Kevin Monahan

Animal chemosensory systems discriminate between complex mixtures of chemical compounds by leveraging large repertoires of chemoreceptor proteins. To organize information from many receptors, these systems often employ a one-receptor-type per cell organization (Fulton et al. 2024). This structure requires a gene regulatory mechanism that can coordinate the generation of many distinct types of sensory neurons, each expressing a different receptor (Yusuf and Monahan 2024; Danoff et al. 2025; Pourmorady and Lomvardas 2022; Bashkirova and Lomvardas 2019; Monahan and Lomvardas 2015; Brann and Datta 2020). Here we show that testis-expressed gene 15 ( Tex15 ) is a critical component in an epigenetic mechanism that safeguards diverse olfactory receptor (OR) choice in the mouse olfactory system. Tex15 is required to inhibit an initial wave of olfactory receptor gene transcription that occurs as olfactory sensory neuron progenitors differentiate. In Tex15 knockout ( Tex15-/- ) mice, this repression fails: the early-transcribed OR genes get expressed at abnormally high levels, get chosen at high rates, and come to dominate the neuronal population. This results in a profound reduction in the diversity of OR gene choice and disrupted spatial patterning of the olfactory epithelium, while maintaining the expression of one receptor per cell. These changes in OR gene expression are accompanied by reduced deposition of H3K9me3 heterochromatin on OR genes and the preferential formation of interchromosomal enhancer hubs around the dominant ORs. We propose that Tex15 directs a heterochromatin-based transcriptional repression mechanism that counter-balances early OR transcription, thereby preventing the heterogeneous onset of OR transcription from skewing OR choice.

Diverse epigenetic regulatory mechanisms ensure and modulate cellular diversity. The histone 3 lysine 9 me3 (H3K9me3) post-translational modification participates in silencing lineage-inappropriate genes by restricting access of transcription factors and other regulatory proteins to genes that control cell fate. Mouse olfactory sensory neurons (OSNs) select one olfactory receptor (OR) gene out of 2600 possibilities. This monoallelic and stochastic OR choice occurs as OSNs differentiate and undergo dramatic changes in nuclear architecture. OR genes from different chromosomes converge into specialized nuclear bodies and chromatin compartments, as H3K9me3 and chromatin binding proteins including heterochromatin protein 1 (HP1) are incorporated. In this work, we have uncovered an unexpected role for HP1β in OR choice and neuronal identity that cannot be rescued by HP1α in vivo. With the use of a conditional knock-in mouse model, that after CRE expression replaces HP1β with HP1α, we observe changes in H3K9me3 levels and DNA accessibility over OR gene clusters. These changes alter the expression patterns that partition the mouse olfactory epithelium into five OR expression zones, which results in a reduced OR repertoire that leads to a loss of olfactory sensory neuron diversity. We propose that HP1β modulates the competition of OR promoters for enhancers to promote receptor diversity by establishing repression gradients in a zonal fashion.

The mouse vomeronasal organ (VNO) detects pheromones, which provide vital information needed to find a mate, detect predators, or alert to the presence of an intruder. Within the VNO, pheromones are sensed by two families of G-protein Coupled Receptors (GPCRs) the type 1 and type 2 vomeronasal receptors (V1Rs and V2Rs). However, little is known about the regulatory mechanisms that control the expression of V1R and V2R genes by vomeronasal sensory neurons (VSNs). Here we identify a transcriptional repressor, Testis-expressed gene 15 ( Tex15 ), that regulates vomeronasal receptor gene choice and is required for the proper functioning of the vomeronasal system in regulating male behavior. We find that Tex15 is transiently expressed by VSN precursors prior to strong VR gene expression. The absence of Tex15 results in a pervasive change in the expression of V1R and V2R genes, which results in a less diverse repertoire of VR expressing cells and includes a dramatic reduction in the expression of specific receptors that have been tied to intermale aggression. Accordingly, Tex15 knockout mice exhibit lowered activation in the Accessory Olfactory Bulb (AOB) after exposure to male odorants, and a loss of stereotyped aggression between male mice. Taken together, these results show that Tex15 plays a critical role in pheromone sensing by ensuring that VSNs express a diverse set of receptor proteins.

The mammalian olfactory system enables the detection of a wide variety of chemical compounds via the expression of a repertoire of olfactory receptors comprising the largest gene family in the mammalian genome. Olfactory sensory neurons (OSNs) each express only 1 odorant receptor (OR) gene. In mice, this requires activation of 1 OR gene and repression of over 1,400 other OR genes. In this review, we describe the mechanisms that support the transcription of OR genes and how these mechanisms impact which OR is expressed in each neuron. First, we discuss what is currently known about the role of transcription in OR choice. We then describe the role of specific features of OR genes and enhancers in the regulation of OR transcription. Finally, we discuss characteristics of OSNs which specify transcription of some OR genes while restricting the transcription of others.

