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Composite DNA storage

ABSTRACT: DNA storage of digital media using composite DNA

PROVIDER: PRJEB32427 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR3308451_1.fastq.gz	Fastqsanger.gz
	ERR3308451_2.fastq.gz	Fastqsanger.gz
	ERR3308811_1.fastq.gz	Fastqsanger.gz
	ERR3308811_2.fastq.gz	Fastqsanger.gz
	ERR3308452_1.fastq.gz	Fastqsanger.gz

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Project description:Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. SPICE de novo predicted known composite elements, including AP1-IRF composite elements (AICE) and STAT5 tetramers, and also predicted a range of novel binding partners, including JUN-IKZF1 composite elements. We confirmed cooperative binding of JUN and IKZF1 to an upstream conserved noncoding region, CNS9, in the human IL10 gene, that contains a non-canonical IKZF1 site, and the activity of an IL10-luciferase reporter construct depended on both this site and the AP1 binding site within this composite element in primary B and T cells. Our findings reveal an unappreciated global association of IKZF1 and AP1, and establish SPICE as a valuable new pipeline for predicting novel transcription binding complexes.

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A Composite DNA Element that Functions as a Maintainer Required for Epigenetic Inheritance of Heterochromatin

Project description:Epigenetic inheritance of heterochromatin requires DNA sequence-independent propagation mechanisms, coupling to RNAi, or input from DNA sequence, but how DNA contributes to inheritance is not understood. Here, we identify a DNA element (termed “maintainer”) that is sufficient for epigenetic inheritance of preexisting histone H3 lysine 9 methylation (H3K9me) and heterochromatin in Schizosaccharomyces pombe, but cannot establish de novo gene silencing in wild-type cells. This maintainer is a composite DNA element with binding sites for the Atf1/Pcr1 and Deb1 transcription factors and the Origin Recognition Complex (ORC), located within a 130-base pair region, and can be converted to a silencer in cells with lower rates of H3K9me turnover, suggesting that it participates in recruiting the H3K9 methyltransferase Clr4/Suv39h. These results suggest that, in the absence of RNAi, histone H3K9me is only heritable when it can collaborate with maintainer-associated DNA-binding proteins that help recruit the enzyme responsible for its epigenetic deposition.

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A composite DNA element that functions as a maintainer required for epigenetic inheritance of heterochromatin

Project description:Epigenetic inheritance of heterochromatin requires sequence - independent propagation mechanisms and input from DNA sequence, but how DNA contributes to inheritance is not understood. Here, we identify a DNA element ( term ed the “maintainer” ) that is necessary and sufficient for epigenetic inheritance of preexisting histone H3 lysine 9 methylation (H3K9me) and heterochromatin i n the fission yeast Schizosaccharomyces pombe . In wild - type cells, d espite its requirement for maintenance of H3K9me, the maintainer cannot establish de novo gene silencing. The maintainer is a composite 1307 - base pair DNA element with binding sites for the Atf1/Pcr1 and Deb1 transcription factors and the O rigin R ecognition C omplex (ORC) and can be converted to a silencer in cells with lower rates of H3K9me turnover , suggesting that it participate s in recruiting the H3K9 methyltransferase Clr4 / Suv39h . T hese results suggest tha t histone H3K9me is only heritable when it can collaborate with maintainer - associated DNA - binding proteins that help recruit the enzyme responsible for its epigenetic deposition .

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