Distinct regulatory functions and biological roles of lncRNA splice variants

Abstract

Alternative splicing (AS) of RNA molecules is a key contributor to transcriptome diversity. In humans, 90%-95% of multi-exon genes produce alternatively spliced RNA transcripts. Therefore, every single gene has the opportunity of producing multiple splice variants, including long non-coding RNA (lncRNA) genes that undergo RNA maturation steps such as conventional and alternative splicing. Emerging evidence suggests significant roles for these lncRNA splice variants in many aspects of cell biology. Differential changes in expression of specific lncRNA splice variants have also been associated with many diseases including cancer. This review covers the current knowledge on this emerging topic of investigation. We provide exclusive insights on the AS landscape of lncRNAs and also describe at the molecular level the functional relevance of lncRNA splice variants, i.e., RNA-based differential functions, production of micropeptides, and generation of circular RNAs. Finally, we discuss exciting perspectives for this emerging field and outline the work required to further develop research endeavors in this field.

Keywords: MT: Non-coding RNAs; alternative splicing; circular RNA; long non-coding RNA; micropeptide; splice variant; therapeutics.

Graphical abstract

Figure 1

Relative percentage of protein-coding genes (PCGs) and lncRNA genes across species The proportion of PCGs and lncRNA genes across species is represented in percentage (%). The calculation was based on numbers from NONCODEv5 and Ensembl databases.

Figure 2

General characteristics of lncRNA genes across species (A) Median length of lncRNA transcripts across species. (B) Median number of exons in lncRNA genes across species. (C) Distribution of the number of exons across species. The calculation was based on numbers from NONCODEv5 and Ensembl databases.

Figure 3

RNA-based molecular functions of alternatively spliced transcripts (A) RP11-369C8.1 gene produces two alternatively spliced transcripts: TRMP and TRMP-S. TRMP competes with p27 mRNA for PTBP1 binding and thus inhibits p27 mRNA translation, leading to cellular senescence. TRMP-S also represses p27 expression. Mechanistically, TRMP-S functions as a scaffold for UHRF1 and USP7 deubiquitinating enzyme to favor UHRF1 deubiquitination and enhance its stability on p27 promoter. UHRF1 acts as an epigenetic silencer of p27 transcription leading to cellular senescence. In addition, TRMP-S can decrease p53 expression by associating with FUBP3 to sequester RPL26, a protein essential for p53 translation. Since p53 is required for p27 transcription, TRMP-S indirectly promotes the decrease of p27 expression to induce cellular senescence. (B) PXN-AS1 gene produces two major splice variants: PXN-AS1-L and PXN-AS1-S lacking exon 4. MBNL3 protein favors the inclusion of exon 4 in PXN-AS1 final transcript. Both isoforms of PNX-AS1 have contrasting functions while regulating PXN protein. PXN-AS1-L isoform binds to 3′ UTR of PXN mRNA and prevents its miR-24-mediated degradation, thus promoting tumorigenesis. PXN-AS1-S binds to the CDS region of PXN mRNA and prevents its translation, thus suppressing tumorigenesis. (Illustrations created with Biorender.com).

Figure 4

Production of micropeptides by lncRNA spliced variants HOXB-AS3 lncRNA gene produces several spliced variants, including NR_033202.2 and NR_033201.2. NR_033202.2 enhances the transcription of ribosomal RNA and therefore promotes cancer cell proliferation in patients with acute myeloid leukemia with mutated NPM1 (NPM1mut). The NR_033201.2 variant harbors a small open reading frame encoding for a functional micropeptide (HOXB-AS3-peptide). This micropeptide regulates PKM splicing and favors the production of PKM1 isoform instead of PKM2 isoform. PKM1 favors the use of pyruvate in the tricarboxylic acid cycle in normal cells, while PKM2 favors the conversion of pyruvate into lactate inducing progression of colorectal cancer (CRC). (Illustrations created with Biorender.com).

Figure 5

Production of circular RNAs (circRNAs) by lncRNA spliced variants ANRIL lncRNA gene can produce multiple splice variants. Transcripts with exons 5, 6, and 7 can generate by backsplicing a stable circRNA named circANRIL. CircANRIL modulates the maturation of the 47S pre-ribosomal RNA (pre-rRNA) by disrupting the WDR12-BOP1-PES1 complex. The absence of 47S pre-rRNA leads to nucleolar stress and p53-induced apoptosis in vascular smooth muscle cells and macrophages, thus contributing to preventing atherosclerosis. (Illustrations created with Biorender.com).

Figure 6

Deregulation of lncRNA spliced variants in diseases and cancer Examples of lncRNA splice variants deregulated in various diseases including multiple cancers. (Illustrations created with Biorender.com).