The genetic architecture of type 2 diabetes

The genetic architecture of common traits, including the number, frequency, and effect sizes of inherited variants that contribute to individual risk, has been long debated. Genome-wide association studies have identified scores of common variants associated with type 2 diabetes, but in aggregate, these explain only a fraction of heritability. To test the hypothesis that lower-frequency variants explain much of the remainder, the GoT2D and T2D-GENES consortia performed whole genome sequencing in 2,657 Europeans with and without diabetes, and exome sequencing in a total of 12,940 subjects from five ancestral groups. To increase statistical power, we expanded sample size via genotyping and imputation in a further 111,548 subjects. Variants associated with type 2 diabetes after sequencing were overwhelmingly common and most fell within regions previously identified by genome-wide association studies. Comprehensive enumeration of sequence variation is necessary to identify functional alleles that provide important clues to disease pathophysiology, but large-scale sequencing does not support a major role for lower-frequency variants in predisposition to type 2 diabetes

Prediction of photoperiodic regulators from quantitative gene circuit models

Photoperiod sensors allow physiological adaptation to the changing seasons. The external coincidence hypothesis postulates that a light-responsive regulator is modulated by a circadian rhythm. Sufficient data are available to test this quantitatively in plants, though not yet in animals. In Arabidopsis, the clock-regulated genes CONSTANS (CO) and FLAVIN, KELCH, F-BOX (FKF1) and their lightsensitive proteins are thought to form an external coincidence sensor. We use 40 timeseries of molecular data to model the integration of light and timing information by CO, its target gene FLOWERING LOCUS T (FT), and the circadian clock. Among other predictions, the models show that FKF1 activates FT. We demonstrate experimentally that this effect is independent of the known activation of CO by FKF1, thus we locate a major, novel controller of photoperiodism. External coincidence is part of a complex photoperiod sensor: modelling makes this complexity explicit and may thus contribute to crop improvement

FLOWERING LOCUS C Mediates Natural Variation in the High-Temperature Response of the Arabidopsis Circadian Clock

Temperature compensation contributes to the accuracy of biological timing by preventing circadian rhythms from running more quickly at high than at low temperatures. We previously identified quantitative trait loci (QTL) with temperature-specific effects on the circadian rhythm of leaf movement, including a QTL linked to the transcription factor FLOWERING LOCUS C (FLC). We have now analyzed FLC alleles in near-isogenic lines and induced mutants to eliminate other candidate genes. We showed that FLC lengthened the circadian period specifically at 27°C, contributing to temperature compensation of the circadian clock. Known upstream regulators of FLC expression in flowering time pathways similarly controlled its circadian effect. We sought to identify downstream targets of FLC regulation in the molecular mechanism of the circadian clock using genome-wide analysis to identify FLC-responsive genes and 3503 transcripts controlled by the circadian clock. A Bayesian clustering method based on Fourier coefficients allowed us to discriminate putative regulatory genes. Among rhythmic FLC-responsive genes, transcripts of the transcription factor LUX ARRHYTHMO (LUX) correlated in peak abundance with the circadian period in flc mutants. Mathematical modeling indicated that the modest change in peak LUX RNA abundance was sufficient to cause the period change due to FLC, providing a molecular target for the crosstalk between flowering time pathways and circadian regulation

