Project description:We report the application of genome architecture mapping in specific cell types in mouse brain. We generated cell-type specific chromatin contact maps in mouse dopaminergic neurons from the midbrain ventral tegmental area (VTA DN), pyramidal glutamatergic neurons from the cornus ammonis 1 region of the hippocampus (CA1 PGN), and non-neuronal post-mitotic oligodendrocytes from the somatosensory cortex (SSC_Olig). We explored cell-type specific chromatin topologies genome-wide at multiple genomic scales. Our data demonstrates that chromatin organization is cell type specific and reflects cell specialization at all genomic scales.
Project description:We report the application of genome architecture mapping in specific cell types in mouse brain. We generated cell-type specific chromatin contact maps in mouse dopaminergic neurons from the midbrain ventral tegmental area (VTA DN), pyramidal glutamatergic neurons from the cornus ammonis 1 region of the hippocampus (CA1 PGN), and non-neuronal post-mitotic oligodendrocytes from the somatosensory cortex (SSC_Olig). We explored cell-type specific chromatin topologies genome-wide at multiple genomic scales. Our data demonstrates that chromatin organization is cell type specific and reflects cell specialization at all genomic scales.
Project description:Inter-microbial and host–microbial interactions are thought to be critical for the functioning of the gut microbiome, but few substantive tools are available to measure these interactions. Here, we report a method for unbiased spatial sampling of microbiome-host interactions in the gut at high spatial resolution. This method combines enzymatic in situ polyadenylation of both bacterial and host transcripts with spatial RNA-sequencing. Application of this method revealed the biogeography of the mouse gut microbiome as function of location in the intestine, short-range intermicrobial interaction, local shaping of the microbiome by the host, and tumor-associated changes in the architecture of the host-microbiome interface. This method is compatible with broadly available commercial platforms for spatial RNA-sequencing, and can therefore be readily adopted to broadly study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.
Project description:Inter-microbial and host–microbial interactions are thought to be critical for the functioning of the gut microbiome, but few substantive tools are available to measure these interactions. Here, we report a method for unbiased spatial sampling of microbiome-host interactions in the gut at high spatial resolution. This method combines enzymatic in situ polyadenylation of both bacterial and host transcripts with spatial RNA-sequencing. Application of this method revealed the biogeography of the mouse gut microbiome as function of location in the intestine, short-range intermicrobial interaction, local shaping of the microbiome by the host, and tumor-associated changes in the architecture of the host-microbiome interface. This method is compatible with broadly available commercial platforms for spatial RNA-sequencing, and can therefore be readily adopted to broadly study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.
Project description:The field of structural biology is increasingly focusing on studying proteins in situ, i.e. in a larger biological context. Crosslinking mass spectrometry is contributing to this effort, typically through the use of MS-cleavable crosslinkers. Here, we apply the popular non-cleavable crosslinker disuccinimidyl suberate to mitochondria and identify 5,518 distance restraints between protein residues. Each distance restraint within or between proteins provides structural information on proteins and their processes within mitochondria. Comparing these restraints to high-throughput comparative models and PDB deposited structures reveals novel protein conformations. Our data suggest substrates and flexibility of mitochondrial heat shock proteins. Crosslinking mass spectrometry is progressing towards large-scale in situ structural biology that reveals protein dynamics in addition to protein-protein interaction topologies.
Project description:Inter-microbial and host-microbial interactions are critical for the functioning of the gut microbiome, but few tools are available to measure these interactions in situ. Here, we report a method for broad spatial sampling of microbiome-host interactions in the gut at high resolution (1 µm). This method combines enzymatic in situ polyadenylation of both bacterial and host RNA with spatial RNA-sequencing to increase bacterial RNA recovery and enable transcriptomic analysis of low-abundance and spatially restricted microbial taxa. We benchmark the method against existing spatial transcriptomic workflows, demonstrating improved sensitivity and resolution. Application of this method in a mouse model of intestinal neoplasia revealed the biogeography of the mouse gut microbiome as function of location in the intestine, frequent strong inter-microbial interactions at short length scales, and tumor-associated changes in the architecture of the host-microbiome interface. This method is compatible with widely available commercial platforms for spatial RNA-sequencing and can therefore be readily adopted to study the role of short-range, bidirectional host-microbe interactions in microbiome health and disease.