It has recently become apparent that RNA, itself the product of transcription, is a major regulator of the transcriptional process. In particular, long noncoding RNAs (lncRNAs), which are so numerous in eukaryotes, function in many cases as transcriptional regulators. These RNAs function through binding to histone-modifying complexes, to DNA binding proteins (including transcription factors), and even to RNA polymerase II. In other cases, it is the act of lncRNA transcription rather than the lncRNA product that appears to be regulatory. Researchers from the University of Colorado, Boulder discuss the recent progress in elucidating the molecular mechanisms by which lncRNAs modulate gene expression and future opportunities in this research field.
ncRNAs regulate transcription through DNA binding proteins
lncRNAs (and sometimes miRNAs) interact with DNMTs, resulting in recruitment or inhibition of DNMTs at chromatin loci. Alteration of DNA methylation (m5C) level generally affects local transcription. lncRNA–transcription factor interactions can either recruit or evict transcription factors from chromatin, and this action can be either in cis (demonstrated in figure) or in trans. eRNA transcribed from an enhancer region can contribute to chromatin looping and gene activation. lncRNAs interact with the chromatin insulator CCCTC-binding factor (CTCF) and regulate transcription. The mechanism may involve CTCF’s action in chromatin looping and nuclear architecture. TSS, transcription start site