Evolutionary conservation of long non-coding RNAs; sequence, structure, function

Abstract

Background: Recent advances in genomewide studies have revealed the abundance of long non-coding RNAs (lncRNAs) in mammalian transcriptomes. The ENCODE Consortium has elucidated the prevalence of human lncRNA genes, which are as numerous as protein-coding genes. Surprisingly, many lncRNAs do not show the same pattern of high interspecies conservation as protein-coding genes. The absence of functional studies and the frequent lack of sequence conservation therefore make functional interpretation of these newly discovered transcripts challenging. Many investigators have suggested the presence and importance of secondary structural elements within lncRNAs, but mammalian lncRNA secondary structure remains poorly understood. It is intriguing to speculate that in this group of genes, RNA secondary structures might be preserved throughout evolution and that this might explain the lack of sequence conservation among many lncRNAs.

Scope of review: Here, we review the extent of interspecies conservation among different lncRNAs, with a focus on a subset of lncRNAs that have been functionally investigated. The function of lncRNAs is widespread and we investigate whether different forms of functionalities may be conserved.

Major conclusions: Lack of conservation does not imbue a lack of function. We highlight several examples of lncRNAs where RNA structure appears to be the main functional unit and evolutionary constraint. We survey existing genomewide studies of mammalian lncRNA conservation and summarize their limitations. We further review specific human lncRNAs which lack evolutionary conservation beyond primates but have proven to be both functional and therapeutically relevant.

General significance: Pioneering studies highlight a role in lncRNAs for secondary structures, and possibly the presence of functional "modules", which are interspersed with longer and less conserved stretches of nucleotide sequences. Taken together, high-throughput analysis of conservation and functional composition of the still-mysterious lncRNA genes is only now becoming feasible.

Keywords: Antisense RNA; Epigenetic; Evolution; Long non-coding RNA; Polypurines; Secondary structure.

Figure 1. HOTAIR mediated chromatin remodeling

LncRNA HOTAIR functions as a scaffold and brings the chromatin remodeling factors PRC2 and LSD1 in close proximity to each other. PRC2 and LSD1 interact with two separate RNA modules in HOTAIR, which are connected with a linker. The HOTAIR:protein complex is recruited to polypurines by a so far unknown mechanism, whereby suppressive epigenetic marks, such as H3K27me3 is induced.

Figure 2. In-cis mediated regulation may be controlled by tethering

(A) Ongoing transcription tethers the asRNA transcript to the genomic locus. A DNA-RNPII-RNA complex maintains the tethering and its cis location. (B) The genomic sequence is not of importance, as long as the transcription, and tethering, is ongoing. (C) The asRNA contain a structure with the capacity to bind and recruit RNA biding proteins and ultimately regulates the expression of the protein coding sense gene. (D) Once transcription of the asRNA stops, the asRNA loses location and capacity to regulate the sense gene.

Figure 3. In-trans mediated asRNA regulation of PTEN

(A) The PTENpg1 locus encodes for three different lncRNAs; PTENpg1 sense, PTENpg1 asRNA alpha and beta. (B) The PTENpg1 asRNA beta interacts with and stabilizes the PTENpg1 sense through RNA:RNA interactions, (C) whereby microRNA sponging and consequently PTEN translation is affected. (D) The PTENpg1 asRNA alpha does not interact with PTENpg1 sense, presumably due to RNA secondary structures. (E) The PTENpg1 asRNA alpha binds the chromatin remodeling factors DNMT3a and EZH2 and (F) is recruited to the PTEN promoter where (G) transcriptional repression is induced by the formation of H3K27me3.