Eukaryotic lncRNAs

lncRNA refers to long noncoding RNA in eukaryotes. These RNAs act to regulate the expression of target genes. The long refers to the fact that RNA of this type is greater than 200 nucleotides in length. This distinguishes them from the shorter regulatory RNAs (miRNA, siRNA and piRNA) that are much less than 200 nucleotides. In fact the shorter regulatory RNAs are generally less than 30 nucleotides in the active form.

Not only is there a significant difference in length but the mechanism of how the RNAs regulate is quite different: unlike the shorter RNA, lncRNA is NOT involved in RNA interference. There is a lot of variation in how different lncRNAs act, including transcriptional and post-transcriptional regulation of targets. But there is one general shared feature: an lncRNA is involved in forming (with proteins) a ribonucleoprotein particle and the RNP is then involved in regulating a target gene. How this is accomplished is where the variation can occur, and in most cases the mechanisms are not well understood. However, the lncRNA component is typically involved in the process by the complementarity it has to some part of the target sequence.

lncRNAs are further subdivided based on the genome location from which the RNA is transcribed. Although they are themselves noncoding - meaning here that they do not code for a protein - the genome location from which they are transcribed can be described relative to locations that do code for proteins:

• asRNA - antisenseRNA. These are lncRNAs that are transcribed from the same genome location as a protein-coding gene. The lncRNA is transcribed from the opposite strand in this region making it complementary to the mRNA. Generally the asRNA is not just a full complement of the mRNA. Instead the asRNA just overlaps part of the mRNA.
• lincRNA - long intergenic noncoding RNA. These are lncRNAs that are transcribed from an intergenic region. They have complementarity to a target sequence and act via this complementarity but they are not transcribed from the same genome location as their target.
• intronic lncRNA. These are transcribed from an intron region of a protein-coding mRNA gene.

A well known example of a lncRNA is the Xist transcript that is involved in X inactivation in mammals as covered here. This provides one example of how an lncRNA can act to regulate gene expression.