Transcription Factors And Their Targets
Our studies of the hypoxia response pathway have recently focused on the pathways terminal effector: the transcription factor HIF-1. An ultimate goal in studying any signaling pathway that regulates gene expression at the transcriptional level is to identify and characterize all of the transcriptional targets of the pathway. To that end, we are using RNA-seq, ChIP-seq, and other Omics techniques to identify all of the target genes regulated by HIF-1. We are employing novel computational approaches to separate true targets from background noise and the technical artifacts that often arise when one uses these technical approaches. We are beginning to collaborate with other C. elegans researchers to use these same approaches to identify transcriptional targets of other interesting transcription factors and signal transduction pathways in the worm.
Questions About Transcription Factors
Where do transcription factors bind in the genome?
What computational tools can we use to identify their true regulatory targets?
How does the transcriptional profile activated by a signal transduction pathway change over time?
What is the relationship between transcription factor binding, the regulation of gene expression, and changes in the epigenetic chromatin landscape?
Dopamine signaling promotes the xenobiotic stress response and protein homeostasis.
Joshi KK, Matlack TL, Rongo C. EMBO J. 2016 Sep 1;35(17):1885-901. doi: 10.15252/embj.201592524. Epub 2016 Jun 3. PMID: 27261197
Multicellular organisms encounter environmental conditions that adversely affect protein homeostasis (proteostasis), including extreme temperatures, toxins, and pathogens. It is unclear how they use sensory signaling to detect adverse conditions and then activate stress response pathways so as to offset potential damage. Here, we show that dopaminergic mechanosensory neurons in C. elegans release the neurohormone dopamine to promote proteostasis in epithelia. Signaling through the DA receptor DOP-1 activates the expression of xenobiotic stress response genes involved in pathogenic resistance and toxin removal, and these genes are required for the removal of unstable proteins in epithelia. Exposure to a bacterial pathogen (Pseudomonas aeruginosa) results in elevated removal of unstable proteins in epithelia, and this enhancement requires DA signaling. In the absence of DA signaling, nematodes show increased sensitivity to pathogenic bacteria and heat-shock stress. Our results suggest that dopaminergic sensory neurons, in addition to slowing down locomotion upon sensing a potential bacterial feeding source, also signal to frontline epithelia to activate the xenobiotic stress response so as to maintain proteostasis and prepare for possible infection.
EGF signalling activates the ubiquitin proteasome system to modulate C. elegans lifespan.
Liu G, Rogers J, Murphy CT, Rongo C. EMBO J. 2011 Jun 14;30(15):2990-3003. doi: 10.1038/emboj.2011.195. PMID:21673654
Epidermal growth factor (EGF) signalling regulates growth and differentiation. Here, we examine the function of EGF signalling in Caenorhabditis elegans lifespan. We find that EGF signalling regulates lifespan via the Ras-MAPK pathway and the PLZF transcription factors EOR-1 and EOR-2. As animals enter adulthood, EGF signalling upregulates the expression of genes involved in the ubiquitin proteasome system (UPS), including the Skp1-like protein SKR-5, while downregulating the expression of HSP16-type chaperones. Using reporters for global UPS activity, protein aggregation, and oxidative stress, we find that EGF signalling alters protein homoeostasis in adults by increasing UPS activity and polyubiquitination, while decreasing protein aggregation. We show that SKR-5 and the E3/E4 ligases that comprise the ubiquitin fusion degradation (UFD) complex are required for the increase in UPS activity observed in adults, and that animals that lack SKR-5 or the UFD have reduced lifespans and indications of oxidative stress. We propose that as animals enter fertile adulthood, EGF signalling switches the mechanism for maintaining protein homoeostasis from a chaperone-based approach to an approach involving protein elimination via augmented UPS activity.