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The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila [ATAC-seq]

ABSTRACT: The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila [ATAC-seq]

PROVIDER: PRJNA1063673 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27503795_1.fastq.gz	Fastqsanger.gz
	SRR27503795_2.fastq.gz	Fastqsanger.gz
	SRR27503796_1.fastq.gz	Fastqsanger.gz
	SRR27503796_2.fastq.gz	Fastqsanger.gz
	SRR27503797_1.fastq.gz	Fastqsanger.gz

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The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila.

Project description:The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila.

| PRJNA1063668 | ENA

The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila [ChIP-seq]

Project description:Evolutionary analyses have estimated that ~60% of nucleotides in intergenic regions of the Drosophila melanogaster genome are functionally relevant, suggesting that regulatory information may be encoded more densely in intergenic regions than has been revealed by most functional dissections of regulatory DNA. Here, we approached this issue through a functional dissection of the regulatory region of the gene shavenbaby (svb). Most of the ~90 kilobases of this large regulatory region is highly conserved in the genus Drosophila, though characterized enhancers occupy a small fraction of this region. By analyzing the regulation of svb in different contexts of Drosophila development, we found that the regulatory information that drives svb expression in the abdominal pupal epidermis is organized in a different way than the elements that drive svb expression in the embryonic epidermis. While in the embryonic epidermis svb is activated by compact enhancers separated by large inactive DNA regions, svb expression in the pupal epidermis is driven by regulatory information distributed over broader regions of svb cis-regulatory DNA. In the same vein, we observed that other developmental genes also display a dense distribution of putative regulatory elements in their regulatory regions. Furthermore, we found that a large percentage of conserved non-coding DNA of the Drosophila genome is contained within regions of open chromatin. These results suggest that part of the evolutionary constraint on non-coding DNA of Drosophila is explained by the density of regulatory information, which may be greater than previously appreciated.

2024-01-16 | GSE253026 | GEO

The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila [ATAC-seq]

2024-01-16 | GSE253025 | GEO

The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila [CUT&RUN]

2024-01-16 | GSE253027 | GEO

The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila [ChIP-seq]

Project description:The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila [ChIP-seq]

| PRJNA1063674 | ENA

The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila [CUT&RUN]

Project description:The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila [CUT&RUN]

| PRJNA1063679 | ENA

The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila.

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-01-16 | GSE253028 | GEO

Breaking constraint of mammalian axial formulae

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Genome-wide chromatin accessibility changes in cultured primary human monocytes cultured at low density and high density.

Project description:ATAC sequencing of primary human monocytes cultured at low and high density. Monocytes isolated from PBMCs of 3 healthy donors were cultured at low density (1 x 10^6 cells/mL) or at high density (1 x10^7 cells/mL) for 24hrs and harvested for ATAC sequencing. Protein expression of FcgR2b is higher on monocytes in high density conditions compared to low density conditions, where expression is negligble. This study provides information on genome-wide chromatin accessibility changes that occur in high density culture in order to study associations with FcgR2b expression.

2022-04-13 | GSE166100 | GEO

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