Rare event of histone demethylation can initiate singular gene expression of olfactory receptors

Abstract

Mammals sense odors through the gene family of olfactory receptors (ORs). Despite the enormous number of OR genes (∼1,400 in mouse), each olfactory sensory neuron expresses one, and only one, of them. In neurobiology, it remains a long-standing mystery how this singularity can be achieved despite intrinsic stochasticity of gene expression. Recent experiments showed an epigenetic mechanism for maintaining singular OR expression: Once any ORs are activated, their expression inhibits further OR activation by down-regulating a histone demethylase Lsd1 (also known as Aof2 or Kdm1a), an enzyme required for the removal of the repressive histone marker H3K9me3 on OR genes. However, it remains unclear at a quantitative level how singularity can be initiated in the first place. In particular, does a simple activation/ feedback scheme suffice to generate singularity? Here we show theoretically that rare events of histone demethylation can indeed produce robust singularity by separating two timescales: slow OR activation by stepwise H3K9me3 demethylation, and fast feedback to turn off Lsd1. Given a typical 1-h response of transcriptional feedback, to achieve the observed extent of singularity (only 2% of neurons express more than one ORs), we predict that OR activation must be as slow as 5-10 d-a timescale compatible with experiments. Our model further suggests H3K9me3-to-H3K9me2 demethylation as an additional rate-limiting step responsible for OR singularity. Our conclusions may be generally applicable to other systems where monoallelic expression is desired, and provide guidelines for the design of a synthetic system of singular expression.neurogenesis | stochastic gene expression | histone modification | kinetics modeling | negative feedback I n mammals, the ability to sense odors relies on the singular expression of the olfactory receptor (OR) gene family. Despite the enormous family size (∼1,400 genes in the mouse genome), each sensory neuron only expresses one single allele of OR (1-4). It has long been thought that this singularity stems from a negative feedback in which the expression of one OR specifically silences all other ORs (5-7). However, this hypothesis has led to the question of how the one, and only one, active OR can escape its own silencing effect. In other words, it was unclear how such silencing can be biologically feasible.A series of recent studies provoked a different mechanism for OR singularity in light of epigenetic regulation. Contrary to previous belief, Magklara et al. (8) found that silencing of OR genes precedes OR expression: The histone marker H3K9me2 on OR genes become methylated into H3K9me3 as early as in the stage of neuronal progenitors, which do not yet express any ORs. H3K9me2 is a marker for localization of inactive genes into facultative heterochromatin; its further methylation into H3K9me3, however, marks OR genes for constitutive heterochromatinnuclear compartments that normally contain pericentromeric and telomeric regions. With this marker, all OR genes are deeply repressed i...

Heterochromatin-Mediated Gene Silencing Facilitates the Diversification of Olfactory Neurons

“…Thus, for most ORs, H3K9 demethylation is necessary but not sufficient for expression at high cellular levels. Although recent theoretical calculations support that a slow demethylation process combined with a fast feedback can explain singular OR expression (Tan et al, 2013), our experimental findings suggest that an additional regulatory layer may also contribute to the singularity of OR choice. Were the absence of H3K9 methylation sufficient for robust OR transcription, then most G9a/GLP KO OSNs should express multiple ORs at high levels.…”

“…Because perturbations in the OR-elicited feedback result in frequent OR switching but not simultaneous co-expression of multiple OR alleles (Dalton et al, 2013; Lyons et al, 2013), the latter hypothesis is more likely. However, recent theoretical models suggest that singular OR expression could also be explained just by a combination of a slow H3K9 demethylation process and a fast feedback that blocks further demethylation(Tan et al, 2013). In this scenario, removal of the repressive histone marks from a randomly chosen OR allele could be essential and sufficient for OR expression, a hypothesis supported by pharmacological inhibition of G9a/GLP in zebrafish embryos(Ferreira et al, 2014).…”

Monoallelic Expression of Olfactory Receptors

“…Recent theoretical studies have shown that monoallelic OR choice can be modeled with mechanisms similar to those described above, namely OR derepression and the subsequent inhibition of the derepressing mechanism (Alsing & Sneppen 2013, Tan et al 2013). The success of this simple activation–feedback mechanism depends on the ratio between the average time it takes to activate an OR and the time it takes for feedback inhibition to occur (Tan et al 2013). Coexpression occurs if the activation of a second OR occurs shortly after the activation of the first—that is, before feedback inhibition can shut off the derepression mechanism.…”

KDM1 Histone Lysine Demethylases as Targets for Treatments of Oncological and Neurodegenerative Disease

“…Once a functional OR has been activated, rapid induction of Adenylyl Cyclase 3 provides feedback downregulation of KDM1A, preventing both the activation of other OR genes and downregulation of the OR by repressive KDM1A complexes. This allows for terminal differentiation and locks each individual OSN in a state of sustained expression of a single olfactory receptor ( Figure 3D) [86,87].…”

“…If the OR is functional, Adcy3 is activated and KDM1A expression downregulated, allowing for the continued expression of that OR. If the OR is not functional, Adcy is not activated and the expression of another OR is attempted [86,87] future science group KDM1 treatments of oncological & neurodegenerative disease Review out that they could not exclude the possibility that the effect was provoked by inhibition of MAOs, which can perturb glucocorticoid receptors in the hippocampus and affect memory consolidation [109]. Indeed, RN-1 was administered as a single high dose which is incompatible with repeated administration [tamara maes, unpublished Data].…”