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Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

ABSTRACT: Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

PROVIDER: PRJNA474531 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7257540.fastq.gz	Fastqsanger.gz
	SRR7257560_1.fastq.gz	Fastqsanger.gz
	SRR7257560_2.fastq.gz	Fastqsanger.gz
	SRR7257541.fastq.gz	Fastqsanger.gz
	SRR7257561_1.fastq.gz	Fastqsanger.gz

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Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants [ChIP-Seq]

Project description:Background: LincRNAs play critical roles in eukaryotic cells, but systematic analyses of lincRNAs of an animal for phenotypes have been missing. We have generated CRISPR knockout strains for C. elegans lincRNAs and have evaluated their phenotypes Results: C. elegans lincRNAs demonstrate global features such as shorter length and fewer exons than mRNAs. For the systematic evaluation of C. elegans lincRNAs, CRISPR knockout strains for 155 out of all the 170 C. elegans lincRNAs were produced. Mutants of 23 lincRNAs have shown phenotypes in 6 traits analyzed. We have investigated these phenotypic lincRNAs for their gene expression patterns and their potential functional mechanisms. Some C. elegans lincRNAs play cis roles to modulate the expression of their neighboring genes, and some other lincRNAs play trans roles as ceRNAs against microRNAs. LincRNAs are extensively regulated by transcription factors, and we dissect the pathway that two transcription factors UNC-30 and UNC-55 control the expression of linc-73 together. Furthermore, linc-73 plays a cis role to modulate the expression of its neighboring gene unc-104, and thus regulates the formation of presynapses. Conclusions: By using CRISPR/cas9 technology, we have generated knockout strains of 155 C. elegans lincRNAs as valuable resources for studies in noncoding RNAs, and we provide biological insights for 23 phenotypic lincRNAs identified from 6 traits examined.

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Project description:Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants [lncRNA-seq]

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Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants [miRNA-seq]

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Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants.

Project description:BACKGROUND:Long intergenic RNAs (lincRNAs) play critical roles in eukaryotic cells, but systematic analyses of the lincRNAs of an animal for phenotypes are lacking. We generate CRISPR knockout strains for Caenorhabditis elegans lincRNAs and evaluate their phenotypes. RESULTS:C. elegans lincRNAs demonstrate global features such as shorter length and fewer exons than mRNAs. For the systematic evaluation of C. elegans lincRNAs, we produce CRISPR knockout strains for 155 of the total 170 C. elegans lincRNAs. Mutants of 23 lincRNAs show phenotypes in 6 analyzed traits. We investigate these lincRNAs by phenotype for their gene expression patterns and potential functional mechanisms. Some C. elegans lincRNAs play cis roles to modulate the expression of their neighboring genes, and several lincRNAs play trans roles as ceRNAs against microRNAs. We also examine the regulation of lincRNA expression by transcription factors, and we dissect the pathway by which two transcription factors, UNC-30 and UNC-55, together control the expression of linc-73. Furthermore, linc-73 possesses a cis function to modulate the expression of its neighboring kinesin gene unc-104 and thus plays roles in C. elegans locomotion. CONCLUSIONS:By using CRISPR/cas9 technology, we generate knockout strains of 155 C. elegans lincRNAs as valuable resources for studies in noncoding RNAs, and we provide biological insights for 23 lincRNAs with the phenotypes identified in this study.

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Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

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

2018-12-27 | GSE115324 | GEO

Systematic evaluation of chromosome conformation capture assays

Project description:Systematic evaluation of chromosome conformation capture assays

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Systematic evaluation of chromosome conformation capture assays [1D]

Project description:Systematic evaluation of chromosome conformation capture assays [1D]

| PRJNA698732 | ENA