Olfactory receptor choice: a case study for gene regulation in a multi-enhancer system

Abstract

The mammalian genome possesses >2000 olfactory receptor (OR) alleles regulated by 63 known OR-Enhancer elements, yet each olfactory sensory neuron (OSN) expresses only a single OR allele. Choreographed changes to OSN nuclear architecture are evidently necessary for OR expression. Additionally, the insulated organization of OR-enhancers around an OR allele is a hallmark of the chosen OR. However, the biology guiding OR choice itself is unclear. Innovations in single-cell and biophysics-based analysis of nuclear architecture are revising previous models of the nucleus to include its dynamic and probabilistic nature. In this review, we ground current knowledge of OR gene regulation in these emerging theories to speculate on mechanisms that may give rise to diverse and singular OR expression.

Figure 1. OSN Development and OR Choice

(A) Differentiating olfactory epithelium stem cells downregulate Lamin b receptor (Lbr) allowing for nuclear inversion. H3K9me3 and H4K20me3 constitutive heterochromatin marks are laid onto OR genes, which organize into several OR compartments around a heterochromatic core, forming the characteristic “fried egg” appearance of mature OSN nuclei. (B) Singular OR expression is maintained by a multi-enhancer hub in mature OSNs. OR-Enhancers, known as Greek Islands, are co-bound by transcription factors EBF and Lhx2. Lhx2 interacts with the Lim-domain binding protein, Ldb1, which supports intra- and inter-chromosomal contact of Greek Islands to the active OR locus. The remaining OR repertoire is heterochromatically silent.

Figure 2. Deterministic and Probabilistic Models of OR Choice

(A & C) In a simple deterministic model of OR choice each of the > 2000 OR alleles has a requirement of specific enhancers, in cis and trans, that will support its expression. Similarly, each of the 126 Greek Island alleles has the capacity to support the expression of one or more specific ORs. While the activation of pink, green, and cyan enhancers individually support the expression of many ORs, only olfr715 has its entire enhancer requirement satisfied. Therefore, only olfr715 can become the chosen OR. (B & D) In a probabilistic model of OR choice low frequency histone demethylation makes few OR alleles available for expression and heterogeneous OSN nuclear architecture is the main driving force for diverse OR choice. Stochastic genome organization randomly supplies OR genes with nearby enhancers and transcriptional machinery. Only the OR that is best positioned and can sufficiently recruit transcriptional resources will then escape re-inhibition to become the chosen OR.

Figure 3. Chromatin Dynamics and Transcription

(A) A representative bulk Hi-C map from a mouse OSN depicts the nested organization of TADs, indicated by overlapping yellow triangles, on chromosome 2. (B) These cartoons illustrate the variable conformations TADs on chromosome 2 can take when observed in single-cell. (C) Looping of the LCR onto the ß-globin gene increases transcription burst frequency. (D) Proximity of the Sox2 enhancer, SCR, to the Sox2 locus, is not correlated with levels of transcription.