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Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo

ABSTRACT: Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo

PROVIDER: PRJNA481951 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6180300_1.fastq.gz	Fastqsanger.gz
	SRR6180300_2.fastq.gz	Fastqsanger.gz
	SRR6180301_1.fastq.gz	Fastqsanger.gz
	SRR6180301_2.fastq.gz	Fastqsanger.gz
	SRR6180302_1.fastq.gz	Fastqsanger.gz

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Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (lungs and spleens)

Project description:Here we compare gene expression profiles between lungs and spleens following LPS in vivo injection into Wild type, lincRNA-Cox2 knockout and lincRNA-Cox2 mutant mice The aim of the experiment is to determine the cis and trans functions for lincRNA-Cox2 following in vivo LPS challenge within the spleen and lung

2018-12-19 | GSE116354 | GEO

Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (lungs)

Project description:Here we compare gene expression profiles between lungs taken from a Wild type mouse to lungs from a lincRNA-Cox2 knockout mouse The aim of the experiment is to determine what impact lincRNA-Cox2 has on gene expression within the lung

2018-12-19 | GSE105068 | GEO

Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (lungs)

Project description:Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (lungs)

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Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (macrophages)

Project description:Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (macrophages)

| PRJNA481949 | ENA

Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (lungs and spleens)

Project description:Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (lungs and spleens)

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Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2.

Project description:An inducible gene expression program is a hallmark of the host inflammatory response. Recently, long intergenic non-coding RNAs (lincRNAs) have been shown to regulate the magnitude, duration, and resolution of these responses. Among these is lincRNA-Cox2, a dynamically regulated gene that broadly controls immune gene expression. To evaluate the in vivo functions of this lincRNA, we characterized multiple models of lincRNA-Cox2-deficient mice. LincRNA-Cox2-deficient macrophages and murine tissues had altered expression of inflammatory genes. Transcriptomic studies from various tissues revealed that deletion of the lincRNA-Cox2 locus also strongly impaired the basal and inducible expression of the neighboring gene prostaglandin-endoperoxide synthase (Ptgs2), encoding cyclooxygenase-2, a key enzyme in the prostaglandin biosynthesis pathway. By utilizing different genetic manipulations in vitro and in vivo, we found that lincRNA-Cox2 functions through an enhancer RNA mechanism to regulate Ptgs2. More importantly, lincRNA-Cox2 also functions in trans, independently of Ptgs2, to regulate critical innate immune genes in vivo.

| S-EPMC6291222 | biostudies-literature

Cis-trans

Project description:Cis-trans

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High-resolution dissection of human cell type-specific enhancers in cis and trans activities

Project description:The spatiotemporal specific gene expression is regulated by cell type-specific regulatory elements including enhancers, silencers and insulators etc. The massively parallel reporter assay (MPRA) methods like STARR-seq facilitate the systematic study of DNA sequence intrinsic enhancer activities in a large scale. However, when applied to human cells, it remains challenging to identify and quantify cell type-specific active enhancers in the genome-wide scale with high-resolution, due to the large size of human genome. In this study, we selected the H3K4me1 associated dinucleosome with the linker DNA sequences as candidate enhancer sequences in two different human cell lines and performed ChIP-STARR-seq to quantify the cell type-specific enhancer activities with high-resolution in a genome-wide scale. Furthermore, we investigated how the activity landscape of enhancer repository would change when transferred from native cells (cis activity) to another cell lines (trans activity). Using ChIP-STARR-seq of the candidate enhancers in native cells and another type of cells, we obtained enhancers cis activity maps and trans activity maps in two different cell lines. The cis and trans activity maps enabled us to identify cell type-specific active enhancers, with enrichment of motifs of differentially expressed TFs. Comparisons between the cis and trans activity maps revealed general consistent regulatory property with different levels of activity in the two cell types, suggesting the sequence intrinsic regulatory properties keep similar in different type of cells. This study provides a new perspective of sequence intrinsic enhancer activities in different types of cells.

2023-09-22 | GSE243793 | GEO

Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo

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

2018-12-19 | GSE117379 | GEO

Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (macrophages)

Project description:Here we amplified a region in exon 5 of Ptgs2 that contains SNPs to allow us to differenitate between the C57 allele and the MOLF allele

2018-12-19 | GSE117377 | GEO

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