Transcriptional gene silencing in humans

Abstract

It has been over a decade since the first observation that small non-coding RNAs can functionally modulate epigenetic states in human cells to achieve functional transcriptional gene silencing (TGS). TGS is mechanistically distinct from the RNA interference (RNAi) gene-silencing pathway. TGS can result in long-term stable epigenetic modifications to gene expression that can be passed on to daughter cells during cell division, whereas RNAi does not. Early studies of TGS have been largely overlooked, overshadowed by subsequent discoveries of small RNA-directed post-TGS and RNAi. A reappraisal of early work has been brought about by recent findings in human cells where endogenous long non-coding RNAs function to regulate the epigenome. There are distinct and common overlaps between the proteins involved in small and long non-coding RNA transcriptional regulatory mechanisms, suggesting that the early studies using small non-coding RNAs to modulate transcription were making use of a previously unrecognized endogenous mechanism of RNA-directed gene regulation. Here we review how non-coding RNA plays a role in regulation of transcription and epigenetic gene silencing in human cells by revisiting these earlier studies and the mechanistic insights gained to date. We also provide a list of mammalian genes that have been shown to be transcriptionally regulated by non-coding RNAs. Lastly, we explore how TGS may serve as the basis for development of future therapeutic agents.

Figure 1.

Regulatory non-coding RNA timeline. A timeline of some important observations in RNA biology are shown leading up to our collective understanding of non-coding RNA-directed transcriptional gene silencing (TGS). (,,–177).

Figure 2.

Small non-coding RNA pathways in human cells. Small non-coding RNAs can be generated as priRNAs where they are (A) processed by Drosha and DGCR8 into miRNAs which are (B) exported from the nucleus and (C) loaded into RISC where they can affect mRNA expression by (D) binding and blocking mRNA translation or (E) cutting the target mRNA. Some miRNAs may also be retained in the nucleus (F) where they can interact with epigenetic remodeling proteins and (G) recruit the complexes to target loci in the genome resulting in (H) localized chromatin compaction and epigenetic silencing.

Figure 3.

Antisense RNA-directed TGS. Small antisense non-coding RNAs can be (A) introduced into the nucleus and (B) interact with and recruit epigenetic silencing complexes consisting of DNMT3a, Ago1, EZH2 and HDAC1 to homology containing targeted loci by interactions with low copy promoter-associated transcripts resulting in (C) epigenetic silencing consisting of histone and DNA methylation and ultimately chromatin compaction of the targeted locus. (D) Long antisense non-coding RNAs have also been observed to interact with similar epigenetic silencing complexes (53,54) and (E) localize with these complexes at targeted loci resulting in (C) epigenetic silencing of the lncRNA targeted locus.

Figure 4.

LncRNA pathways of transcriptional silencing and de-repression. LncRNAs can be expressed in (A) Cis or trans and can (B) interact with those proteins involved in epigenetic silencing. The lncRNAs act to (C) target and tether the epigenetic silencing complexes to homology containing loci resulting in (D) chromatin compaction and transcrtiptinal gene silencing of the targeted locus. These endogenous regulatory lncRNAs can be targeted with (E) antisense oligonucleotides or (F) siRNAs, which results in the loss of the lncRNA and activation/de-repression of those loci actively under lncRNA regulation.