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

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

PROVIDER: PRJNA474535 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7257560_1.fastq.gz	Fastqsanger.gz
	SRR7257560_2.fastq.gz	Fastqsanger.gz
	SRR7257561_1.fastq.gz	Fastqsanger.gz
	SRR7257561_2.fastq.gz	Fastqsanger.gz
	SRR7257562_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants [lncRNA-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.

2018-12-27 | GSE115320 | GEO

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

2018-12-27 | GSE122973 | GEO

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

2018-12-27 | GSE115321 | GEO

Systematic evaluation of C. elegans lincRNAs with CRISPR knockout mutants

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

| PRJNA474531 | ENA

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

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

| PRJNA507090 | ENA

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

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

| PRJNA474534 | ENA

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.

| S-EPMC6325887 | biostudies-literature

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

| PRJNA698572 | ENA

Reevaluation by CRISPR-Cas9 approach reveals multiple lincRNAs dispensable for pluripotency maintenance and SNORA73 essential for pluripotency exit (scRNA-Seq)

Project description:Many lincRNAs have been identified as essential regulators for ESC pluripotency through siRNA-based screening. However, the biological and molecular functions of the large intergenic noncoding RNAs (lincRNAs) remain unclear. Here, we employed CRISPR/Cas9-mediated knockout technology to explore the functions of 8 previously annotated lincRNAs in ESCs. Unexpectedly, it was found that most lincRNAs are dispensable for pluripotency maintenance, cloning formation ability, proliferation and apoptosis in ESCs when we disrupted these lincRNAs individually or in combinations. Single-cell transcriptomic analysis of a set of lncRNA knockout ESCs showed consistent results, indicating that previously observed functions of lincRNAs on ESC pluripotency maintenance may be due to off-targeted effects. Interestingly, deletion and transcriptional repression of linc1343 disrupts embryoid body (EB) differentiation in ESC. Notably, GM17300 and two small RNAs (Snora73a, Snora73b) derived from the lnc1343 locus are highly expressed in ESCs. Further overexpression of Snora73a and Snora73b in linc1343 knockout cells rescue the phenotype, suggesting that snoRNAs derived from linc1343 are the responders for EB differentiation. Taken together, our results demonstrate the divergent effects of lincRNAs on regulating ESC pluripotency and EB differentiation.

2024-08-07 | GSE225238 | GEO

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