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The genome is partitioned into topologically associated domains and genomic compartments with shared chromatin valence. More...

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. Overall design: lab: Stavros Lomvardas, COLUMBIA award: 1U01DA040582-01 accession: 4DNES425UDGS condition: Immediate Neuronal Precursor cells submitted_by: Adan Horta dataset_label: Hi-C on Mouse Olfactory System cells experiment_type: in situ Hi-C url: https://data.4dnucleome.org/experiment-set-replicates/4DNES425UDGS/ number_of_experiments: 2 experiment: 4DNEXKO3TRJT; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEXTDMNUOO; replicate_number: Biorep 2, Techrep 1 Series supplementary files: *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/6aa74f2a-2d5f-4132-9cd0-ac178f752d4e/ genome_assembly: GRCm38 derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIDFRSE2G.pairs.gz, 4DNFIBO9M2WY.pairs.gz, 4DNFI3HVC1SE.txt description: This is an output file of the Hi-C processing pipeline file_type: contact list-combined file_format: pairs file name: 4DNFI1QBCSKR.pairs.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/6aa74f2a-2d5f-4132-9cd0-ac178f752d4e/ genome_assembly: GRCm38 derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIDFRSE2G.pairs.gz, 4DNFIBO9M2WY.pairs.gz, 4DNFI3HVC1SE.txt description: This is an output file of the Hi-C processing pipeline file_type: contact matrix file_format: mcool file name: 4DNFICUQ1N7S.mcool *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/c8f95f43-1f95-4e07-8a82-647951bf7579/ genome_assembly: GRCm38 derived_from: 4DNFICUQ1N7S.mcool description: Boundaries calls on Hi-C contact matrices file_type: boundaries file_format: bed file name: 4DNFI2YHK51M.bed.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/c8f95f43-1f95-4e07-8a82-647951bf7579/ genome_assembly: GRCm38 derived_from: 4DNFICUQ1N7S.mcool description: Diamond insulation scores calls on Hi-C contact matrices file_type: insulation score-diamond file_format: bw file name: 4DNFICXGHQP3.bw *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/96e31197-b1ca-4921-b833-9b6c1132d770/ genome_assembly: GRCm38 derived_from: 4DNFICUQ1N7S.mcool, 4DNFIOFXJOUA.bedGraph.gz description: Compartments signals on Hi-C contact matrices file_type: compartments file_format: bw file name: 4DNFIKXATLSH.bw Less...