Sizing up long non-coding RNAs: do lncRNAs have secondary and tertiary structure?

Abstract

Long noncoding RNAs (lncRNAs) play a key role in many important areas of epigenetics, stem cell biology, cancer, signaling and brain function. This emerging class of RNAs constitutes a large fraction of the transcriptome, with thousands of new lncRNAs reported each year. The molecular mechanisms of these RNAs are not well understood. Currently, very little structural data exist. We review the available lncRNA sequence and secondary structure data. Since almost no tertiary information is available for lncRNAs, we review crystallographic structures for other RNA systems and discuss the possibilities for lncRNAs in the context of existing constraints.

Keywords: HOTAIR; MALAT; RNA; RNA structure; cancer; epigenetics; hormone receptor; lincRNA; lncRNA; long noncoding RNA; non-coding; secondary structure; structural biology.

Figure 1. The first experimentally determined secondary structure of an intact lncRNA, to our knowledge. The steroid receptor RNA activator (SRA) lncRNA contains 4 subdomains, and 25 helices. The structure was determined using four methods of chemical (SHAPE, in-line, DMS) or enzymatic (RNase V1) probing. Covariance analysis based on multiple sequence alignment across vertebrates was used to help validate the structure. In SHAPE probing (selective 2’-hydroxyl acylation analyzed by primer extension), high reactivity corresponds to high mobility and low likelihood for base pairing; low reactivity corresponds to low mobility and high likelihood for base pairing. Orange, high SHAPE reactivity. Yellow, medium reactivity. Grey, low reactivity. Black, no reactivity. Insets: Red, SHAPE reactivity capillary electrophoresis trace for lncRNA. Green, raw blank trace.

Figure 2. Examples of RNA tertiary structures solved by crystallography. (A) Group II intron, solved by Pyle, Toor and coworkers. The intron is a highly-structured isolated RNA with compact core. (B) Telomerase RNA solved by Skordalakes and coworkers. (C) RNase P solved by Mondragon and coworkers. RNase P is a highly structured RNA with a single protein binding domain. (D) Ribosome, Ramakrishnan and coworkers. The ribosome is a highly structured and highly compact RNA complex containing ~50 proteins that help stabilize the RNA structure. The ribosome contains a limited number of factor binding sites. Different factors bind to the same binding sites, regulating protein synthesis.

Figure 3. Possibilities for lncRNA three-dimensional architecture. These homology models represent concepts for possible lncRNA 3D structures. (A) lncRNA (pink) contains a compact tertiary core. The lncRNA may have a main protein (green) binding site, responsible for binding various protein factors. (B) De-centralized scaffold. In this scenario, the lncRNA does not have a compact core. The lncRNA may have several protein (yellow) binding sites. (C) Loosely organized protein binding domain with regions of unstructured RNA. The lncRNA may contain several long stretches of disordered single stranded RNA.

Figure 4. An example of potentially relevant time scales for lncRNA activity: DBE-T lncRNA. DBE-T is a cis-acting tether than recruits epigenetic factors to chromatin. Steps af each have an associated timescale, t. (A) Initial state. (B) Transcription of DBE-T. (C) DBE-T folding. (D) The epigenetic factor binds to the lncRNA. (E) The epigenetic factor binds to chromatin. (F) The epigenetic factor marks the chromatin (e.g., histone methylation).