Molecular time sharing through dynamic pulsing in single cells

In cells, specific regulators often compete for limited amounts of a core enzymatic resource. It is typically assumed that competition leads to partitioning of core enzyme molecules among regulators at constant levels. Alternatively, however, different regulatory species could time share, or take turns utilizing, the core resource. Using quantitative time-lapse microscopy, we analyzed sigma factor activity dynamics, and their competition for RNA polymerase, in individual Bacillus subtilis cells under energy stress. Multiple alternative sigma factors were activated in ∼1-hr pulses in stochastic and repetitive fashion. Pairwise analysis revealed that two sigma factors rarely pulse simultaneously and that some pairs are anti-correlated, indicating that RNAP utilization alternates among different sigma factors. Mathematical modeling revealed how stochastic time-sharing dynamics can emerge from pulse-generating sigma factor regulatory circuits actively competing for RNAP. Time sharing provides a mechanism for cells to dynamically control the distribution of cell states within a population. Since core molecular components are limiting in many other systems, time sharing may represent a general mode of regulation.This work was supported by NIH grants R01 GM079771B and R01 HD075605A (to M.B.E.), T32 GM07616 (to J.P.), and NIHGMSK99BM118910 (to S.H.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. It was also supported by National Science Foundation grant 1547056 and the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 (KK9150) from the U.S. Army Research Office. The content of the information does not necessarily reflect the position or the policy of the government, and no official endorsement should be inferred. J.G.-O. and M.D. were supported by the Spanish Ministry of Economy and Competitiveness (MINECO) and FEDER (project FIS2015-66503-C3-1-P), the ICREA Academia program, and the Maria de Maeztu Program for Units of Excellence in R&D (MINECO, project MDM-2014-0370). Work in the Locke laboratory was supported by the European Research Council under the European Union's Seventh Framework Program (FP/2007-2013)/ERC Grant Agreement 338060, a fellowship from the Gatsby Foundation (GAT3272/GLC), and an award from the Human Frontier Science Program (CDA00068/2012)

Molecular time sharing through dynamic pulsing in single cells

In cells, specific regulators often compete for limited amounts of a core enzymatic resource. It is typically assumed that competition leads to partitioning of core enzyme molecules among regulators at constant levels. Alternatively, however, different regulatory species could time share, or take turns utilizing, the core resource. Using quantitative time-lapse microscopy, we analyzed sigma factor activity dynamics, and their competition for RNA polymerase, in individual Bacillus subtilis cells under energy stress. Multiple alternative sigma factors were activated in ∼1-hr pulses in stochastic and repetitive fashion. Pairwise analysis revealed that two sigma factors rarely pulse simultaneously and that some pairs are anti-correlated, indicating that RNAP utilization alternates among different sigma factors. Mathematical modeling revealed how stochastic time-sharing dynamics can emerge from pulse-generating sigma factor regulatory circuits actively competing for RNAP. Time sharing provides a mechanism for cells to dynamically control the distribution of cell states within a population. Since core molecular components are limiting in many other systems, time sharing may represent a general mode of regulation.This work was supported by NIH grants R01 GM079771B and R01 HD075605A (to M.B.E.), T32 GM07616 (to J.P.), and NIHGMSK99BM118910 (to S.H.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. It was also supported by National Science Foundation grant 1547056 and the Institute for Collaborative Biotechnologies through grant W911NF-09-0001 (KK9150) from the U.S. Army Research Office. The content of the information does not necessarily reflect the position or the policy of the government, and no official endorsement should be inferred. J.G.-O. and M.D. were supported by the Spanish Ministry of Economy and Competitiveness (MINECO) and FEDER (project FIS2015-66503-C3-1-P), the ICREA Academia program, and the Maria de Maeztu Program for Units of Excellence in R&D (MINECO, project MDM-2014-0370). Work in the Locke laboratory was supported by the European Research Council under the European Union's Seventh Framework Program (FP/2007-2013)/ERC Grant Agreement 338060, a fellowship from the Gatsby Foundation (GAT3272/GLC), and an award from the Human Frontier Science Program (CDA00068/2012)

Weather and seasons together demand complex biological clocks

The 24-hour rhythms of the circadian clock [1] allow an organism to anticipate daily environmental cycles, giving it a competitive advantage [2, 3]. Although clock components show little protein sequence homology across phyla, multiple feedback loops and light inputs are universal features of clock networks [4, 5]. Why have circadian systems evolved such a complex structure? All biological clocks entrain a set of regulatory genes to the environmental cycle, in order to correctly time the expression of many downstream processes. Thus the question becomes: What aspects of the environment, and of the desired downstream regulation, are demanding the observed complexity? To answer this, we have evolved gene regulatory networks in silico, selecting for networks that correctly predict particular phases of the day under light/dark cycles. Gradually increasing the realism of the environmental cycles, we have tested the networks for the minimal characteristics of clocks observed in nature: oscillation under constant conditions, entrainment to light signals, and the presence of multiple feedback loops and light inputs. Realistic circadian gene networks are found to require a nontrivial combination of conditions, with seasonal differences in photoperiod as a necessary but not sufficient component