Whole transcriptome analyses in many organisms have revealed that most transcribed RNAs do not encode proteins. These non-coding RNAs likely contribute to the regulation of gene expression during the development of multicellular organisms. In eukaryotes, the roles of small RNAs, one class of non-coding RNAs, in transcriptional and post-transcriptional regulation have been well characterized. However, the functions of a second class of non-coding RNAs, long intergenic noncoding (linc) RNAs, are relatively unknown, especially in plants. Recent advances in RNA-seq and tiling microarray technologies have revealed the presence of many lincRNAs across plant species.
One of the most well characterized functions of lincRNAs is to epigenetically regulate gene expression by recruiting proteins for chromosome modification to specific loci. Second, lincRNAs are known to inhibit the physical interaction between microRNAs (miRNAs) and their target mRNAs thus controling protein levels of the target mRNAs. Lastly, lincRNAs control alternative splicing by binding and sequestering the proteins required for alternative splicing.
Functions of lincRNAs in plants
a Transcriptional regulation of the PIF3 gene by HID1 under red light. Red light induces accumulation of HID1. HID1 physically associates with the proximal region of the PIF3 promoter. That binding negatively regulates transcription of the PIF3 gene. HID1 may recruit PRC2 complex for transcriptional regulation of PIF3. b Function of a lincRNA (IPS1) as endogenous target mimicry (eTM). In normal concentrations of phosphorus (Pi), PHO2 mRNA is degraded by miR399 guided cleavage via sequence complementary (left). IPS1 is induced under low Pi concentrations and binds to miR399 (right). However, the pairing is interrupted by a mismatch loop at the expected miR399 cleavage site, because degradation of IPS1 is impaired. That results in sequestering miR399 from PHO2 mRNAs. Finally, PHO2 mRNA is more intact by eTM effect of IPS1. c Alternative splicing regulation by ASCO-lncRNA. NSRs are required for alternative splicing to produce isoform1. For example, the intron between exon1 and exon2 is spliced out by NSRs (left). However, ASCO-lncRNA binds to NSRs and inhibits physical interaction between NSRs and the intron of pre-mRNA (right). Isoform2 is produced more efficiently by ASCO-lncRNA.