Stochastic gene expression in mammals: lessons from olfaction

Abstract

One of the remarkable characteristics of higher organisms is the enormous assortment of cell types that emerge from a common genome. The immune system, with the daunting duty of detecting an astounding number of pathogens, and the nervous system with the equally bewildering task of perceiving and interpreting the external world, are the quintessence of cellular diversity. As we began to appreciate decades ago, achieving distinct expression programs among similar cell types cannot be accomplished solely by deterministic regulatory systems, but by the involvement of some type of stochasticity. In the last few years our understanding of these non-deterministic mechanisms is advancing, and this review will provide a brief summary of the current view of stochastic gene expression with focus on olfactory receptor (OR) gene choice, the epigenetic underpinnings of which recently began to emerge.

Keywords: antigen receptors; clustered protocadherins; epigenetic mechanisms; nuclear architecture; olfactory receptors; stochasticity.

Figure I

Genomic organization and recombination in the immunoglobulin family

Figure 1. Allelic exclusion takes place in two phases where epigenetic mechanisms and nuclear repositioning play an important role

(a) In progenitor B cells both Igκ alleles are initially DNA hypermethylated (red circle). At a later stage one allele becomes histone acetylated (green circle) and subsequently it undergoes demethylation, it while the other allele is recruited to heterochromatin. Finally, VJ recombination is initiated at the “active” allele leading to juxtaposition of the segments, while the “repressed” allele remains unrearranged [18]. (b) In the maintenance phase the rearranged (active) IgH allele remains in an euchromatic region, is marked by histone acetylation (green stars) and H3K4me3 (blue circles) and can undergo transcription (arrow) [49]. The unrearranged allele is recruited to pericentromeric heterochromatin, adopts a “closed” chromatin structure [19] and is probably marked by DNA hypermethylation (red stars) and repressive histone modifications (yellow circles) that prevent a secondary rearrangement.

Figure 2. Stochastic choice and stabilization of expression in OR genes

The OR genes are marked by H3K9me3 (in pink) and H4K20me3 (in purple) and they form specific nuclear foci. The repressive histone marks serve as docking sites for HP1 proteins that play an essential role in heterochromatin packaging and spreading. Each OR cluster may be regulated by a distant enhancer element (H-like element). A stochastically chosen OR allele moves out of the repressive nuclear focus into a permissive transcriptional environment, where it can interact with its cognate enhancer. Enzymatic complex(es) with histone demethylase and/or methylase activities carry out the epigenetic switch from H3K9me3/H4K20me3 to H3K4me3. Once a functional OR protein is produced, a feedback signal is initiated that prevents de-silencing of the rest of the OR genes probably through targeting a histone demethylase complex.

Figure 3. Genomic organization and stochastic promoter choice in the mouse Pcdhα cluster

(a) The Pcdhα gene cluster consists of 14 variable and 3 constant exons. The black blocks indicate identified enhancers. (b) The promoter of the variable exon a7 is stochastically chosen and activated, probably via its interaction with cis-regulatory sequences (HS5-1 and HS7), leading to the splicing of exon a7 to the set of constant exons and generation of the mature mRNA (c). (d) Most of the promoters of the variable exons and the enhancer HS5-1 are bound by complexes of CTCF/cohesin, while the c2 promoter and the HS7 enhancer are bound only by cohesin[42]. (e) The activated promoter a7 and the enhancers form a DNA-loop that is mediated by the CTCF/cohesin complexes. The rest of the variable promoters are getting marked by DNA methylation and histone modifications (H3K9me3 and H4K20me3), while they lose the CTCF/cohesin complexes, thus they are led to a repressive state.