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STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [single_cell_RNA-Seq]

ABSTRACT: STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [single_cell_RNA-Seq]

PROVIDER: PRJNA600930 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10877362_1.fastq.gz	Fastqsanger.gz
	SRR10877362_2.fastq.gz	Fastqsanger.gz
	SRR10877363_1.fastq.gz	Fastqsanger.gz
	SRR10877363_2.fastq.gz	Fastqsanger.gz
	SRR10877364_1.fastq.gz	Fastqsanger.gz

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STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells

Project description:STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells

| PRJNA600923 | ENA

STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [ChIP-seq]

Project description:STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [ChIP-seq]

| PRJNA600928 | ENA

STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [RNA-Seq]

Project description:STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [RNA-Seq]

| PRJNA600932 | ENA

STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [single_cell_RNA-Seq]

Project description:Enhancers are distal regulators of gene expression that shape cell identity and regulate cell fate transitions. Mouse embryonic stem cells (mESCs) are a typical example of cells whose pluripotent identity is maintained by a complex enhancer landscape, that is drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for enhancer location, strength and dynamics. Here, we applied STARR-seq, a genome-wide plasmid-based assay, to measure the enhancer potential of genomic loci in a plasmid context in “ground-state” (2i+LIF; 2iL-ESCs) and “metastable” (serum+LIF; SL-ESCs) embryonic stem cells.

2020-08-16 | GSE143545 | GEO

STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [RNA-Seq]

2020-08-16 | GSE143543 | GEO

STARR-seq identifies chromatin masked enhancers in pluripotent mouse embryonic stem cells [ChIP-seq]

2020-08-16 | GSE143541 | GEO

STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells.

Project description:BackgroundEnhancers are distal regulators of gene expression that shape cell identity and control cell fate transitions. In mouse embryonic stem cells (mESCs), the pluripotency network is maintained by the function of a complex network of enhancers, that are drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for identifying putative enhancers and for describing their activity levels and dynamics.ResultsHere, we applied STARR-seq, a genome-wide plasmid-based assay, as a read-out for the enhancer landscape in "ground-state" (2i+LIF; 2iL) and "metastable" (serum+LIF; SL) mESCs. This analysis reveals that active STARR-seq loci show modest overlap with enhancer locations derived from peak calling of ChIP-seq libraries for common enhancer marks. We unveil ZIC3-bound loci with significant STARR-seq activity in SL-ESCs. Knock-out of Zic3 removes STARR-seq activity only in SL-ESCs and increases their propensity to differentiate towards the endodermal fate. STARR-seq also reveals enhancers that are not accessible, masked by a repressive chromatin signature. We describe a class of dormant, p53 bound enhancers that gain H3K27ac under specific conditions, such as after treatment with Nocodazol, or transiently during reprogramming from fibroblasts to pluripotency.ConclusionsIn conclusion, loci identified as active by STARR-seq often overlap with those identified by chromatin accessibility and active epigenetic marking, yet a significant fraction is epigenetically repressed or display condition-specific enhancer activity.

| S-EPMC7488044 | biostudies-literature

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.

2013-01-17 | E-GEOD-40739 | biostudies-arrayexpress

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

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.

2024-06-17 | GSE267075 | GEO

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