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Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila [Hi-C]

ABSTRACT: Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila [Hi-C]

PROVIDER: PRJNA1145315 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30167991_1.fastq.gz	Fastqsanger.gz
	SRR30167991_2.fastq.gz	Fastqsanger.gz
	SRR30167992_1.fastq.gz	Fastqsanger.gz
	SRR30167992_2.fastq.gz	Fastqsanger.gz
	SRR30167993_1.fastq.gz	Fastqsanger.gz

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Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila [Cut&Run]

Project description:Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila [Cut&Run]

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Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila [RNA-seq]

Project description:Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila [RNA-seq]

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Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila [Hi-C]

Project description:The tight correlation between topologically associating domains (TADs) and epigenetic domains in Drosophila suggests that the epigenome contributes to define TADs. However, it is still unknown whether histone modifications are essential for TAD formation and structure. By either deleting or shifting key regulatory elements needed to establish the epigenetic signature of Polycomb TADs, we show that the epigenome is not a major driving force for the establishment of TADs. On the other hand, physical domains have an important impact on the formation of epigenetic domains, as they can restrict spreading of repressive histone marks and looping between cis-regulatory elements.

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Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila [RNA-seq]

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Determining the functional relationship between epigenetic and physical chromatin domains in Drosophila [Cut&Run]

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Gene Density, Transcription and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains (Hi-C analysis of Drosophila melanogaster Kc167 genome)

Project description:The mechanisms responsible for the establishment of physical domains in metazoan chromosomes are poorly understood. Here we find that physical domains in Drosophila chromosomes are demarcated at regions of active transcription and high gene density that are enriched for transcription factors and specific combinations of insulator proteins. Physical domains contain different types of chromatin defined by the presence of specific proteins and epigenetic marks, with active chromatin preferentially located at the borders and silenced chromatin in the interior. Domain boundaries participate in long-range interactions that may contribute to the clustering of regions of active or silenced chromatin in the nucleus. Analysis of transgenes suggests that chromatin is more accessible and permissive to transcription at the borders than inside domains, independent of the presence of active or silencing histone modifications. These results suggest that the higher-order physical organization of chromatin may impose an additional level of regulation over classical epigenetic marks. We carried out Hi-C experiment using HindIII on Kc167 cells and generate two libraries separately. One library was sequenced once more as technical replicates (TR1 and TR2), the other library was sequenced as biological replicate (BR). processed files contain the following: Column 1: chromosome ID in which the first read in a pair locates Column 2: coordinate of the first read Column 3: chromosome ID in which the second read in a pair locates Column 4: coordinate of the second read

2012-10-04 | E-GEOD-38468 | biostudies-arrayexpress

Gene Density, Transcription and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains (Hi-C analysis of Drosophila melanogaster Kc167 genome)

2012-10-04 | GSE38468 | GEO

Temperature Sensitive Remodeling of Fruit Fly Physical Chromosomal Domains upon Heat Shock

Project description:Metazoan chromosomes in interphase nucleus are partitioned into discrete three dimensional physical domains which confine epigenetically modified chromatin and are relative stable across different cell types even species1-4. Physical domains are segregated preferentially at DNase I hypersensitive sequences of high density of active gene and insulator proteins which are hypothesized contributing together to domain border formation3,4. However, whether physical domain structure can be maintained without insulator proteins and transcription is unknown5-8. Transcription of most genes and the insulator proteins binding can be severely impaired in heat shocked (HS) fruit fly nuclei9. Here we show that chromatin contact frequency increases within and decreases beyond ~100kb after HS respectively accompanied by repartitioning of the Drosophila chromosomes into a different array of physical domain. Prominently, domains tend to merge because borders disappeared are more than borders newly emerged which are located more frequently in repressive chromatin. In contrast to previous hypothesis1,3,4, changes in insulator proteins enrichment and RNAPII show no noticeable difference at lost or emerged borders. Our results show a metazoan genome can be quickly reconfigured as cells undergo brief physiological stress. In addition to insulator proteins and transcription, we speculate that extra trans-factors binding and various biological activities are required for the establishment and maintenance of physical domains. Moreover, we found long-range chromatin interaction network is reshaped after HS implying long-range chromatin interactions can be formed due to domain level reorganization of chromosomes despite functional relevance. We anticipate our analysis to be a starting point for more intensive experimental investigation into the elusive mechanisms behind the physical domain partition and dynamic reconfiguration of metazoan genomes.

2016-03-18 | GSE45293 | GEO

Setdb1 regulates Cohesin at H3K9me3-independent topological domains [Hi-C]

Project description:Setdb1 regulates Cohesin at H3K9me3-independent topological domains [Hi-C]

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Protect-seq: Genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin

Project description:Protect-seq: Genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin

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