Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE81807 | GEO | 2016/12/26
SECONDARY ACCESSION(S): PRJNA322612
REPOSITORIES: GEO
Similar Datasets
Project description:Chromatin structure at the length scale encompassing local nucleosome-nucleosome interactions is thought to play a crucial role in regulating transcription and access to DNA. However, this secondary structure of chromatin remains poorly understood compared with the primary structure of single nucleosomes or the tertiary structure of long-range looping interactions. Here we report the first genome-wide map of chromatin conformation in human cells at the 1-3 nucleosome (50-500?bp) scale, obtained using ionizing radiation-induced spatially correlated cleavage of DNA with sequencing (RICC-seq) to identify DNA-DNA contacts that are spatially proximal. Unbiased analysis of RICC-seq signal reveals regional enrichment of DNA fragments characteristic of alternating rather than adjacent nucleosome interactions in tri-nucleosome units, particularly in H3K9me3-marked heterochromatin. We infer differences in the likelihood of nucleosome-nucleosome contacts among open chromatin, H3K27me3-marked, and H3K9me3-marked repressed chromatin regions. After calibrating RICC-seq signal to three-dimensional distances, we show that compact two-start helical fibre structures with stacked alternating nucleosomes are consistent with RICC-seq fragmentation patterns from H3K9me3-marked chromatin, while non-compact structures and solenoid structures are consistent with open chromatin. Our data support a model of chromatin architecture in intact interphase nuclei consistent with variable longitudinal compaction of two-start helical fibres.
| S-EPMC5526328 | biostudies-literature
Project description:Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping
| PRJNA322612 | ENA
Project description:Chromatin structure at the length scale encompassing nucleosome-nucleosome interactions is thought to play a crucial role in regulating transcription and access to DNA. However, this chromatin secondary structure remains poorly understood compared to the primary structure of single nucleosomes or the tertiary structure of long-range looping interactions. Here we report the first genome-wide map of chromatin conformation in human cells at the 1-3 nucleosome (50-500 bp) scale, obtained using ionizing radiation-induced spatially correlated cleavage of DNA with sequencing (RICC-seq). Unbiased analysis of RICC-seq DNA fragments in 1 Mb windows reveals a similar fragment length profile across the genome, with regional enrichment of characteristic fragments spanning tri-nucleosome units in heterochromatin. We observe differences in nucleosome-nucleosome contacts among euchromatin, H3K27me3-marked heterochromatin, and H3k9me3-marked heterochromatin. After calibrating RICC-seq signal to 3D distances, we show that compact 2-start helical fiber structures with stacked alternating nucleosomes are consistent with RICC-seq fragmentation patterns from H3K9me3-marked heterochromatin, while non-compact zig-zags and other extended structures are preferred in open chromatin. Our data support a model of heterochromatin condensation in native, intact nuclei consistent with longitudinal compaction of two-start helical fibers.
2016-12-26 | GSE81806 | GEO
Project description:Chromatin structure at the length scale encompassing nucleosome-nucleosome interactions is thought to play a crucial role in regulating transcription and access to DNA. However, this chromatin secondary structure remains poorly understood compared to the primary structure of single nucleosomes or the tertiary structure of long-range looping interactions. Here we report the first genome-wide map of chromatin conformation in human cells at the 1-3 nucleosome (50-500 bp) scale, obtained using ionizing radiation-induced spatially correlated cleavage of DNA with sequencing (RICC-seq). Unbiased analysis of RICC-seq DNA fragments in 1 Mb windows reveals a similar fragment length profile across the genome, with regional enrichment of characteristic fragments spanning tri-nucleosome units in heterochromatin. We observe differences in nucleosome-nucleosome contacts among euchromatin, H3K27me3-marked heterochromatin, and H3k9me3-marked heterochromatin. After calibrating RICC-seq signal to 3D distances, we show that compact 2-start helical fiber structures with stacked alternating nucleosomes are consistent with RICC-seq fragmentation patterns from H3K9me3-marked heterochromatin, while non-compact zig-zags and other extended structures are preferred in open chromatin. Our data support a model of heterochromatin condensation in native, intact nuclei consistent with longitudinal compaction of two-start helical fibers.
2016-12-26 | GSE81736 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-11-07 | GSE216132 | GEO
Project description:Eukaryotic DNA replication origins differ both in their efficiency and in the characteristic time during S phase when they become active. The biological basis for these differences remains unknown, but they could be a consequence of chromatin structure. The availability of genome-wide maps of nucleosome positions has led to an explosion of information about how nucleosomes are assembled at transcription start sites, but no similar maps exist for DNA replication origins. Here we combine high-resolution genome-wide nucleosome maps with comprehensive annotations of DNA replication origins to identify patterns of nucleosome occupancy at eukaryotic replication origins. On average, replication origins contain a nucleosome depleted region centered next to the ACS element, flanked on both sides by arrays of well-positioned nucleosomes. Our analysis identified DNA sequence properties that correlate with nucleosome occupancy at replication origins genome-wide and that are correlated with the nucleosome-depleted region. Clustering analysis of all annotated replication origins revealed a surprising diversity of nucleosome occupancy patterns. We provide evidence that the origin recognition complex, which binds to the origin, acts as a barrier element to position and phase nucleosomes on both sides of the origin. Finally, analysis of chromatin reconstituted in vitro reveals that origins are inherently nucleosome depleted. Together our data provide a comprehensive, genome-wide view of chromatin structure at replication origins and suggest a model of nucleosome positioning at replication origins in which the underlying sequence occludes nucleosomes to permit binding of the origin recognition complex, which then (likely in concert with nucleosome modifiers and remodelers) positions nucleosomes adjacent to the origin to promote replication origin function.
| S-EPMC2932696 | biostudies-literature
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.
2021-08-27 | GSE148792 | GEO
Project description:Chromatin accessibility mapping is a powerful approach to identify potential regulatory elements. A popular example is ATAC-seq, whereby Tn5 transposase inserts sequencing adapters into accessible DNA ('tagmentation'). CUT&Tag is a tagmentation-based epigenomic profiling method in which antibody tethering of Tn5 to a chromatin epitope of interest profiles specific chromatin features in small samples and single cells. Here we show that by simply modifying the tagmentation conditions for histone H3K4me2 or H3K4me3 CUT&Tag, antibody-tethered tagmentation of accessible DNA sites is redirected to produce chromatin accessibility maps that are indistinguishable from the best ATAC-seq maps. Thus, chromatin accessibility maps can be produced in parallel with CUT&Tag maps of other epitopes with all steps from nuclei to amplified sequencing-ready libraries performed in single PCR tubes in the laboratory or on a home workbench. As H3K4 methylation is produced by transcription at promoters and enhancers, our method identifies transcription-coupled accessible regulatory sites.
| S-EPMC7721439 | biostudies-literature
Project description:Technological advances have made it possible to measure spatially resolved gene expression at high throughput. However, methods to analyze these data are not established. Here we describe SpatialDE, a statistical test to identify genes with spatial patterns of expression variation from multiplexed imaging or spatial RNA-sequencing data. SpatialDE also implements 'automatic expression histology', a spatial gene-clustering approach that enables expression-based tissue histology.
| S-EPMC6350895 | biostudies-literature
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.
2021-08-27 | GSE174024 | GEO