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Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice [olfactory, single-cell RNA & Hi-C]

ABSTRACT: The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding our genome’s structure–function relation, yet is extremely challenging for existing methods. Here we present Linking mRNA to Chromatin Architecture (LiMCA), which jointly profiles 3D genome and transcriptome with exceptional sensitivity and from low-input materials. Combining LiMCA and our high-resolution scATAC-seq assay, METATAC, we profiled the developing mouse olfactory epithelium and reported the first chromatin accessibility profiles and the first paired 3D genome structures and gene expression information of single neurons. We greatly expanded the repertoire of known OR enhancers, and discovered unexpected rules of their dynamics: ORs and their enhancers are most accessible during early differentiation, and the active OR typically does not associate with the largest enhancer hub. These findings offer valuable insights into how 3D connectivity of ORs and enhancers dynamically orchestrate the “one neuron–one receptor” selection process.

ORGANISM(S): Mus musculus

PROVIDER: GSE239969 | GEO | 2024/01/15

REPOSITORIES: GEO

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Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice [scATAC-Seq, scRNA-seq]

Project description:The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding our genome’s structure–function relation, yet is extremely challenging for existing methods. Here we present Linking mRNA to Chromatin Architecture (LiMCA), which jointly profiles 3D genome and transcriptome with exceptional sensitivity and from low-input materials. Combining LiMCA and our high-resolution scATAC-seq assay, METATAC, we profiled the developing mouse olfactory epithelium and reported the first chromatin accessibility profiles and the first paired 3D genome structures and gene expression information of single neurons. We greatly expanded the repertoire of known OR enhancers, and discovered unexpected rules of their dynamics: ORs and their enhancers are most accessible during early differentiation, and the active OR typically does not associate with the largest enhancer hub. These findings offer valuable insights into how 3D connectivity of ORs and enhancers dynamically orchestrate the “one neuron–one receptor” selection process.

2024-01-15 | GSE239876 | GEO

Simultaneous single-cell three-dimensional genome and gene expression profiling Uncovers Dynamic Enhancer Connectivity Underlying Olfactory Receptor Choice [cell line, single-cell RNA-Seq & Hi-C]

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Olfactory receptor accessory proteins play crucial roles in receptor gene choice

Project description:Mice with olfactry accessory protein RTP1 and RTP2 knocked out show severe bias in their olfactory receptor repertoire. Surprisingly, even though RTP1,2(-/-) animals have fewer OSNs, we discovered ~8% of the ORs are expressed in larger numbers than the wild type.

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RNA-Chromatin Interactome Reveals Enhancer-Promoter Connectivity in 3D Genome

Project description:High eukaryotic genomes are populated with enhancers, but it has been a major challenge in defining specific enhancer-promoter relationship. Enhancers can also be divided into typical and super-enhancers, yet their functional distinctions remain to be understood. Here, we report a strategy to capture in situ Global RNA Interactions with DNA by deep sequencing (GRID-seq). By deducing general RNA background on chromatin, we unexpectedly detect a highly selective set of RNAs (including both lncRNAs and protein-coding pre-mRNAs) decorated on enhancers, particularly super-enhancers. Based on the origins of those RNAs and functional perturbation of enhancer activities, we are able to infer global enhancer-promoter connectivity, which is significantly beyond the traditional framework. These findings provide a functional RNA-chromatin interactome in 3D genome.

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Transcriptome Analysis of Dihydrotestosterone-treated 2D- and 3D-cultured Dermal Papilla Cells

Project description:Hair follicle growth inhibitory effect of dihydrotestosterone (DHT)-treated two-dimensional (2D)- and 3D-cultured DPCs were evaluated. 2D- and 3D-cultured DPC proliferation was inhibited after co-culturing with outer root sheath (ORS) cells under DHT treatment. Moreover, gene expression levels of β‐catenin and neural cell adhesion molecule (NCAM) were significantly decreased and those of cleaved caspase-3 significantly increased in 2D- and 3D-cultured DPCs with increasing DHT concentrations. ORS cell proliferation also significantly increased after co-culturing in the control-3D model compared with the control-2D model. ki67 downregulation and cleaved caspase-3 upregulation in DHT-2D and 3D groups significantly inhibited ORS cell proliferation. Sequencing showed an increase in the expression of genes related to extracellular matrix synthesis in the 3D model group. Additionally, the top 10 hub genes were identified, and the expression of nine chemokine-related genes in DHT-treated DPCs was found significantly increased. We also identified the interactions between transcription factor (TF)–genes and microRNAs with hub genes and the TF–microRNA coregulatory network. Overall, the findings indicate that 3D-cultured DPCs are more representative of in vivo conditions than are 2D-cultured DPCs, and contribute to our understanding of the molecular mechanisms underlying androgen-induced alopecia.

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HiChIP: Efficient and sensitive analysis of protein-directed genome architecture

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Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-01-15 | GSE240128 | GEO

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NFI transcription factors regulate zonal olfactory receptor expression

Project description:Expression of one out of > 1000 olfactory receptor (OR) genes is stochastic, yet organized into anatomic "zones" along the dorsoventral axis of the olfactory epithelium. Here we profile the gene expression, chromatin state and nuclear architecture of olfactory sensory neurons and olfactory progenitors of different zones. We discovered that zonal OR expression is specified by two processes: low-level polygenic transcription of OR genes in olfactory progenitors, as wells as the chromatin structure and nuclear architecture during olfactory differentiation. Specifically, in cells of any zonal segment, polygenic transcription in olfactory progenitors defines the OR repertoire eligible for OR choice as the cells mature, while an increased level of heterochromatin and chromatin compaction represses ectopic more dorsally expressed ORs. We find that this process is regulated by the NFI family of transcription factors that are expressed in a graded fashion in the olfactory epithelium. Conditional deletion of NFI A, B, and X results in a transformation of the chromatin state and nucellar architecture and an accompanying shift in the preferred OR repertoire.

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KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure

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