Conservation and tissue-specific transcription patterns of long noncoding RNAs

Abstract

Over the past decade, the focus of molecular biology has shifted from being predominately DNA and protein-centric to having a greater appreciation of RNA. It is now accepted that the genome is pervasively transcribed in tissue- and cell-specific manner, to produce not only protein-coding RNAs, but also an array of noncoding RNAs (ncRNAs). Many of these ncRNAs have been found to interact with DNA, protein and other RNA molecules where they exert regulatory functions. Long ncRNAs (lncRNAs) are a subclass of ncRNAs that are particularly interesting due to their cell-specific and species-specific expression patterns and unique conservation patterns. Currently, individual lncRNAs have been classified functionally; however, for the vast majority the functional relevance is unknown. To better categorize lncRNAs, an understanding of their specific expression patterns and evolutionary constraints are needed.

Keywords: RNA-Seq; comparative genomics; gene regulation; lncRNAs; transcriptome.

Figure 1.

Genomic localization-based classes of lncRNAs. Upper panel: Intronic lncRNA: the lncRNA is transcribed from an intronic region of a protein-coding gene. Antisense lncRNA: the lncRNA is transcribed from the strand opposite to protein-coding gene, with partial or complete overlap of any intronic or exonic regions. Intergenic/intervening lncRNA: the lncRNA is transcribed from a region located between other genes. There is no overlap with any protein-coding genes. Overlapping lncRNA: The intron of the lncRNA encompasses a protein-coding gene. Bidirectional lncRNA: The lncRNA shares its transcription start site with a protein-coding gene on the opposite strand. Arrows indicate orientation of transcription. Lower panel: lncRNAs can be alternatively spliced to produce numerous splice variants. Here, the intervening lncRNA is spliced to produce two variants. Each of these variants produces RNAs with unique secondary structure. The unique RNA secondary structure can determine function of the lncRNA isoform.