Real-time monitoring of gene expression reveals transcription kinetics of mammalian genes.

We study the effect of conservation laws on the finite-temperature transport properties in one-dimensional integrable quantum many-body systems. We show that the energy current is closely related to the first conservation law in these systems and therefore the thermal transport coefficients are anomalous. Using an inequality on the time decay of current correlations we show how the existence of conserved quantities implies a finite charge stiffness (weight of the zero-frequency component of the conductivity) and so ideal conductivity at finite temperatures.

The mammalian circadian clock uses interlocked negative feedback loops in which the heterodimeric basic helix-loop-helix transcription factor BMAL1/CLOCK is a master regulator. While there is prominent control of liver functions by the circadian clock, the detailed links between circadian regulators and downstream targets are poorly known. Using chromatin immunoprecipitation combined with deep sequencing we obtained a time-resolved and genome-wide map of BMAL1 binding in mouse liver, which allowed us to identify over 2,000 binding sites, with peak binding narrowly centered around Zeitgeber time 6. Annotation of BMAL1 targets confirms carbohydrate and lipid metabolism as the major output of the circadian clock in mouse liver. Moreover, transcription regulators are largely overrepresented, several of which also exhibit circadian activity. Genes of the core circadian oscillator stand out as strongly bound, often at promoter and distal sites. Genomic sequence analysis of the sites identified E-boxes and tandem E1-E2 consensus elements. Electromobility shift assays showed that E1-E2 sites are bound by a dimer of BMAL1/CLOCK heterodimers with a spacing-dependent cooperative interaction, a finding that was further validated in transactivation assays. BMAL1 target genes showed cyclic mRNA expression profiles with a phase distribution centered at Zeitgeber time 10. Importantly, sites with E1-E2 elements showed tighter phases both in binding and mRNA accumulation. Finally, analyzing the temporal profiles of BMAL1 binding, precursor mRNA and mature mRNA levels showed how transcriptional and post-transcriptional regulation contribute differentially to circadian expression phase. Together, our analysis of a dynamic protein-DNA interactome uncovered how genes of the core circadian oscillator crosstalk and drive phase-specific circadian output programs in a complex tissue. The circadian clock is a timing system that allows organisms to keep behavioral, physiological, and cellular rhythms in resonance with daily environmental cycles. In mammals, such clocks use transcriptional regulatory loops in which the heterodimeric transcription factor BMAL1/CLOCK plays a central role. While defects in circadian clock function have been associated with diabetes, obesity, and cancer, the molecular links between the circadian clock and such output pathways are poorly characterized. Here, we mapped DNA-binding sites of BMAL1 in mouse liver during one circadian cycle. Our temporal analysis revealed widespread daily rhythms in DNA binding, with maximum levels peaking at midday. In the list of candidates, core circadian genes stood out as the most strongly bound, often showing multiple binding sites. Interestingly, BMAL1 targets were highly enriched in genes involved in carbohydrate and lipid metabolism, and also in transcription factors, in particular nuclear receptors. Our results suggest that the mammalian clock uses BMAL1 to control transcriptional output programs both directly and indirectly. Additionally, the DNA specificity of BMAL1 binding revealed the importance of tandem E-box elements, which may favor strong binding and precise timing of daily gene expression. Taken together, our work confirms BMAL1's primary function as a master regulator of the core circadian oscillator, while demonstrating that it also contributes in a more distributed fashion to a variety of output programs.