Long Non-Coding RNA in Controlling Chromatin Modification and Transcription.

Abstract

Long non-coding RNAs (lncRNAs) are present in many eukaryotes and have an important function in controlling transcription. In the Transcriptional Gene Silencing (TGS) pathway lncRNAs can act as scaffolds for RNA binding proteins to target specific loci and affect chromatin structure. In many organisms genetic studies of TGS are limited because lncRNAs are produced by RNA Polymerase II (Pol II), the same polymerase responsible for transcribing protein coding genes. This limitation is overcome by using the model organism Arabidopsis thaliana in which lncRNA is produced by Pol V. Pol V is a specialized RNA polymerase which recently has evolutionarily diverged from Pol II in plants. Knockout mutants of Pol V allow the study of pathways involving lncRNA without disrupting the essential Pol II machinery. This tool has allowed discovery of many mechanistic principles of TGS. In this pathway, ARGONAUTE 4 binds to small interfering RNA (siRNA) and to lncRNA for chromatin targeting. Other proteins, SUPRESSOR OF TY INSERTION 5-LIKE (SPT5L) and INVOLVED IN DE NOVO 2 (IDN2) also bind to Pol V transcripts and are important for TGS. Components of TGS are essential for directing histone modification and de novo DNA methylation to affect Pol II transcription at specific loci. While this was thought to mainly occur to silence transposons, this work shows that TGS components localize to promoters and function in controlling gene expression. I also demonstrate that TGS is important for positioning nucleosomes, and that AGO4, IDN2, and SPT5L are all important for this function. This is in contrast to directing DNA methylation where AGO4 plays a large role, while the contribution of SPT5L and IDN2 is minor. I also find that TGS can control gene expression long-range by inhibiting long distance chromatin interactions. Overall this work revolutionizes how we think of TGS and is a major contribution to the mechanistic knowledge on the functions of lncRNA.