Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons

Monahan, Kevin D.; Schieren, Ira; Cheung, Jonah; Mumbey-Wafula, Alice; Monuki, Edwin S.; Lomvardas, Stavros

doi:10.7554/elife.28620

Cited by 118 publications

(185 citation statements)

References 97 publications

(129 reference statements)

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“…These functions were emphasized in our study, as activation of PGNs coincided with immediate early gene and synaptic plasticity related gene expression, activation of Trim genes and de-repression of neighbouring Olfr genes. Olfr genes are highly repressed in mature olfactory sensory neurons, where they form a large inter-chromosomal hub to regulate specificity of single Olfr gene activation 56,57 . Our results expand these previous findings, highlighting that alternative long-range mechanisms of Olfr repression may reflect their specialized roles in different cell types of the brain.…”

Section: Discussionmentioning

confidence: 99%

Cell-type specialization in the brain is encoded by specific long-range chromatin topologies

Winick-Ng

Kukalev

Harabula

et al. 2020

Preprint

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Neurons and oligodendrocytes are terminally differentiated cells that perform highly specialized functions, which depend on cascades of gene activation and repression to retain homeostatic control over a lifespan. Gene expression is regulated by threedimensional (3D) genome organisation, from local levels of chromatin compaction to the organisation of topological domains and chromosome compartments. Whereas our understanding of 3D genome architecture has vastly increased in the past decade, it remains difficult to study specialized cells in their native environment without disturbing their activity. To develop the application of Genome Architecture Mapping (GAM) in small numbers of specialized cells in complex tissues, we combined GAM with immunoselection. We applied immunoGAM to map the genome architecture of specific cell populations in the juvenile/adult mouse brain: dopaminergic neurons (DNs) from the midbrain, pyramidal glutamatergic neurons (PGNs) from the hippocampus, and oligodendrocyte lineage cells (OLGs) from the cortex. We integrate 3D genome organisation with single-cell transcriptomics data, and find specific chromatin structures that relate with cell-type specific patterns of gene expression. We discover abundant changes in compartment organisation, especially a strengthening of heterochromatin compartments which establish strong contacts spanning tens of megabases, especially in brain cells. These compartments contain olfactory and taste receptor genes, which are de-repressed in a subpopulation of PGNs with molecular signatures of long-term potentiation (LTP). We also show extensive reorganisation of topological domains where activation of neuronal or oligodendrocyte genes coincides with formation of new TAD borders.Finally, we discover loss of TAD organisation, or 'TAD melting', at long (>1Mb) neuronal genes when they are most highly expressed. Our work shows that the 3D 3 organisation of the genome is highly cell-type specific in terminally differentiated cells of the brain, and essential to better understand brain-specific mechanisms of gene regulation.

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Section: Discussionmentioning

confidence: 99%

Cell-type specialization in the brain is encoded by specific long-range chromatin topologies

Winick-Ng

Kukalev

Harabula

et al. 2020

Preprint

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“…All experiments were performed on dissected olfactory epithelium tissue or on dissociated cells prepared from whole olfactory epithelium tissue. Dissociated cells were prepared using papain (Worthington Biochemical) and FAC sorted as previously described 5 .…”

Section: Animal Modelsmentioning

confidence: 99%

“…Conditional deletion of Ldb1 in OSNs was achieved by crossing Ldb1 conditional allele mice (Ldb1-fl: Ldb1 tm2Lmgd ) 16 with OMP-ires-Cre mice (OMP-Cre, Omp tm1(cre)Jae ) 17 . For experiments on purified Ldb1KO mOSNs, a Cre-inducible tdtomato allele (ROSA26-tdtomato, Gt(ROSA)26Sor tm14(CAG-tdTomato)Hze/J ) 18 was included in the cross and tdtomato+ cells were purified by FACS as previously described 5 . Conditional deletion of Lhx2 in mOSNs was achieved by crossing Lhx2 conditional allele mice (Lhx2-fl: Lhx2 tm1Monu ) 32 with OMP-Cre mice.…”

