Similar Datasets
Project description:Spatial transcriptomics aims to understand how the ensemble of RNA molecules in tissues and cells is organized in 3D space. Here we introduce Proximity RNA-seq, which identifies co-localization preferences for pairs or groups of chromatin-associated, nuclear-retained and nascent RNAs in cell nuclei. Proximity RNA-seq is based on massive-throughput RNA barcoding of sub-nuclear particles in water-in-oil emulsion droplets, followed by sequencing.
2019-05-03 | GSE129732 | GEO
Project description:Enhancers can regulate the promoters of their target genes over very large genomic distances. It is widely assumed that mechanisms of enhancer action involve the reorganization of three-dimensional chromatin architecture, but this is poorly understood. The predominant model involves physical enhancer-promoter interaction by looping out the intervening chromatin. However, studying the enhancer-driven activation of the Sonic hedgehog gene (Shh), we have identified a change in chromosome conformation that is incompatible with this simple looping model. Using super-resolution 3D-FISH and chromosome conformation capture, we observe a decreased spatial proximity between Shh and its enhancers during the differentiation of embryonic stem cells to neural progenitors. We show that this can be recapitulated by synthetic enhancer activation, is impeded by chromatin-bound proteins located between the enhancer and the promoter, and appears to involve the catalytic activity of poly (ADP-ribose) polymerase. Our data suggest that models of enhancer-promoter communication need to encompass chromatin conformations other than looping.
| S-EPMC6838673 | biostudies-literature
Project description:RNA proximity sequencing reveals properties of spatial transcriptome organization in the nucleus
| PRJNA532610 | ENA
Project description:Chromosome structure in mammals is thought to regulate transcription by modulating spatial proximity between enhancers and promoters. However, the mechanisms by which this occurs remain elusive, and reports suggested moderate to no correlation between physical proximity and transcription. Whether and how chromosome structure is actually translated into transcriptional outputs thus remains unclear. Here we use a novel assay to position an enhancer at hundreds of different chromosomal sites relative to a fixed promoter and quantitatively measure promoter output.
2021-04-26 | GSE172253 | GEO
Project description:Chromosome structure in mammals is thought to regulate transcription by modulating spatial proximity between enhancers and promoters. However, the mechanisms by which this occurs remain elusive, and reports suggested moderate to no correlation between physical proximity and transcription. Whether and how chromosome structure is actually translated into transcriptional outputs thus remains unclear. Here we use a novel assay to position an enhancer at hundreds of different chromosomal sites relative to a fixed promoter and quantitatively measure promoter output.
2021-11-05 | GSE188266 | GEO
Project description:Chromosome structure in mammals is thought to regulate transcription by modulating spatial proximity between enhancers and promoters. However, the mechanisms by which this occurs remain elusive, and reports suggested moderate to no correlation between physical proximity and transcription. Whether and how chromosome structure is actually translated into transcriptional outputs thus remains unclear. Here we use a novel assay to position an enhancer at hundreds of different chromosomal sites relative to a fixed promoter and quantitatively measure promoter output.
2021-04-26 | GSE172255 | GEO
Project description:Chromosome structure in mammals is thought to regulate transcription by modulating spatial proximity between enhancers and promoters. However, the mechanisms by which this occurs remain elusive, and reports suggested moderate to no correlation between physical proximity and transcription. Whether and how chromosome structure is actually translated into transcriptional outputs thus remains unclear. Here we use a novel assay to position an enhancer at hundreds of different chromosomal sites relative to a fixed promoter and quantitatively measure promoter output.
2021-04-26 | GSE172256 | GEO
Project description:The extent to which the three-dimensional organization of the genome contributes to chromosomal translocations is an important question in cancer genomics. We now have generated a high-resolution Hi-C spatial organization map of the G1-arrested mouse pro-B cell genome and mapped translocations from target DNA double-strand breaks (DSBs) within it via high-throughput genome-wide translocation sequencing. RAG endonuclease-cleaved antigen-receptor loci are dominant translocation partners for target DSBs regardless of genomic position, reflecting high frequency DSBs at these loci and their co-localization in a fraction of cells. To directly assess spatial proximity contributions, we normalized genomic DSBs via ionizing-radiation. Under these conditions, translocations were highly enriched in cis along single chromosomes containing target DSBs and within other chromosomes and sub-chromosomal domains in a manner directly related to pre-existing spatial proximity. Our studies reveal the power of combining two high-throughput genomic methods to address long-standing questions in cancer biology. Hi-C interaction maps for WT and ATM -/- G1-arrested AMuLV-transformed pro-B cell lines.
2012-02-16 | E-GEOD-35519 | biostudies-arrayexpress
Project description:Rapid advances in high-throughput DNA sequencing technologies are accelerating the pace of research into personalized medicine. While methods for variant discovery and genotyping from whole genome sequencing (WGS) datasets have been well established, linking variants together into a single haplotype remains a challenge. An understanding of complete haplotypes of an individual will help clarify the consequences of inheriting multiple alleles in combination, identify novel disease associations, and augment studies of gene regulation. Although numerous methods have been developed to reconstruct haplotypes from WGS data, chromosome-span haplotypes at high resolution have been difficult to obtain. Here we present a novel method to accurately reconstruct chromosome-span haplotypes from proximity-ligation and DNA shotgun sequencing. We demonstrate the utility of this approach in producing high-resolution chromosome-span haplotype phasing in mouse and human. While proximity-ligation based methods were originally designed to investigate spatial organization of the genome, our results lend support for their use as a general tool for haplotyping in the future. Hi-C experiments in two replicates of Human GM12878 Lymphoblastoid cells and two replicates of F123 mouse ES cells (4 total samples)
2013-11-03 | E-GEOD-48592 | biostudies-arrayexpress
Project description:Though important for gene regulation most studies of genome organisation use either fluorescence in situ hybridisation (FISH) or chromosome conformation capture (3C) methods. FISH directly visualises the spatial relationship of sequences, but is usually applied to a few loci at a time. The frequency at which sequences are ligated together by formaldehyde crosslinking can be measured genome-wide by 3C methods, with higher frequencies thought to reflect shorter distances. FISH and 3C should therefore give the same views of genome organisation, but this has not been tested extensively. We investigate the murine HoxD locus with 5C and FISH in different developmental and activity states, and in the presence or absence of epigenetic regulators. We identify situations where the two datasets are concordant, but find other conditions where chromatin topographies extrapolated from 5C or FISH data are not compatible. We conclude that products captured by 3C do not always reflect spatial proximity, with ligation occurring between sequences located hundreds of nanometers apart – influenced by nuclear environment and chromatin composition. We conclude that results obtained at high-resolution with either 3C methods or by FISH alone must be interpreted with caution and that conclusions about genome organisation should be validated by independent methods. 5C oligonucleotides were designed around EcoRI restriction sites following an alternative scheme
2015-01-02 | E-GEOD-61814 | biostudies-arrayexpress