RNA polymerase II (Pol II) transcribes two classes of RNAs, protein-coding and non-protein-coding (ncRNA) genes. ncRNAs are also synthesized by RNA polymerases I and III (Pol I and III). In humans, the number of ncRNA genes exceeds more than twice that of protein-coding genes. However, the history of studying Pol II-synthesized ncRNA is relatively short. Since early 2000s, important biological and pathological functions of these ncRNA genes have begun to be discovered and intensively studied. And transcription mechanisms of long non-coding RNA (lncRNA) have been recently reported. Transcription of lncRNAs utilizes some transcription factors and mechanisms shared in that of protein-coding genes. In addition, tissue specificity in lncRNA gene expression has been shown. LncRNAs play essential roles in regulating the expression of neighboring or distal genes through different mechanisms. This leads to the implication of lncRNAs in a wide variety of biological pathways and pathological development.
LncRNA-mediated gene expression regulation
The difference between mRNA and ncRNA is whether an RNA molecule is encoded into a protein (mRNA) or not (ncRNA, depicted in a red curvy line with a red star). In the nucleus, lncRNAs regulate transcription in cis or in trans. In cis means when lncRNA-mediated transcriptional regulation occurs at a gene(s) on the same chromosome. In contrast, lncRNA-mediated transcription regulation in trans occurs at a gene(s) on a different chromosome. Expressed lncRNAs can stabilize and protect mRNAs from miRNA-induced degradation and also facilitate translation of their client mRNAs in the cytoplasm. Ribosomes are shown in light blue circles aligned on an mRNA in an orange line. In addition, lncRNAs can be processed to generate hairpin-structured pre-miRNAs in nucleus and then transported to the cytoplasm where they become to be matured into miRNAs