C. elegans microarrays: daf-2(-) vs. daf-2(-) xbp-1(-)
ABSTRACT: Transcriptional profiling of day 1 animals comparing untreated daf-2(-) animals and daf-2(-) xbp-1(-) animals. Goal was to identify genes whose expression in daf-2 mutants is dependent (directly or indirectly) on xbp-1. Two-condition experiment, daf-2(-) animals and daf-2(-) xbp-1(-) animals. 4 Biological replicates in daf-2(e1370) background: 4 sets of daf-2(e1370) animals and their matching daf-2(e1370) xbp-1(zc12) animals. 4 Biological replicates in daf-2(e1368) background: 4 sets of daf-2(e1368) animals and their matching daf-2(e1368) xbp-1(zc12) animals.
Project description:Transcriptional profiling of day 1 animals comparing untreated daf-2(-) animals and daf-2(-) xbp-1(-) animals. Goal was to identify genes whose expression in daf-2 mutants is dependent (directly or indirectly) on xbp-1. Overall design: Two-condition experiment, daf-2(-) animals and daf-2(-) xbp-1(-) animals. 4 Biological replicates in daf-2(e1370) background: 4 sets of daf-2(e1370) animals and their matching daf-2(e1370) xbp-1(zc12) animals. 4 Biological replicates in daf-2(e1368) background: 4 sets of daf-2(e1368) animals and their matching daf-2(e1368) xbp-1(zc12) animals.
Project description:In order to understand the complexity of gene regulation downstream of IIS, we did RNA-seq in mixed culture in wild-type, daf-2(e1370), daf-16(mgDf50);daf-2(e1370) and daf-2(e1370);daf-12(m20 and correlated it with ChIP-seq data RNA-seq profile of different mutants in mix stage
Project description:In order to understand the complexity of gene regulation downstream of IIS, we used anti-DAF-16 antibody, we report the first genome-wide ChIP-sequencing study of endogenous DAF-16 recruitment in daf-2(e1370). We also report the average bin-wise normalized read count of ZFP-1 and DAF-16 on DAF-16 summits ChIP-Seq profile of DAF-16 in mix stage
Project description:To exmine the role of nonsense-mediated mRNA decay process in the longevity regulation of daf-2 mutants, we sequenced transcriptomes from day 1 adult Caenorhabditis elegans: Bristol N2 (wild-type), and smg-2(qd101), daf-2(e1370) and smg-2(qd101); daf-2(e1370) mutants. Overall design: Determination of transcript levels in N2 (wild-type), smg-2(qd101), daf-2(e1370), and smg-2(qd101); daf-2(e1370) animals by using deep sequencing, in duplicate
Project description:In this study we have investigated the effect of loss of math-33 activity on DAF-16-mediated target gene regulation in C. elegans under conditions of reduced Insulin/IGF-1 signaling (IIS). Using whole nematode RNA sequencing experiments we found that the daf-2(e1370)-mediated induction and repression of DAF-16 target genes was decreased in daf-2(e1370); math-33(tm3561) mutant animals. Our data suggest that the downregulation of endogenous DAF-16 isoforms in the absence of a functional MATH-33 severely affects the global expression of DAF-16 targets when IIS activity is reduced. Therefore, MATH-33 is essential for DAF-16-mediated target gene activation and repression in the context of IIS. DAF-16 mediated target gene regulation was analyzed in daf-2(e1370) nematodes and compared to daf-2(e1370); math-33(tm3561) mutant animals. daf-16(mu86); daf-2(e1370); N2 (wild type) and math-33(tm3561) single mutant animals were used as controls.
