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Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

ABSTRACT: Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

PROVIDER: PRJNA322612 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3571010_1.fastq.gz	Fastqsanger.gz
	SRR3571010_2.fastq.gz	Fastqsanger.gz
	SRR3571020_1.fastq.gz	Fastqsanger.gz
	SRR3571020_2.fastq.gz	Fastqsanger.gz
	SRR3571011_1.fastq.gz	Fastqsanger.gz

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Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping

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Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping.

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.

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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.

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