Thesis (doctoral)--Ludwig-Maximilians-Universität München, 2008. / Title from PDF t.p. (viewed on Jan. 8, 2009). Some chapters co-authored with others. Includes bibliographical references (p. 117-127).

Pattern formation during development is guided by tightly controlled gene regulatory networks that lead to reproducible cell fate outcomes. However, stochastic choices are often employed to further diversify cell fates. These two mechanisms are closely interlinked in the mouse olfactory system, where stochastic expression of one of one out of >1,000 olfactory receptor (OR) genes is restricted to anatomical segments, or “zones”, organized along the dorsoventral axis of the olfactory epithelium (OE). Despite recent progress in understanding the processes underlying OR choice, the mechanism by which the dorsoventral position of an olfactory sensory neuron (OSN) dictates its OR repertoire has remained elusive and is the focus of this thesis. To gain insight into a possible mechanism I compared the transcriptomes, chromatin landscape, and nuclear architecture of cells isolated from ventral and dorsal zonal segments of the OE. I determined the developmental window in which cells become restricted in their zonal OR repertoire and found this coincided with both the deposition of heterochromatic histone marks H3K9me3 and H3K79me3 on OR genes and their coalescence into a multi-chromosomal compartment. Comparing heterochromatin levels and OR compartment composition in OSNs from different zones, I determined in each case OR genes with more dorsal indexes have higher levels of H3K9me3/H3K79me3 and thus become silenced, while OR genes with more ventral indexes have no heterochromatin and consequently are excluded from OR compartments. Thus, ORs that are “competent” for activation are relatively more accessible, while still being recruited into the OR compartment where they can interact with the proximally positioned enhancer hub. I found that this mechanism is regulated by Nfi family transcription factors that are expressed in a ventral (high) to dorsal (low) gradient in the OE. Deletion of Nfi A, B and X transforms the heterochromatin and OR compartmentalization in ventral OSNs to a more dorsal state, and shifts their preferred OR repertoire towards more dorsal ORs. This result implicates Nfi proteins as key regulators of zonal OR expression. Finally, I probed the nuclear architecture in single cells to look for the source of stochastic choice within zonal segments. I found high variability in inter-chromosomal OR compartment and enhancer hub composition between individual OSNs that stemmed from the unpredictable and variable positioning of chromosomes in the interphase nucleus. Overall, this thesis provides evidence for a mechanism of zonal OR choice that combines deterministic restrictions imposed by a gradient of Nfi with random inter-chromosomal contacts.

Some of life’s most important behaviors are guided by the sense of smell. Detecting and interpreting odor information influences food-seeking, predator avoidance, sociality, competition, mating rituals, and more, shaping how organisms interact with their environment. In vertebrates, odors are detected by olfactory sensory neurons (OSNs) of the main olfactory epithelium (MOE). OSNs rely on olfactory receptors (ORs) to recognize odorants and trigger neural activation. The OR gene pool is typically vast, containing between 200-4000 olfactory receptor genes across mammals, yet mature OSNs stably express only one gene from one allele. Data from mice show that ORs are anatomically restricted to designated sections of the MOE, but within these zones, OR expression appears mosaic and random. Since the discovery of the OR gene pool 30 years ago, deciphering how OSNs choose which OR they are going to express remains a central question. While multiple differentiation-dependent alterations to the OSN nucleus are required for OR expression, the most notable contribution comes from the organization of OR-gene specific enhancers, called Greek Islands (GIs), around the chosen allele. GIs use the transcription factors Lhx2 and Ebf1, as well as the coactivator Ldb1, to form a nucleoprotein complex known as the Greek Island Hub (GIH) to associate with the active OR gene and support its transcription. Bulk Hi-C data show that GIs form strong, specific, and singular associations with the active OR gene, suggesting a possible role for the GIH in singular OR choice. However, single-cell Hi-C analysis shows that multiple GIHs exist in every OSN with no clear differences between them, complicating the contribution of the GIH. Furthermore, ectopic OR gene activation is sufficient to drive association of an OR locus with a GIH and bias choice, suggesting a role for OR transcription itself in supporting its own stable expression. To clarify the genomic transformations that result in the formation of multiple GIHs, I performed combined scRNA-seq and scATAC-seq in the MOE. I determined that a selective inactivation event was taking place during the INP3-to-iOSN transition, where OSNs would silence a large fraction of the GI pool. GI inactivation takes place during a phase preceding OR choice, where OR expression is polygenic but skewed towards one OR. My single-cell Hi-C analysis verifies the presence of multiple GIHs per cell, with similar GI-GI interaction properties, but I also observe that the single active GIH contains much more specific GI-OR gene interactions than those in inactive GIHs. These architectural differences are supported by Liquid Hi-C and H3K27ac HiChIP analysis where I observe that the active GIH is more highly acetylated than inactive GIHs and possesses more euchromatic physical properties. Taken together these data show that while most GIs were initially euchromatic during the polygenic phase of OR expression, once choice has taken place, GIHs possess distinct OR interaction properties, chromatin marks, and physical features that are determined by their association with the active OR gene. I believe that these data are best explained by a winner-takes-all event, where GIHs containing transcribed OR genes during the polygenic phase are in competition for choice. Once one OR begins to win, it recruits resources to maintain its expression which consequently results in the silencing of other GIHs. Ectopic induction of OR gene transcription is sufficient to bias choice and silence other ORs by impeding their specific association with a GIH. I find that this does not depend on the coding properties of OR protein, as the transcription of non-coding OR mRNAs still results in OR gene silencing. I describe this competition as a symmetry breaking process, where asymmetrical reorganization of transcriptional resources to a single GIH is mediated by non-coding properties of a single highly expressed OR mRNA, culminating in the stable expression of that allele alone for the remainder of a cell’s lifetime.

