Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals

Abstract

Transcriptional regulation lies at the core of the circadian clockwork, but how the clock-related transcription machinery controls the circadian phase is not understood. Here, we show both in human cells and in mice that RuvB-like ATPase 2 (RUVBL2) interacts with other known clock proteins on chromatin to regulate the circadian phase. Pharmacological perturbation of RUVBL2 with the adenosine analog compound cordycepin resulted in a rapid-onset 12-hour clock phase-shift phenotype at human cell, mouse tissue, and whole-animal live imaging levels. Using simple peripheral injection treatment, we found that cordycepin penetrated the blood-brain barrier and caused rapid entrainment of the circadian phase, facilitating reduced duration of recovery in a mouse jet-lag model. We solved a crystal structure for human RUVBL2 in complex with a physiological metabolite of cordycepin, and biochemical assays showed that cordycepin treatment caused disassembly of an interaction between RUVBL2 and the core clock component BMAL1. Moreover, we showed with spike-in ChIP-seq analysis and binding assays that cordycepin treatment caused disassembly of the circadian super-complex, which normally resides at E-box chromatin loci such as PER1, PER2, DBP, and NR1D1. Mathematical modeling supported that the observed type 0 phase shifts resulted from derepression of E-box clock gene transcription.

Proteomic analysis of Drosophila CLOCK complexes identifies rhythmic interactions with SAGA and Tip60 complex component NIPPED-A

“…Since clock gene transcript abundance was measured in heads 20 , and the vast majority of clock gene expression in heads is from photoreceptors 56 , such differential use of NIPPED-A in the Tip60 and SAGA complexes could result from tissue-specific interactions with CLK-CYC complexes. Our data strongly support an interaction between NIPPED-A and the CLK-CYC complex, consistent with recent work showing that mammalian TRRAP is present in CLOCK-BMAL1 complexes in mice 7 . Thus, our results suggest that interactions between NIPPED-A and CLK-CYC promote histone modifications via the SAGA and Tip60 complexes, thereby translating CLK-CYC binding into target gene transcription.…”

“…6 Significantly longer than w 1118 , UAS-dcr; + / + ; pdf-Gal4/ + control flies (p < 0.05). 7 Significantly lower power than w 1118 , UAS-dcr; tim-Gal4/ + ; + / + control flies (p < 0.05). 8 Significantly lower power than w 1118 , UAS-dcr; + / + ; pdf-Gal4/ + control flies (p < 10 -2 ).…”

“…As in flies, rhythmic transcription coincides with rhythms in clock protein phosphorylation and chromatin modifications 3 . PER-containing complexes contain multiple chromatin modifiers that repress transcription, including histone deacetylases 6 , helicases 7 , 8 , histone methyltransferases 9 , 10 , and nucleosome remodelers 11 . Factors that activate clock-dependent transcription have also been identified in mammals including MLL1 histone methyltransferase (HMT) 12 , Jarid1a histone demethylase (HDM) 13 , and histone acetyltransferases (HATs) 14 , 15 .…”

Go Human! Circadian translational medicine has come of age

“…Chemical screens to identify small molecules directly targeting the circadian phase will be the potential therapeutic approach. Recently, a paper authored by Ju et al reported that a natural compound, cordycepin, dramatically induces "type 0" phase shifts in mammalian cells and animals [3], while its clinical relevance needs further evaluation. Third, although we live in and follow the same solar/social time‐schedule, each individual person has a unique chronotype for his/her own.…”

Regulation of RUVBL1-RUVBL2 AAA-ATPases by the nonsense-mediated mRNA decay factor DHX34, as evidenced by Cryo-EM

“…RUVBL2 binds RPAP3 and PIH1D1, two subunits of the R2TP complex, functions not shared by RUVBL1. Interestingly, cordycepin, a derivative of the nucleoside adenosine affects the circadian clock in mammals by targeting RUVBL2 (Ju et al, 2020). A crystal structure of RUVBL1-RUVBL2 bound to cordycepin (PDB 6K0R) shows that the compound interacted with all RUVBL2 subunits but not with RUVBL1 and the N-termini of RUVBL2 were visible and folded into the protein.…”