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A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes [RIBO_RNA]

ABSTRACT: A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes [RIBO_RNA]

PROVIDER: PRJNA927287 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23217391_1.fastq.gz	Fastqsanger.gz
	SRR23217391_2.fastq.gz	Fastqsanger.gz
	SRR23217392_1.fastq.gz	Fastqsanger.gz
	SRR23217392_2.fastq.gz	Fastqsanger.gz
	SRR23217393_1.fastq.gz	Fastqsanger.gz

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A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes [RIBO_RNA]

Project description:The genome is pervasively transcribed to produce a vast array of non-coding RNAs (ncRNAs). Long noncoding RNAs (lncRNAs) are transcripts of > 200 nucleotides and are best known for their ability to regulate gene expression. Enhancer RNAs (eRNAs) are subclass of lncRNAs that are synthesized from enhancer regions and have also been shown to coordinate gene expression. The biological function and significance of most lncRNAs and eRNAs remain to be determined. Epithelial to mesenchymal transition (EMT) is a ubiquitous cellular process that occurs during cellular migration, homeostasis, fibrosis, and cancer-cell metastasis. EMT-transcription factors, such as SNAI1 induce a complex transcriptional program that coordinates the morphological and molecular changes associated with EMT. Such complex transcriptional programs are often subject to coordination by networks of ncRNAs and thus can be leveraged to identify novel functional ncRNA loci. Here, using a genome-wide CRISPR activation (CRISPRa) screen targeting ~10,000 lncRNA loci we identified ncRNA loci that could either promote or attenuate EMT. We discovered a novel locus that we named SCREEM (SNAI1 cis-regulatory eRNAs expressed in monocytes). The SCREEM locus contained a cluster of eRNAs that when activated using CRISPRa induced expression of the neighboring gene SNAI1, driving concomitant EMT. However, the SCREEM eRNA transcripts themselves appeared dispensable for the induction of SNAI1 expression. Interestingly, the SCREEM eRNAs and SNAI1 were co-expressed in activated monocytes, where the SCREEM locus demarcated a monocyte-specific super-enhancer. These findings suggest an unexpected role for SNAI1 in monocytes. Exploration of the SCREEM-SNAI axis could reveal novel aspects of monocyte biology.

2023-03-02 | GSE223681 | GEO

A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes [gRNA_SCREEN]

2023-03-02 | GSE223683 | GEO

A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes [SNA1_RNA-Seq]

2023-03-02 | GSE223682 | GEO

A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes

Project description:A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes

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A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes [gRNA_SCREEN]

Project description:A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes [gRNA_SCREEN]

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A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes [SNA1_RNA-Seq]

Project description:A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes [SNA1_RNA-Seq]

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A genome–wide CRISPR activation screen identifies SCREEM a novel SNAI1 super-enhancer demarcated by eRNAs in monocytes

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

2023-03-02 | GSE223684 | GEO

Assessing eRNAs associated with a cytokine-sensing mammary super-enhancer

Project description:Enhancers are transcription factor platforms that also bind RNA polymerase II and generate enhancer RNAs (eRNA). Although eRNAs have been suggested as predictors of enhancer activities and possibly key components facilitating transcription, there is little genetic evidence to support this. We address the biology of eRNAs in vivo and investigate eRNA patterns, expression levels and possible functions within a mammary-specific super-enhancer that is composed of three units with distinct transcriptional capacities. We show that eRNA levels do not correspond with the activities of their respective enhancer units. However, changes in eRNA expression upon deletion of individual enhancer units reflect the change in overall super-enhancer activity. These data provide genetic evidence that eRNA levels are not a reliable readout of individual enhancers, but they predict superenhancer activity in the absence of constituent elements.

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Project description:Prostate cancer (PCa) is one of the most commonly diagnosed cancers in males worldwide. lncRNAs (long non-coding RNAs) play a significant role in the occurrence and development of PCa. eRNAs (enhancer RNA) and SE-lncRNAs (super-enhancer lncRNA) are important elements of lncRNAs, but the role of eRNAs and SE-lncRNAs in PCa remains largely unclear. In this work, we identified 681 eRNAs and 292 SE-lncRNAs that were expressed differentially in PCa using a microarray. We constructed a transcriptional regulation network that eRNA related enhancer and the target genes shared the same TF binding motifs. Further, we investigated whether CTCF played a role in mediating the transcriptional regulation network. eRNAs, especially those that regulate androgen response genes, may be candidates for prognostic biomarkers and therapy targets. Our work provide a new perspective for developing medical treatments and therapies for prostate cancer.

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Project description:Assessing eRNAs associated with a cytokine-sensing mammary super-enhancer

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