The adaptability and robustness of the central nervous system is partially explained by the vast diversity of neuronal identities. Molecular mechanisms generating such heterogeneity have evolved through multiple independent pathways. The olfactory sensory system provides a unique and tractable platform for investigating at least two orthogonal gene expression systems that generate neuronal diversity through stochastic promoter choice: olfactory receptor genes and clustered protocadherins. Olfactory sensory neuron identity is defined by the specific olfactory receptor (OR) gene chosen. Greater than 1300 OR genes are scattered throughout the mouse genome, and expression of an OR defines a unique sensory neuron class that responds to a selective set of odorants. This work further delineated an unprecedented network interchromosomal (trans) interactions indispensable for singular OR choice. In a largely orthogonal gene expression system, I sought to understand the molecular mechanisms governing stochastic protocadherin choice. Clustered protocadherins are an evolutionary- conserved system that is involved in cell-cell identification through a series of homo- and heterophilic interactions. This work uncovered a methylation-dependent mechanism for generating stochastic gene expression in the context of cis-regulatory elements. Overall, this work highlighted divergent cis and trans transcriptional regulatory mechanisms for generating stochastic gene expression and neuronal diversity.

No description available.

The olfactory sensitivity of five male CD-1 mice (Mus musculus) for six amino acids was determined using an operant conditioning paradigm. All animals significantly distinguished dilutions as low as 0.01 mM L-cysteine, 3.3 mM L-methionine, 10 mM L-proline, 0.03 mM D-cysteine, 0.3 mM D-methionine and 10 mM D-proline from the odorless solvent, with individual animals displaying even lower detection thresholds. Among the three different L-forms of the amino acids the mice were most sensitive for cysteine and least sensitive for proline, and among the three D-forms the animals displayed a lower sensitivity for D-proline compared to D-cysteine and D-methionine. A comparison between the present data and results obtained with other species showed that the CD-1 mice displayed a higher sensitivity than human subjects and spider monkeys with three (L-Cysteine, D-cysteine and L-proline) of the six amino acids. Results from this report support the idea that the number of functional olfactory receptor genes is not suitable to predict a species’ olfactory sensitivity.

Thesis (Ph. D.)--Oregon State University, 2009. / Printout. Includes bibliographical references (leaves 93-102). Also available on the World Wide Web.

Thesis (Ph. D.)--Oregon State University, 2011. / Printout. Includes bibliographical references (leaves 92-102). Also available on the World Wide Web.

Mammalian olfaction requires the enduring expression of a single olfactory receptor (OR) gene for the life of each sensory neuron. This is due to the fact that OR proteins play multiple roles in the coherent perception of odors, first by sensing molecular cues from the external environment, and by directing the wiring of neuronal projections faithfully from the peripheral sensory neurons to the brain. Both of these processes require singular and stable OR expression in olfactory sensory neurons (OSNs. The transcription factor Atf5 has previously been shown to enforce these modes of expression, through a process that requires the unfolded protein response (UPR). The work presented in this thesis deciphers how Atf5 enables proper OR expression and neuronal function in the olfactory system. We identify the developmental window in which UPR is activated, and provide evidence that Atf5 protein expression coincides with the assembly of a multi-chromosomal enhancer hub that drives singular and robust OR transcription, opposing a model in which precocious polygenic OR transcription initiates UPR. Further, we show that Atf5 directly regulates a collection of genes that facilitate proper OR trafficking, axonogenesis, as well as transcription factors and chromatin modifiers, which we propose to be involved in stable OR expression and neuronal maturation. Finally, we find that Atf5 has a special role in the olfactory system that cannot be replaced by its ubiquitously expressed homologue, Atf4, and that this is due to a requisite interaction between Atf5 and the bZIP transcription factor Cebpγ, and potentially other transcription factors known to be critical for olfactory function.