Genome regulation by long noncoding RNAs

Abstract

The central dogma of gene expression is that DNA is transcribed into messenger RNAs, which in turn serve as the template for protein synthesis. The discovery of extensive transcription of large RNA transcripts that do not code for proteins, termed long noncoding RNAs (lncRNAs), provides an important new perspective on the centrality of RNA in gene regulation. Here, we discuss genome-scale strategies to discover and characterize lncRNAs. An emerging theme from multiple model systems is that lncRNAs form extensive networks of ribonucleoprotein (RNP) complexes with numerous chromatin regulators and then target these enzymatic activities to appropriate locations in the genome. Consistent with this notion, lncRNAs can function as modular scaffolds to specify higher-order organization in RNP complexes and in chromatin states. The importance of these modes of regulation is underscored by the newly recognized roles of long RNAs for proper gene control across all kingdoms of life.

Figure 1

Timeline of discoveries of RNAs in biological regulation.

Figure 2. Anatomy of lncRNA loci

lncRNAs are often defined by their location relative to nearby protein coding genes. Antisense lncRNAs are lncRNAs that initiate inside of a protein coding gene and transcribe in the opposite direction that overlaps coding exons. Intronic lncRNAs are lncRNAs that initiate inside of an intron of a protein coding gene in either direction and terminates without overlapping exons. Bidirectional lncRNAs are transcripts that initiate in a divergent fashion from a promoter of a protein coding gene; the precise distance cut-off that constitutes bidirectionality is not defined but is generally within a few hundred base pairs. Finally, intergenic lncRNAs (also termed large intervening noncoding RNAs or lincRNAs) are lncRNAs with separate transcriptional units from protein coding genes. One definition required lincRNAs to be 5 kb away from protein coding genes (44).

Figure 3. Functional discovery pipeline of lncRNAs

A, Genome-wide discovery of lncRNAs. Chromatin marks of transcription initiation (H3K4me3) and elongation (H3K36me3) define transcribed regions of the genome, while sequencing of capped RNA fragments (CAGE-tag) or poly-adenylation ends (3P-seq) defined the precise beginning and ends of transcripts. RNA-seq can directly define the primary structure of lncRNAs. B, Multiple bioinformatic tools and functional studies refine the set of lncRNAs associated with specific biological functions.

Figure 4. Models of lncRNA mechanisms of action

LncRNA can act as decoys that titrate away DNA-binding proteins such as transcription factors. LncRNAs may act as scaffolds to bring two or more proteins into a complex or spatial proximity. LncRNAs may also act as guides to recruit proteins, such as chromatin modification enzymes, to DNA; this may occur through RNA-DNA interactions or RNA interaction with a DNA binding protein. LncRNA guidance can also be exerted through chromosome looping in an enhancer-like model, where the looping defines the cis nature and spread of the lncRNA effect.