splicing and interactions with miRNA. Mechanisms that have been described for MEG3, HEIH, HULC and MALAT-1 are depicted to illustrate the diversity of interactions between lncRNA and other proteins and RNA molecules. (A) miRNA dependent regulation of lncRNA expression. Methylation at the MEG3 promoter is regulated by DNMTs. Modulation of DNMTs by miR-29 contributes to regulation of MEG3 expression. (B) Epigenetic regulation. HEIH associates with the EZH2 subunit of the PRC2 complex, and recruits this complex to a specific gene locus and contributes to the expression of EZH2-regulated target genes. (C) Targeting miRNA. HULC acts as a molecular sponge to sequester miR-372 and reduce the repression of its target gene PRKACB thereby enabling phosphorylation and activation of the CREB transcription factor, which in turn stimulates HULC expression. (D) Regulation of alternative splicing. The full length of MALAT-1 transcript is processed to generate two non-coding RNAs. The larger MALAT-1 RNA transcript is retained in the nuclear speckles and can modulate the activity of serine/arginine (SR) splicing factors to potentially regulate alternative splicing.