Neuronal connectivity is essential for adaptive brain responses and can be modulated by dendritic spine plasticity and the intrinsic excitability of individual neurons. Dysregulation of these processes can lead to aberrant neuronal activity, which has been associated with numerous neurological disorders including autism, epilepsy, and Alzheimer's disease. Nonetheless, the molecular mechanisms underlying abnormal neuronal connectivity remain unclear. We previously found that the serine/threonine kinase Microtubule Affinity Regulating Kinase 2 (MARK2), also known as Partitioning Defective 1b (Par1b), is important for the formation of dendritic spines in vitro. However, despite its genetic association with several neurological disorders, the in vivo impact of MARK2 on neuronal connectivity and cognitive functions remains unclear. Here, we demonstrate that the loss of MARK2 in vivo results in changes to dendritic spine morphology, which in turn leads to a decrease in excitatory synaptic transmission. Additionally, the loss of MARK2 produces substantial impairments in learning and memory, reduced anxiety, and defective social behavior. Notably, MARK2 deficiency results in heightened seizure susceptibility. Consistent with this observation, electrophysiological analysis of hippocampal slices indicates underlying neuronal hyperexcitability in MARK2‐deficient neurons. Finally, RNAseq analysis reveals transcriptional changes in genes regulating synaptic transmission and ion homeostasis. These results underscore the in vivo role of MARK2 in governing synaptic connectivity, neuronal excitability, and cognitive functions.

Olfactory receptor (OR) choice provides an extreme example of allelic competition for transcriptional dominance, where every olfactory neuron stably transcribes one of approximately 2,000 or more OR alleles^1,2. OR gene choice is mediated by a multichromosomal enhancer hub that activates transcription at a single OR^3,4, followed by OR-translation-dependent feedback that stabilizes this choice^5,6. Here, using single-cell genomics, we show formation of many competing hubs with variable enhancer composition, only one of which retains euchromatic features and transcriptional competence. Furthermore, we provide evidence that OR transcription recruits enhancers and reinforces enhancer hub activity locally, whereas OR RNA inhibits transcription of competing ORs over distance, promoting transition to transcriptional singularity. Whereas OR transcription is sufficient to break the symmetry between equipotent enhancer hubs, OR translation stabilizes transcription at the prevailing hub, indicating that there may be sequential non-coding and coding mechanisms that are implemented by OR alleles for transcriptional prevalence. We propose that coding OR mRNAs possess non-coding functions that influence nuclear architecture, enhance their own transcription and inhibit transcription from their competitors, with generalizable implications for probabilistic cell fate decisions.

Neuronal connectivity is essential for adaptive brain responses and can be modulated by dendritic spine plasticity and the intrinsic excitability of individual neurons. Dysregulation of these processes can lead to aberrant neuronal activity, which has been associated with numerous neurological disorders including autism, epilepsy, and Alzheimer’s disease. Nonetheless, the molecular mechanisms underlying aberrant neuronal connectivity remains unclear. We previously found that the serine/threonine kinase Microtubule Affinity Regulating Kinase 2 (MARK2), also known as Partitioning Defective 1b (Par1b), is important for the formation of dendritic spines in vitro. However, despite its genetic association with several neurological disorders, the in vivo impact of MARK2 on neuronal connectivity and cognitive functions remains unclear. Here, we demonstrate that loss of MARK2 in vivo results in changes to dendritic spine morphology, which in turn leads to a decrease in excitatory synaptic transmission. Additionally, loss of MARK2 produces substantial impairments in learning and memory, anxiety, and social behavior. Notably, MARK2 deficiency results in heightened seizure susceptibility. Consistent with this observation, RNAseq analysis reveals transcriptional changes in genes regulating synaptic transmission and ion homeostasis. These findings underscore the in vivo role of MARK2 in governing synaptic connectivity, cognitive functions, and seizure susceptibility.

The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. This architecture is constrained by the DNA polymer, which precludes interactions between genes on different chromosomes. Here we report a marked divergence from this pattern of nuclear organization that occurs in mouse olfactory sensory neurons. Chromatin conformation capture using in situ Hi-C on fluorescence-activated cell-sorted olfactory sensory neurons and their progenitors shows that olfactory receptor gene clusters from 18 chromosomes make specific and robust interchromosomal contacts that increase with differentiation of the cells. These contacts are orchestrated by intergenic olfactory receptor enhancers, the ‘Greek islands’, which first contribute to the formation of olfactory receptor compartments and then form a multi-chromosomal super-enhancer that associates with the single active olfactory receptor gene. The Greek-island-bound transcription factor LHX2 and adaptor protein LDB1 regulate the assembly and maintenance of olfactory receptor compartments, Greek island hubs and olfactory receptor transcription, providing mechanistic insights into and functional support for the role of trans interactions in gene expression.