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Oryza sativa Japonica Group cultivar:Nipponbare

ABSTRACT: Global Quantitative Mapping of Enhancer Activity in Rice Genome by STARR-seq

PROVIDER: PRJNA494898 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7983752_1.fastq.gz	Fastqsanger.gz
	SRR7983752_2.fastq.gz	Fastqsanger.gz
	SRR7990773_1.fastq.gz	Fastqsanger.gz
	SRR7990773_2.fastq.gz	Fastqsanger.gz
	SRR7990674_1.fastq.gz	Fastqsanger.gz

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Oryza sativa Japonica Group strain:Nipponbare

Project description:Mapping of rice endosperm starch altered gelatinization mutant

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Genome-wide quantitative enhancer activity maps identified by STARR-seq

Project description:Genomic enhancers are important regulators of gene expression, but their identification is a challenge and methods depend on indirect measures of activity. We developed a method termed STARR-seq to directly and quantitatively assess enhancer activity for millions of candidates from arbitrary sources of DNA, enabling screens across entire genomes. When applied to the Drosophila genome, STARR-seq identifies thousands of cell type-specific enhancers across a broad continuum of strengths, linking differential gene expression to differences in enhancer activity and creating a genome-wide quantitative enhancer map. This map reveals the highly complex regulation of transcription, with several independent enhancers for both developmental regulators and ubiquitously expressed genes. STARR-seq can be used to identify and quantitate enhancer activity in other eukaryotes, including human. STARR-seq was performed in S2 and OSC cells with paired-end sequencing in two replicates and respective inputs. DHS-seq was done with single-end sequencing in two replicates for S2 and OSC cells. RNA-seq was performed with a strand-specific protocol using single-end sequencing in two replicates within S2 and OSC cells. STARR-seq was also performed in HeLa cells with single-end sequencing with a respective input.

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Oryza sativa Japonica Group strain:Nipponbare

Project description:International Rice Genome Sequencing Project

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Oryza sativa Japonica Group strain:Nipponbare

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Global Quantitative Mapping of Enhancer Activity in Rice Genome by STARR-seq

Project description:Enhancers are important regulators of gene expression, but their identification is a challenge in plants. STARR-seq is a method measuring directly the enhancer activity of millions fragments in parallel, which had been successfully used to identify enhancers in Drosophila and human genomes. Here we present a global map of rice enhancers whose activities are quantitatively determined by STARR-seq.We also predicted intergenic enhancers based on DNase I hypersensitivity as described in a previously published work. Predicted enhancers overlap poorly with STARR-seq enhancers, only about 400 sites accounting for 3-4% of total enhancers identified by these two different methods. In summary, our results of STARR-seq reveal that enhancers in a plant genome differ from animal enhancers in several aspects and provide a regulatory element resource for further functional and mechanistic studies in different contexts

2018-11-08 | GSE121231 | GEO

Genome-wide quantitative enhancer activity maps identified by STARR-seq

Project description:Genome-wide quantitative enhancer activity maps identified by STARR-seq

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Oryza sativa Japonica Group strain:Nipponbare

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STARR-seq enhancer activity determined following hydrodynamic delivery of STARR-seq plasmid library to mouse liver using three different STARR-seq promoters: Super Core promoter, ORI promoter, and minimal Albumin promoter [G173]

Project description:Massively parallel reporter assays (MPRA) are widely used to discover functional enhancers but have largely been limited to transfected cell models. Here, we combine hydrodynamic injection with a modified STARR-seq-based MPRA to determine condition-specific enhancer activity in mouse liver at scale, and we examine how different promoters affect STARR-seq reporter activity. Strong liver enhancer activity was observed with STARR-seq libraries containing an Albumin minimal promoter but not when using a Super Core promoter or an origin of replication (ORI) promoter. This work is part of a larger study where we prepare a global STARR-seq library, comprised of ~50,000 genomic sequences released by DNase-I digestion of mouse liver nuclei, and where we identify condition-specific enhancers with strong correlations between liver enhancer activity and the chromatin state of the corresponding endogenous genomic regions.

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Oryza sativa Japonica Group strain:Nipponbare

Project description:Comparison of spontaneous and somaclonal mutations of rice

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