Genome-wide endogenous DAF-16/FOXO recruitment dynamics during lowered insulin signalling inC. elegans

Abstract

Lowering insulin-IGF-1-like signalling (IIS) activates FOXO transcription factors (TF) to extend life span across species. To study the dynamics of FOXO chromatin occupancy under this condition in C. elegans, we report the first recruitment profile of endogenous DAF-16 and show that the response is conserved. DAF-16 predominantly acts as a transcriptional activator and binding within the 0.5 kb promoter-proximal region results in maximum induction of downstream targets that code for proteins involved in detoxification and longevity. Interestingly, genes that are activated under low IIS already have higher DAF-16 recruited to their promoters in WT. DAF-16 binds to variants of the FOXO consensus sequence in the promoter proximal regions of genes that are exclusively targeted during low IIS. We also define a set of ‘core’ direct targets, after comparing multiple studies, which tend to co-express and contribute robustly towards IIS-associated phenotypes. Additionally, we show that nuclear hormone receptor DAF-12 as well as zinc-finger TF EOR-1 may bind DNA in close proximity to DAF-16 and distinct TF classes that are direct targets of DAF-16 may be instrumental in regulating its indirect targets. Together, our study provides fundamental insights into the transcriptional biology of FOXO/DAF-16 and gene regulation downstream of the IIS pathway.

MiR-150 promotes cellular metastasis in non-small cell lung cancer by targeting FOXO4

“…FOXO proteins use the forkhead box domain to bind as monomers to the consensus sequence (5′-TTGTTTAC-3′) and hence negatively or positively regulate gene expression, depending on the promoter context and extracellular conditions141516. FOXO proteins are subject to multiple posttranslational regulations typically from the PI3K-AKT/SGK pathway (phosphorylation), the stress-activated JNK pathway (phosphorylation) and other posttranslational modifications such as acetylation and methylation, which decide on the subcellular localization (nuclear-cytoplasmic shuttling), DNA binding affinity and transcriptional activity17.…”

A chromatin modifier integrates insulin/IGF‐1 signalling and dietary restriction to regulate longevity

“…Pharynx is marked by arrow head. (C) UCSC browser view of DAF ‐16/ FOXO peaks as determined by Ch IP ‐seq using anti‐ DAF ‐16/ FOXO antibody (Kumar et al ., ). Red boxes indicate the promoter regions of zfp‐1(2a) and zfp‐1(2c) where DAF ‐16/ FOXO peaks are observed.…”

“…We hypothesized that because DAF‐16 and ZFP‐1 may be part of a larger complex (Riedel et al ., ), they would possibly influence the expression of DAF‐16 target genes. To study this aspect of regulation, we focused on the well‐known DAF‐16 direct target, sod‐3 (Oh et al ., ; Mukhopadhyay et al ., ; Kumar et al ., ). Under conditions of low insulin signalling, as seen in daf‐2(‐) , sod‐3 is chronically upregulated in a daf‐16 ‐dependent manner (Libina et al ., ).…”

“…While the zfp‐1(2c) promoter drove GFP expression uniformly in the worm, the zfp‐1(2a) promoter‐driven expression was noticeably absent from the pharynx, germline and the tail regions. A genome‐wide endogenous DAF‐16/FOXO ChIP sequencing study in our laboratory (Kumar et al ., ) showed that the transcription factor binds to the promoters of both the zfp‐1 isoforms in the temperature‐sensitive daf‐2(e1370) allele of daf‐2 (Fig. C; see supplementary Materials and methods for analysis details and data access links).…”

Universal transcriptomic signature of age reveals temporal scaling ofCaenorhabditis elegansaging trajectories

“…The MetaWorm dataset is sufficiently large to generate the cross-validation ensemble of single-gene association tests using random resampling. We further reduced the number of candidate genes by thresholding the transcripts by the frequency Geneset FDR DAF-16 targets [30] 4.6e-7 CEC-3 targets (spr-5 mutant, generation 10) [31] 2.0e-4 small RNAs decreased by starvation at P0 [32] 1.3e-3 PQM-1 L3 targets [33] 1.4e-3 Rb/E2F pathway (DPL-1,EFL-1,LIN-35), intestine [34] 2.7e-3 PMK-1 targets down in Day 15 vs. Day 6 [35] 3.8e-3 age-regulated ELT-2 targets [36] 3.8e-3 up by CSR-1 and w/out CSR-1-bound 22G RNA [37] 7.1e-3…”