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Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C

ABSTRACT: Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C

PROVIDER: PRJNA555717 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9720470_1.fastq.gz	Fastqsanger.gz
	SRR9720470_2.fastq.gz	Fastqsanger.gz
	SRR9720480_1.fastq.gz	Fastqsanger.gz
	SRR9720480_2.fastq.gz	Fastqsanger.gz
	SRR9720490_1.fastq.gz	Fastqsanger.gz

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Compartment-dependent chromatin interaction dynamics revealed by liquid chromatin Hi-C

Project description:Chromosomes are folded so that active and inactive chromatin domains are spatially segregated to form a variety of sub-nuclear neighborhoods. Compartmentalization is thought to occur through polymer phase/microphase separation mediated by interactions between loci of similar type. The nature and dynamics of these interactions are not known. We developed liquid chromatin Hi-C to map the stability of associations between loci genome-wide. Before fixation and Hi-C, chromosomes are fragmented removing the strong polymeric constraint to enable detection of intrinsic locus-locus interaction stabilities. We find that chromosome compartmentalization is dependent on the length of chromatin fragments. Compartmentalization is stable when fragments are over 10-25 kb. Fragmenting chromatin into pieces smaller than 6 kb leads to gradual loss of spatial genome organization. In addition to fragmentation level dissolution kinetics of chromatin interactions vary for different chromatin domains. Lamin associated domains are most stable, and speckle-associated loci are more dynamic. The polycomb-enriched B1 sub-compartment also displays highly unstable interactions. Cohesin-mediated loops dissolve after fragmentation, possibly because cohesin rings slide off nearby DNA ends. Liquid chromatin Hi-C provides a genome-wide view of chromosome interaction dynamics, revealing a range of conformational stabilities at different sub-nuclear structures.

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Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics.

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Project description:H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [Hi-C 1]

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Project description:H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [Hi-C 2b]

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H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [Hi-C 2a]

Project description:H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [Hi-C 2a]

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H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [Hi-C 2]

Project description:H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [Hi-C 2]

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H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [Hi-C 2b]

Project description:Chromatin compartments reorganize dramatically during cell cycle transitions, shifting from a compartmentalized interphase to a condensed mitotic configuration in which large-scale compartment signals are attenuated. While histone modifications are linked to compartment identity, their contribution to compartment organization remains unclear. Using meiotic (mouse spermatogenesis) and mitotic (mouse neuronal progenitor cell, mNPC) models, we mapped histone landscapes alongside compartment dynamics. We found that histone H4 lysine 16 acetylation (H4K16ac) strongly tracked compartment reorganization, remaining enriched in A compartments during compartmentalization but redistributing upon chromatin compaction. In spermatogenesis, H4K16ac loss on the X chromosome coincided with condensation and H3K9me3 spreading. Machine learning highlighted H4K16ac as a stronger predictor of compartment transitions than H3K27ac. Acute degradation of MOF, the principal H4K16ac acetyltransferase, disrupted both the spatial distribution and global abundance of H4K16ac and progressively impaired compartmentalization in mNPCs. These results position H4K16ac as a histone modification selectively coupled to chromatin compartment transitions.

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H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [Hi-C 1]

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H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [Hi-C 2a]

Project description:Chromatin compartments reorganize dramatically during cell cycle transitions, shifting from a compartmentalized interphase organization to a condensed mitotic configuration in which large-scale compartment signals are attenuated. While histone modifications are linked to compartment identity, their causal contribution to compartment organization remained unclear. Using meiotic (mouse spermatogenesis) and mitotic (mouse neuronal progenitor cells, mNPCs) models, we mapped histone landscapes alongside compartment dynamics. We found that histone H4 lysine 16 acetylation (H4K16ac) strongly tracked compartment reorganization, remaining enriched in A compartments during compartmentalization but redistributing upon chromatin compaction. In spermatogenesis, H4K16ac loss on the X chromosome coincided with condensation and H3K9me3 spreading. Machine learning highlighted H4K16ac as a stronger predictor of compartment transitions than H3K27ac. To probe causality, we acutely degraded MOF, the principal H4K16ac acetyltransferase, which disrupted both the spatial distribution and global abundance of H4K16ac and progressively impaired compartmentalization in mNPCs. Together, these results position H4K16ac as a selectively coupled and influential histone modification of chromatin compartment transitions.

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