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The role of insulators and transcription in 3D chromatin organisation of flies

ABSTRACT: The role of insulators and transcription in 3D chromatin organisation of flies

PROVIDER: PRJNA612860 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11314400_1.fastq.gz	Fastqsanger.gz
	SRR11314400_2.fastq.gz	Fastqsanger.gz
	SRR11314401_1.fastq.gz	Fastqsanger.gz
	SRR11314401_2.fastq.gz	Fastqsanger.gz
	SRR11314402_1.fastq.gz	Fastqsanger.gz

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The role of insulators and transcription in 3D chromatin organisation of flies

Project description:The DNA in humans and many animals is compartmentalised in topologically associating domains (TADs). In Drosophila, several architectural proteins are enriched at TAD borders, but we are still missing evidence that these proteins have a functional role in TAD maintenance. Here, we show that depletion of BEAF-32, Cp190 and Chro leads to changes in TAD organisation and chromatin loops. Their depletion affects mainly TAD borders in heterochromatin, while euchromatin TAD borders are resilient to these mutants. Furthermore, transcriptomic data identified thousands of genes displaying differential expression in these mutants and that majority of differentially expressed genes are in TADs that are reorganised. In contrast, we observed a lower effect on gene expression by the loss of chromatin loops. Our work identified for the first time a functional role for architectural proteins at TAD borders in Drosophila and a strong link between TAD reorganisation and changes in gene expression.

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The role of insulators and transcription in 3D chromatin organization of flies.

Project description:The DNA in many organisms, including humans, is shown to be organized in topologically associating domains (TADs). In Drosophila, several architectural proteins are enriched at TAD borders, but it is still unclear whether these proteins play a functional role in the formation and maintenance of TADs. Here, we show that depletion of BEAF-32, Cp190, Chro, and Dref leads to changes in TAD organization and chromatin loops. Their depletion predominantly affects TAD borders located in regions moderately enriched in repressive modifications and depleted in active ones, whereas TAD borders located in euchromatin are resilient to these knockdowns. Furthermore, transcriptomic data has revealed hundreds of genes displaying differential expression in these knockdowns and showed that the majority of differentially expressed genes are located within reorganized TADs. Our work identifies a novel and functional role for architectural proteins at TAD borders in Drosophila and a link between TAD reorganization and subsequent changes in gene expression.

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Project description:gene expression profiles in fly brains between wildtype and miR-34 null flies gene expression profiles in fly brains, wild type (3d, 20d) and miR-34 null flies (3d, 20d)

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Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [IV]

Project description:By CRISPR DNA-fragment editing, in conjunction with chromosome conformation capture, we find that CBSs, if located between enhancers and promoters in the clustered Pcdh and b-globin clusters, function as an enhancer-blocking insulator by forming distinct directional chromatin loops, regardless whether enhancers contain CBS or not. Moreover, computational simulation in silico and genetic deletions in vivo revealed balanced promoter usage in cell populations and stochastic monoallelic expression in single cells by large arrays of tandem variable CBSs. Finally, gene expression levels are negatively correlated with CBS insulators located between enhancers and promoters on a genome-wide scale. Thus, single CBS insulators ensure proper enhancer insulation and promoter activation while tandem-arrayed CBS insulators determine balanced promoter choice. This finding has interesting implications on the role of topological insulators in 3D genome folding and developmental gene regulation.

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Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [VIII]

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Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [VII]

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Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [VI]

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Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [V]

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