The Evolution and Expression Pattern of Human Overlapping lncRNA and Protein-coding Gene Pairs

Abstract

Long non-coding RNA overlapping with protein-coding gene (lncRNA-coding pair) is a special type of overlapping genes. Protein-coding overlapping genes have been well studied and increasing attention has been paid to lncRNAs. By studying lncRNA-coding pairs in human genome, we showed that lncRNA-coding pairs were more likely to be generated by overprinting and retaining genes in lncRNA-coding pairs were given higher priority than non-overlapping genes. Besides, the preference of overlapping configurations preserved during evolution was based on the origin of lncRNA-coding pairs. Further investigations showed that lncRNAs promoting the splicing of their embedded protein-coding partners was a unilateral interaction, but the existence of overlapping partners improving the gene expression was bidirectional and the effect was decreased with the increased evolutionary age of genes. Additionally, the expression of lncRNA-coding pairs showed an overall positive correlation and the expression correlation was associated with their overlapping configurations, local genomic environment and evolutionary age of genes. Comparison of the expression correlation of lncRNA-coding pairs between normal and cancer samples found that the lineage-specific pairs including old protein-coding genes may play an important role in tumorigenesis. This work presents a systematically comprehensive understanding of the evolution and the expression pattern of human lncRNA-coding pairs.

Non-Coding RNAs in Cutaneous Melanoma Development, Progression and Dissemination

“…Among more than 3,000 miRNAs [90] and 24,793 annotated lncRNAs that have been identified within the human genome [91], only a few show deregulations in cutaneous melanoma (Table 1). Nevertheless, we are only at the beginning of our understanding and identification of ncRNAs; recent computational analyses using high-throughput expression data, including microarrays and RNA sequencing, have helped us identify deregulated mRNAs, lncRNAs and pseudogenes in melanoma [92,93].…”

Natural Antisense Transcripts at the Interface between Host Genome and Mobile Genetic Elements

“…The observation in early computational experiments that antisense transcripts show splicing differences and often minimal sequence identity between closely related species argued against stringent conservation ( Veeramachaneni et al, 2004 ; Wood et al, 2013 ). However, recent reports based on microarray or RNAseq data, taking conserved transcription or expression patterns into account, confirm phylogenetic conservation of antisense transcription ( Ling et al, 2013 ; Hezroni et al, 2015 ; Ning et al, 2017 ).…”

“…Secondly, the complementary sense and antisense transcripts can hybridize and form a dsRNA intermediate ( Figure 2A ). This interaction potentially interferes with the processing of both RNAs, their splicing, nuclear export or even translation ( Hastings et al, 2000 ; Ning et al, 2017 ). Alternatively, dsRNA is recognized by enzymes that resolve the double-strand structure and trigger various cellular responses ( Wang and Carmichael, 2004 ).…”

Elucidating the Role of Host Long Non-Coding RNA during Viral Infection: Challenges and Paths Forward

“…When portions of lncRNAs overlap a coding gene, it is expected that this region be conserved and under a strong selective pressure. A recent study found that the evolutionary age, overlapping configuration, and local genomic environment of an lncRNA-coding gene pair influence the expression correlation of the pair [ 96 ]. While there needs to be further research of lncRNA-coding pairs in more well-annotated genomes, it is clear that positional information is important in understanding their functional relationship.…”