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Caenorhabditis elegans

ABSTRACT: RNA-seq quantification of expression changes upon unc-62 knockdown in adult Caenorhabditis elegans.

PROVIDER: PRJNA171150 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR525286.fastq.gz	Fastqsanger.gz
	SRR525287.fastq.gz	Fastqsanger.gz
	SRR525288.fastq.gz	Fastqsanger.gz
	SRR525289.fastq.gz	Fastqsanger.gz
	SRR525290.fastq.gz	Fastqsanger.gz

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RNA-seq quantification of expression changes upon unc-62 knockdown in adult Caenorhabditis elegans.

Project description:We performed RNA-seq to quantify gene expression changes in adult worms upon knockdown of transcription factor unc-62/Homothorax. unc-62 is a developmental regulator that binds proximal to age-regulated transcripts and modulates lifespan. In the intestine (in which tissue-specific unc-62 knockdown increases lifespan), we identify multiple effects of unc-62 knockdown linked to extension of longevity. First, unc-62 RNAi decreases the expression of yolk proteins (vitellogenins) that aggregate in the body cavity and become toxic in old age. Second, unc-62 RNAi results in a broad increase in expression of intestinal genes that typically decrease expression with age, suggesting that unc-62 activity balances intestinal resource allocation between yolk protein expression and fertility on the one hand and somatic functions on the other. mRNA profiling by Illumina HiSeq of 3 biological replicates of day 4 adult Caenorhabditis elegans that were fed either control or unc-62 RNAi beginning at day 1 of adulthood.

2012-09-01 | E-GEOD-39574 | biostudies-arrayexpress

RNA-seq quantification of expression changes upon unc-62 knockdown in adult Caenorhabditis elegans.

2012-09-01 | GSE39574 | GEO

CCAR-1 regulates the alternative splicing of multiple genes in Caenorhabditis elegans

Project description:The Cell Division Cycle and Apoptosis Regulator (CCAR) protein family members have recently emerged as regulators of alternative splicing and transcription, as well as having other key physiological functions. For example, mammalian CCAR2/DBC1 forms a complex with the zinc factor protein ZNF326 to integrate alternative splicing with RNA polymerase II transcriptional elongation in AT-rich regions of the DNA. Additionally, Caenorhabditis elegans CCAR-1, a homolog to mammalian CCAR2, facilitates the alternative splicing of the perlecan unc-52 gene. However, much about the CCAR family's role in alternative splicing is unknown. We are interested in uncovering the role of the CCAR family in alternative splicing in vivo using Caenorhabditis elegans. We examined the role of CCAR-1 in genome-wide alternative splicing and identified new alternative splicing targets of CCAR-1 using RNA sequencing. Also, we found that CCAR-1 interacts with the spliceosome factors UAF-1 and UAF-2 using mass spectrometry, and that knockdown of ccar-1 affects alternative splicing patterns, motility, and proteostasis of UAF-1 mutant worms. Collectively, we demonstrate a role for CCAR-1 in the regulation of global alternative splicing in C. elegans and in conjunction with UAF-1

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Changes in Caenorhabditis elegans proteome after dnj-21 knockdown

Project description:Dysfunction of the motor subunit of the TIM23 translocase, the PAM complex located on the matrix side of the mitochondrial inner membrane in Saccharomyces cerevisiae, was shown to cause a decrease in mitochondrial protein import and precursor accumulation in the cytosol. We used an analogous model to study the non-mitochondrial response to defective mitochondrial import machinery in Caenorhabditis elegans in which we depleted DNJ-21 as the functional homolog of yeast Pam18. To gain a broader insight in potential changes in Caenorhabditis elegans proteome upon DNJ-21 depletion we performed a quantitative, label-free proteomics analysis. We compared protein levels upon knockdown of dnj-21 (dnj-21 RNAi) with control conditions (Empty vector RNAi). Synchronized N2 wild type worms were grown on NGM plates seeded with E. coli HT115(DE3) transformed with a construct targeting dnj-21 gene or with empty vector L4440 as a control.

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