4DNES54YB6TQ - Replicate experiments of in situ Hi-C on olfactory receptor cell with DpnII

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. lab: Stavros Lomvardas, COLUMBIA award: 1U01DA040582-01 accession: 4DNES54YB6TQ condition: Mature Olfr16 expressing olfactory sensory neurons 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/4DNES54YB6TQ/ number_of_experiments: 2 experiment: 4DNEXMM7MN7V; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEXBSGTVWJ; replicate_number: Biorep 2, Techrep 1 Series supplementary files: *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/5d0e1af2-be6a-41b8-96ad-84eb6a6ab4ba/ genome_assembly: GRCm38 derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIBEV8M9E.pairs.gz, 4DNFI3O8M6SZ.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: 4DNFIOW2L46Z.pairs.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/5d0e1af2-be6a-41b8-96ad-84eb6a6ab4ba/ genome_assembly: GRCm38 derived_from: 4DNFI3UBJ3HZ.chrom.sizes, 4DNFIBEV8M9E.pairs.gz, 4DNFI3O8M6SZ.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: 4DNFIMV54HXI.mcool *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/2341d653-648b-4f43-9c23-9893464835d8/ genome_assembly: GRCm38 derived_from: 4DNFIMV54HXI.mcool description: Boundaries calls on Hi-C contact matrices file_type: boundaries file_format: bed file name: 4DNFIQI43DO2.bed.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/2341d653-648b-4f43-9c23-9893464835d8/ genome_assembly: GRCm38 derived_from: 4DNFIMV54HXI.mcool description: Diamond insulation scores calls on Hi-C contact matrices file_type: insulation score-diamond file_format: bw file name: 4DNFIP7U355R.bw *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/a5b6ce84-8f6d-4f57-a496-97c4a27adc27/ genome_assembly: GRCm38 derived_from: 4DNFIMV54HXI.mcool, 4DNFIOFXJOUA.bedGraph.gz description: Compartments signals on Hi-C contact matrices file_type: compartments file_format: bw file name: 4DNFI5F17SZD.bw

基因组被划分为拓扑关联结构域（topologically associated domain, TAD）与具有共享染色质价键的基因组区室。该三维架构受DNA聚合物的约束，从而阻断了不同染色体上基因间的相互作用。
本研究报道了小鼠嗅觉感觉神经元中存在的与该核组织模式显著背离的现象。通过对荧光激活细胞分选（fluorescence-activated cell sorting, FACS）得到的嗅觉感觉神经元及其祖细胞进行原位Hi-C（in situ Hi-C）染色质构象捕获实验，研究发现来自18条染色体的嗅觉受体基因簇会形成特异性且稳定的染色体间相互作用，且这类相互作用随细胞分化程度增强而增多。
这些染色体间相互作用由基因间嗅觉受体增强子——“希腊岛（Greek islands）”所调控：这类增强子首先参与嗅觉受体区室的构建，随后形成多染色体超级增强子，并与单个活跃的嗅觉受体基因相结合。结合于希腊岛的转录因子LHX2以及衔接蛋白LDB1可调控嗅觉受体区室、希腊岛枢纽的组装与维持，同时调控嗅觉受体的转录，这为反式（trans）相互作用在基因表达中的作用提供了机制解析与功能支持。

研究实验室：Stavros Lomvardas
哥伦比亚大学资助项目编号：1U01DA040582-01
数据入库编号：4DNES54YB6TQ
实验条件：表达Olfr16的成熟嗅觉感觉神经元
提交人：Adan Horta
数据集标签：小鼠嗅觉系统细胞Hi-C实验
实验类型：原位Hi-C（in situ Hi-C）
数据链接：https://data.4dnucleome.org/experiment-set-replicates/4DNES54YB6TQ/
实验总数：2
实验1：4DNEXMM7MN7V；生物学重复1，技术重复1
实验2：4DNEXBSGTVWJ；生物学重复2，技术重复1

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工作流程运行链接：https://data.4dnucleome.org/workflow-runs-awsem/5d0e1af2-be6a-41b8-96ad-84eb6a6ab4ba/
基因组组装版本：GRCm38
来源文件：4DNFI3UBJ3HZ.chrom.sizes、4DNFIBEV8M9E.pairs.gz、4DNFI3O8M6SZ.pairs.gz、4DNFI3HVC1SE.txt
文件说明：本文件为Hi-C处理流程的输出结果
文件类型：合并式接触列表
文件格式：pairs文件
文件名：4DNFIOW2L46Z.pairs.gz
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工作流程运行链接：https://data.4dnucleome.org/workflow-runs-awsem/5d0e1af2-be6a-41b8-96ad-84eb6a6ab4ba/
基因组组装版本：GRCm38
来源文件：4DNFI3UBJ3HZ.chrom.sizes、4DNFIBEV8M9E.pairs.gz、4DNFI3O8M6SZ.pairs.gz、4DNFI3HVC1SE.txt
文件说明：本文件为Hi-C处理流程的输出结果
文件类型：接触矩阵
文件格式：mcool文件
文件名：4DNFIMV54HXI.mcool
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工作流程运行链接：https://data.4dnucleome.org/workflow-runs-awsem/2341d653-648b-4f43-9c23-9893464835d8/
基因组组装版本：GRCm38
来源文件：4DNFIMV54HXI.mcool
文件说明：Hi-C接触矩阵的边界调用结果
文件类型：边界文件
文件格式：bed文件
文件名：4DNFIQI43DO2.bed.gz
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工作流程运行链接：https://data.4dnucleome.org/workflow-runs-awsem/2341d653-648b-4f43-9c23-9893464835d8/
基因组组装版本：GRCm38
来源文件：4DNFIMV54HXI.mcool
文件说明：Hi-C接触矩阵的菱形绝缘评分调用结果
文件类型：菱形绝缘评分文件
文件格式：bw文件
文件名：4DNFIP7U355R.bw
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工作流程运行链接：https://data.4dnucleome.org/workflow-runs-awsem/a5b6ce84-8f6d-4f57-a496-97c4a27adc27/
基因组组装版本：GRCm38
来源文件：4DNFIMV54HXI.mcool、4DNFIOFXJOUA.bedGraph.gz
文件说明：Hi-C接触矩阵的区室信号文件
文件类型：区室文件
文件格式：bw文件
文件名：4DNFI5F17SZD.bw