Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of C. elegans young adult hermaphrodites to detect differentially expressed genes in the absence of lsl-1 activity

ABSTRACT: LSL-1 is a novel Zinc-finger transcription factor that we identified in a genome wide RNAi screen as a suppressor of ectopic germline gene expression associated with mutations in let-418, which encodes an ATP-dependent chromatin remodeler. RNA for three different biological replicates was isolated from at least 1000 animals of each genotype: wild type, lsl-1(tm4769) and lsl-1(ljm-1); and then sequence to detect differentially expressed genes in both lsl-1 mutant genotypes compared to wild type animals.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Chantal Wicky

PROVIDER: E-MTAB-11199 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Recently, more than a thousand large intergenic non-coding RNAs (lincRNAs) have been reported. These RNAs are evolutionarily conserved in mammalian genomes and thus presumably function in diverse biological processes. Here, we report the identification of lincRNAs that are regulated by p53. One of these lincRNAs (lincRNA-p21) serves as a repressor in p53-dependent transcriptional responses. Inhibition of lincRNA-p21 affects the expression of hundreds of gene targets enriched for genes normally repressed by p53. The observed transcriptional repression by lincRNA-p21 is mediated through the physical association with hnRNP-K. This interaction is required for proper genomic localization of hnRNP-K at repressed genes and regulation of p53 mediated apoptosis. We propose a model whereby transcription factors activate lincRNAs that serve as key repressors by physically associating with repressive complexes and modulating their localization to sets of previously active genes. Gene expression profiles of different p53 inducible mouse embryonic fibroblasts (p53LSL/LSL MEFs) across different time points after DNA damage. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 transcriptional response. [1] MEF profiling: p53 LSL/LSL MEFs were treated with adenoCRE for p53 restoration or adenoGFP as control for 24h and treated with 500nM doxorubicin for the indicated times. [2] hnRNPKKD profiling: p53 LSL/LSL MEFs were treated with adenoCRE for p53 restoration for 24h, transfected with siRNA oligos targeting different transcripts for 24h and then treated with 100nM doxorubicin for 13h. [3] lincP21KD profiling: p53 LSL/LSL MEFs were treated with adenoCRE for p53 restoration for 24h, transfected with siRNA oligos targeting different transcripts for 24h and then treated with 100nM doxorubicin for 13h. [4] RAS profiling: For p53 restoration, cultured tumor cell lines were incubated with 500nM 4-hydroxytamoxifen for the indicated times.

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RNA-seq of C. elegans young adult hermaphrodites to detect differentially expressed genes in the absence of lsl-1 activity

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