Section: Animal Modelsmentioning

confidence: 99%

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Ldb1 mediates trans enhancement in mammals

Monahan

Horta

Mumbay-Wafula

et al. 2018

Preprint

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Singular olfactory receptor (OR) gene expression 1,2 coincides with the formation of a multichromosomal enhancer hub that associates with the only transcribed OR allele in each cell 3,4 . This hub consists of converging transcriptional enhancers 3 , or "Greek Islands", defined by stereotypic binding of Lhx2 and Ebf on a shared, composite DNA motif 5 . How this multi-chromosomal hub, or any other genomic compartment, assembles is unknown, and so is the significance of compartmentalization in transcription. Here, we report that LIM domain binding protein 1 (Ldb1), which is recruited by Lhx2 and Ebf to Greek Islands, promotes robust and specific trans interactions between these enhancers. In addition to disrupting Greek Island hubs, Ldb1 deletion also causes significant downregulation of OR transcription. Thus, our data provide insight to the formation of genomic compartments, confirm the

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“…The interactions described thus far involve heterochromatic regions, which may compartmentalize due to phase transition properties of heterochromatin proteins 17,18 . Within the OR clusters, however, reside 63 euchromatic transcriptional enhancers, the Greek Islands, which regulate the transcription of proximal ORs 5,19 .…”

mentioning

confidence: 99%

Cell type-specific interchromosomal interactions as a mechanism for transcriptional diversity

Horta

Monahan

Bashkirova

et al. 2018

Preprint

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The eukaryotic genome is partitioned into topologically associated domains (TADs) that assemble into compartments of shared chromatin valance. This architecture is influenced by the physical constraints imposed by the DNA polymer, which restricts DNA interactions predominantly to genomic segments from the same chromosome. Here, we report a dramatic divergence from this pattern of nuclear organization that occurs during the differentiation and specification of mouse olfactory sensory neurons (OSNs). In situ HiC on FAC-sorted OSNs shows that olfactory receptor (OR) genes from numerous chromosomes make frequent, extensive, and highly specific interchromosomal contacts that strengthen with differentiation. Moreover, in terminally differentiated OSNs, >30 intergenic enhancers generate a multi-chromosomal hub that associates only with the single active OR from a pool of ~1400 genes. Our data reveal that interchromosomal interactions can form with remarkable stereotypy between like neurons, generating a regulatory landscape for stochastic, monogenic, and monoallelic gene expression.Mouse ORs are encoded by a family of ~1400 genes that are organized in 69 heterochromatic genomic clusters distributed across most chromosomes. Every mature OSN (mOSN) expresses one OR gene from one allele in a seemingly stochastic fashion 1-3 . Previous work suggested that repressive and activating interchromosomal interactions contribute to the singular OR expression 4-6 . However, these interactions have only been analyzed with the use of biased and low-throughput approaches (3C, 4C, capture HiC, and DNA FISH), which have either limited genomic resolution or restricted genomic coverage. Thus, it remains unknown how prevalent and specific these interactions are, and how they form in relationship to OSN differentiation and OR expression. Moreover, in situ HiC 7 , which reduces the occurrence of non-specific ligation events observed in dilution HiC, revealed that interchromosomal associations between non-repetitive, genic regions are extremely infrequent 8,9 , and only emerge upon depletion of cohesin complexes 10,11 . Thus, to explore the landscape of interchromosomal interactions in a biological system that likely depends on them, and to provide a conclusive answer into whether interchromosomal contacts actually occur with biologically meaningful frequency and specificity, we performed in situ HiC in distinct cell populations of the main olfactory epithelium (MOE).

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Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons

Cited by 118 publications

References 97 publications

Cell-type specialization in the brain is encoded by specific long-range chromatin topologies

Cell-type specialization in the brain is encoded by specific long-range chromatin topologies

Ldb1 mediates trans enhancement in mammals

Cell type-specific interchromosomal interactions as a mechanism for transcriptional diversity

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