Project description:The gene daf-2 encodes the single insulin/insulin growth factor-1-like receptor of Caenorhabditis elegans. The reduction-of-function allele e1370 induces several metabolic alterations and doubles lifespan.We found that the e1370 mutation alters aerobic energy production substantially. In wild-type worms the abundance of key mitochondrial proteins declines with age, accompanied by a dramatic decrease in energy production, although the mitochondrial mass, inferred from the mitochondrial DNA copy number, remains unaltered. In contrast, the age-dependent decrease of both key mitochondrial proteins and bioenergetic competence is considerably attenuated in daf-2(e1370) adult animals. The increase in daf-2(e1370) mitochondrial competence is associated with a higher membrane potential and increased reactive oxygen species production, but with little damage to mitochondrial protein or DNA. Together these results point to a higher energetic efficiency of daf-2(e1370) animals.We conclude that low daf-2 function alters the overall rate of ageing by a yet unidentified mechanism with an indirect protective effect on mitochondrial function.
Project description:Organisms and their cells vary greatly in their tolerance of low oxygen environments (hypoxia). A delineation of the determinants of hypoxia tolerance is incomplete, despite intense interest for its implications in diseases such as stroke and myocardial infarction. The insulin/IGF-1 receptor (IGFR) signaling pathway controls survival of Caenorhabditis elegans from a variety of stressors including aging, hyperthermia, and hypoxia. daf-2 encodes a C. elegans IGFR homolog whose primary signaling pathway modulates the activity of the FOXO transcription factor DAF-16. DAF-16 regulates the transcription of a large number of genes, some of which have been shown to control aging. To identify genes that selectively regulate hypoxic sensitivity, we compared the whole-organismal transcriptomes of three daf-2 reduction-of-function alleles, all of which are hypoxia resistant, thermotolerant, and long lived, but differ in their rank of severities for these phenotypes. The transcript levels of 172 genes were increased in the most hypoxia resistant daf-2 allele, e1370, relative to the other alleles whereas transcripts from only 10 genes were decreased in abundance. RNAi knockdown of 6 of the 10 genes produced a significant increase in organismal survival after hypoxic exposure as would be expected if down regulation of these genes by the e1370 mutation was responsible for hypoxia resistance. However, RNAi knockdown of these genes did not prolong lifespan. These genes definitively separate the mechanisms of hypoxic sensitivity and lifespan and identify biological strategies to survive hypoxic injury.
Project description:FoxO transcription factors promote longevity across taxa. How they do so is poorly understood. In the nematode Caenorhabditis elegans, the A- and F-isoforms of the FoxO transcription factor DAF-16 extend life span in the context of reduced DAF-2 insulin-like growth factor receptor (IGFR) signaling. To elucidate the mechanistic basis for DAF-16/FoxO-dependent life span extension, we performed an integrative analysis of isoform-specific daf-16/FoxO mutants. In contrast to previous studies suggesting that DAF-16F plays a more prominent role in life span control than DAF-16A, isoform-specific daf-16/FoxO mutant phenotypes and whole transcriptome profiling revealed a predominant role for DAF-16A over DAF-16F in life span control, stress resistance, and target gene regulation. Integration of these data sets enabled the prioritization of a subset of 92 DAF-16/FoxO target genes for functional interrogation. Among 29 genes tested, two DAF-16A-specific target genes significantly influenced longevity. Our discovery of new longevity genes underscores the efficacy of our integrative strategy while providing a general framework for identifying specific downstream gene regulatory events that contribute substantially to transcription factor functions. As FoxO transcription factors have conserved functions in promoting longevity and may be dysregulated in aging-related diseases, these findings promise to illuminate fundamental principles underlying aging in animals. Whole-transcriptome profiling of daf-16/FoxO isoform-specific deletion mutants in the long-lived daf-2(e1370) background. Included are daf-16 wild-type, daf-16 null mutation, daf-16a/f mutation, two independent daf-16a mutations, and daf-16f mutation. N2 wild-type controls are also included.
Project description:Analysis of gene expression in long-lived daf-2 mutants for the insulin/IGF-1 receptor. daf-2(e1370) and daf-2(m577) alleles each examined as single and as double mutations with the daf-16(df50) allele. DAF-2 regulates DAF-16, a transcription factor. Results provide insight into longevity.