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Drosophila melanogaster

ABSTRACT: Widespread rearrangement of 3D chromatin organization underlies Polycomb-mediated stress-induced silencing [Hi-C]

PROVIDER: PRJNA268118 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1658530_1.fastq.gz	Fastqsanger.gz
	SRR1658530_2.fastq.gz	Fastqsanger.gz
	SRR1658531_1.fastq.gz	Fastqsanger.gz
	SRR1658531_2.fastq.gz	Fastqsanger.gz
	SRR1658532_1.fastq.gz	Fastqsanger.gz

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Drosophila melanogaster

Project description:Widespread rearrangement of 3D chromatin organization underlies Polycomb-mediated stress-induced silencing [ChIP]

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Project description:Widespread rearrangement of 3D chromatin organization underlies Polycomb-mediated stress-induced silencing

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Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development

Project description:Interphase chromatin is organized into topologically associating domains (TADs). Within TADs, chromatin looping interactions are formed between DNA regulatory elements, but their functional importance for the establishment of the 3D genome organization and gene regulation during development is unclear. Using high-resolution Hi-C experiments, we analyze higher order 3D chromatin organization during Drosophila embryogenesis and identify active and repressive chromatin loops that are established with different kinetics and depend on distinct factors: Zelda-dependent active loops are formed before the midblastula transition between transcribed genes over long distances. Repressive loops within polycomb domains are formed after the midblastula transition between polycomb response elements by the action of GAGA factor and polycomb proteins. Perturbation of PRE function by CRISPR/Cas9 genome engineering affects polycomb domain formation and destabilizes polycomb-mediated silencing. Preventing loop formation without removal of polycomb components also decreases silencing efficiency, suggesting that chromatin architecture can play instructive roles in gene regulation during development.

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Project description:Drosophila Haspin kinase phosphorylates Histone H3 at threonine 3 at centromeric heterochromatin and either lamin- or polycomb-enriched euchromatic regions, being required for nuclear organization of interphase cells and polycomb-dependent gene silencing.

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Hi-C data from Drosophila melanogaster cell line Kc167 in different osmostress conditions.

Project description:Chromatin is organized into a 3D interwoven tapestry of multi-layer architectural features important for controlling gene expression. How distinct layers influence each other and quickly they quickly they respond to cellular environment is unclear. Using Hi-C in Drosophila melanogaster, we measure how 3D chromatin organization responds to cellular hyperosmotic stress. In combination with the hd-pairing method, we demonstrate that chromosome unpairing represents a fast an reversible response to hyperosmotic stress. We identify a novel function of the Z4 protein as an anti-pairer, which we demonstrate is necessary for changes to chromatin organization during hyperosmotic stress. Finally, we demonstrate how changes to pairing impacts the other interwoven layers of 3D chromatin organization.

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ATAC-seq data from Drosophila melanogaster cell line Kc167 in different osmostress conditions

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ChIP-seq and data from Drosophila melanogaster cell line Kc167 in different osmostress conditions.

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Project description:Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development

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Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of lincRNA genes in human cells

Project description:Characterizing the relationship between genome form and function requires methods both for zooming out, to globally survey the genomic architectural landscape, and for zooming in, to investigate regions of interest at high resolution. High throughput methods based on chromosome conformation capture (3C) have greatly advanced our understanding of the three-dimensional (3D) organization of genomes, but are limited in resolution by their reliance on restriction enzymes. Here we describe a method for comprehensively mapping global chromatin contacts that uses DNaseI for chromatin fragmentation, leading to greatly improved efficiency and resolution. Coupling this method with DNA capture technology provides a high-throughput approach for targeted mapping of fine-scale chromatin architecture. We applied targeted DNase Hi-C to characterize the 3D organization of 1,030 lincRNA promoters in two human cell lines, and identified thousands of high-confidence lincRNA promoter-associated chromatin contacts at 1 kilobase pair (kbp) resolution. Detailed analysis of these contacts reveals that expression of lincRNAs is tightly controlled by complex mechanisms involving both super-enhancers and the polycomb repressive complex. Our results provide the first glimpse of the cell-type-specific 3D organization of lincRNA genes. DNase Hi-C assay (x1 replicate) in H1 and K562 cells, respectively. Targeted DNase Hi-C assays of the 220kb promoter-enhancer library (x1 replicate) and the 5Mb lincRNA promoter library (x2 replicate), in H1 and K562 cells, respectively.

2014-11-01 | E-GEOD-56869 | biostudies-arrayexpress

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