Non-canonical functions of enhancers: regulation of RNA polymerase III transcription, DNA replication, and V(D)J recombination

Abstract

Enhancers are the key regulators of other DNA-based processes by virtue of their unique ability to generate nucleosome-depleted regions in a highly regulated manner. Enhancers regulate cell-type-specific transcription of tRNA genes by RNA polymerase III (Pol III). They are also responsible for the binding of the origin replication complex (ORC) to DNA replication origins, thereby regulating origin utilization, replication timing, and replication-dependent chromosome breaks. Additionally, enhancers regulate V(D)J recombination by increasing access of the recombination-activating gene (RAG) recombinase to target sites and by generating non-coding enhancer RNAs and localized regions of trimethylated histone H3-K4 recognized by the RAG2 PHD domain. Thus, enhancers represent the first step in decoding the genome, and hence they regulate biological processes that, unlike RNA polymerase II (Pol II) transcription, do not have dedicated regulatory proteins.

Keywords: DNA replication; Enhancers; RNA polymerase III; V(D)J recombination; chromatin accessibility; gene expression.

Figure 1:

Mechanism by which enhancers stimulate Pol II transcription. (A) A segment of DNA (black bars) containing nucleosomes (Nuc; red ovals) with X, Y, Z binding sites for transcription factors (different colored shapes). (B) The combined action of the activator proteins recruits chromatin modifying complexes (yellow shapes) that remodel nucleosomes (e.g., Swi/Snf) or acetylate histones (e.g. SAGA). (C) Structure of enhancer-modified chromatin showing depleted nucleosomes (light red oval) acetylated histones (green asterisks). (D) Bidirectional transcription from enhancers (purple arrows) and associated recruitment of Set1/MLL histone methylases and generation of localized H3K4me3 regions of chromatin (blue number sign).

Figure 2:

Enhancers, via effects on chromatin, regulate Pol III transcription, DNA replication, and V(D)J recombination. (A) TFIIIC binds the A and B boxes in accessible chromatin, thereby permitting recruitment of TFIIIB and Pol III resulting in transcription. Cell types where the enhancer is inactive are unable to bind TFIIIC and support Pol III transcription. (B) The origin replication complex (ORC) binds enhancer-mediated regions depleted for nucleosomes but having acetylated histones. ORC recruits the MCM helicase to start the process of bidirectional DNA replication. (C) The RAG1/RAG2 V(D)J recombinase binds target sequences (RSS) in enhancer-mediated regions depleted for nucleosomes. Binding of RAG2 is facilitated by binding of the PHD domain of RAG2 to H3K4me3 marks (blue box; arrows pointing to methylation marks) generated by recruitment of Set1/MLL histone methylases during the generation of enhancer-RNAs.