A New Promoter Element Associated with Daily Time Keeping in Drosophila

Abstract

Circadian clocks are autonomous daily timekeeping mechanisms that allow organisms to adapt to environmental rhythms as well as temporally organize biological functions. Clock-controlled timekeeping involves extensive regulation of rhythmic gene expression. To date, relatively few clock-associated promoter elements have been identified and characterized. In an unbiased search of core clock gene promoters from 12 species of Drosophila, we discovered a 29-bp consensus sequence that we designated as the Clock-Associated Transcriptional Activation Cassette or 'CATAC'. To experimentally address the spatiotemporal expression information associated with this element, we generated constructs with four separate native CATAC elements upstream of a basal promoter driving expression of either the yeast Gal4 or firefly luciferase reporter genes. Reporter assays showed that presence of wild-type, but not mutated CATAC elements, imparted increased expression levels as well as rhythmic regulation. Part of the CATAC consensus sequence resembles the E-box binding site for the core circadian transcription factor CLOCK/CYCLE (CLK/CYC), and CATACmediated expression rhythms are lost in the presence of null mutations in either cyc or the gene encoding the CLK/CYC inhibitor, period (per). Nevertheless, our results indicate that CATAC's enhancer function persists in the absence of CLK/CYC. Thus, CATAC represents a novel cis-regulatory element encoding clock-controlled regulation.

A deep sleep stage in Drosophila with a functional role in waste clearance

“…Flies were transferred to a black 96-well plate, placed under domes [c.f. (48)]. Flies are in a checkerboard pattern so flies are only in diagonally adjacent wells (i.e., up to 48 flies per plate).…”

TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data

“…Using real time series RNA-seq data collected after insulin stimulation (Zirin et al, 2019), TIMEOR discovered a novel ordered cascade of TF-TF interactions, providing a new link between insulin stimulation and a validated circadian clock GRN (Fathallah-Shaykh, 2010;Kadener et al, 2007;Maury, 2019;Zhou et al, 2016). TIMEOR revealed that insulin regulates several key circadian clock TFs, providing a new molecular mechanism linking a high sugar diet to sleep disruption (Qian and Scheer, 2016;Sharp et al, 2017;Stenvers et al, 2019). Overall, TIMEOR facilitates future analyses of integrated omics data to uncover novel biological and disease mechanisms from temporal gene expression data sets.…”