Enhancer-promoter communication and transcriptional regulation of Igh

Abstract

Transcriptional regulation of eukaryotic protein-coding genes requires the participation of site-specific transcription factors that bind distal regulatory elements, as well as factors that, together with RNA polymerase II, form the basal transcription machinery at the core promoter. Gene regulation requires proper communication between promoters and enhancers, often over great distances. Therefore, it is important to understand the potentially inter-related transcription factor interactions at both of these elements. How this is achieved on tissue-specific genes, such as the immunoglobulin heavy chain (IgH) in B cells remains unclear. Here, we review known interactions at the Igh variable region (V(H)) promoters and present our perspective on promoter-enhancer interactions that are likely important for Ig gene regulation in B cells.

Figure 1

Model for formation of a pre-initiation complex (PIC) on the core promoter following local chromatin modifications. a) A chromatin template that has been remodeled through the action of histone modifying and ATP-dependent nucleosome remodeling factors (not shown). Ac, Me, and Ph represent acetylation, methylation and phosphorylation marks on histone tails, respectively. It is believed that nucleosomal displacement around the core promoter facilitates interactions of the general transcription machinery that result in formation of a preinitiation complex. b) A pre-initiation complex on a core promoter containing TATA, Inr and DPE elements at the normal positions. The minimal preinitiation complex contains RNA polymerase II (RNAPII) and the six GTFs (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that comprise the general transcriptional machinery, with site-specific TATA box interactions mediated exclusively by TBP and potential Inr and DPE interactions mediated by the TBP-associated factors (TAFs) that, for simplicity, are not shown individually. Following interactions with transcriptional activators at distal sites (not shown), the general transcriptional cofactors PC4 and Mediator may target multiple components of the general machinery and facilitate formation and/or function (initiation) of the pre-initiation complex.

Figure 2. Location and diversity of V_H promoters

(a) Architecture of the VDJ rearranged Igh gene. The locations of Eμ and the 3′-RR enhancers are shown. The V_H promoter is upstream of the recombined VDJ region. Various constant (C)-region genes are also indicated along with their promoters (distances are not to scale) (b) Diversity and architectures of various families of V_H promoters. Although the majority of the family members show the depicted architecture, there still exists considerable heterogeneity (ref. 9). While the positions and functions of both TATA box and octamer (Oct) elements are experimentally determined, the positions of the Inr, DICE and Pu.1 elements are based on sequence analyses (ref. 9). Functional contributions of the DICE element, both in isolation and in conjunction with Eμ have been shown in vitro. The functional significance of the putative Inr and Pu.1 elements in Igh transcription is predicted but experimentally undetermined.

Figure 3. Model for Igh promoter-enhancer communication

Due to potential interactions of TFII-I with both Inr and DICE (particularly in J558 V_H promoters), TFII-I is likely to have stable interactions with the core promoter. Because TFII-I also interacts with OCA-B, the latter is recruited to the V_H promoter as well. In this model, TFII-I also interacts with MAR-bound Bright transcription factor. By virtue of its interaction with both TFII-I and OCT1, OCA-B can facilitate communication between the core promoter, upstream octamer and the downstream 3′-RR, resulting in looping and juxtaposition of upstream and downstream elements. Although an interaction between the V_H promoter and the intronic/Eμ enhancer has not yet been shown, the fact that that Eμ harbors octamer sites that can bind OCT1/2-OCA-B raises the possibility that core promoter-bound TFII-I–OCA-B can also interact with Eμ-bound OCT1/2-OCA-B during early stages of B cell development. Likewise, proximal promoter-bound OCT1/2-OCA-B can interact with core promoter-bound TFII-I–OCA-B. Dotted arrows depict the presumptive interactions, while the solid arrow indicates the demonstrated interaction. Ikaros interacts with the 3′-RR and inhibits transcription, although its role in promoter-enhancer communication is untested. In addition, both TFII-I and OCA-B appear to be downstream of the BCR/Btk signaling cascade, thereby potentially connecting BCR signaling to IgH transcription.