Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

https://www.cell.com/cell/pdf/S0092-8674(09)01418-4.pdf

H2A.Z-Containing Nucleosomes Mediate the Thermosensory Response in Arabidopsis

In plants, the circadian clock functions as an endogenous pacemaker that anticipates and responds to a changing environment in order to optimize the timing of physiological and developmental events. Nusinow et al. elucidate the mechanism by which the circadian clock controls growth of the model plant Arabidopsis thaliana. A novel trimeric complex called the evening complex is regulated by the clock and has a peak of expression at dusk. The complex represses the expression of two transcription factors, PIF4 and PIF5, which are part of a light-signalling cascade that controls the timing of plant growth in response to light conditions. The circadian clock is required for adaptive responses to daily and seasonal changes in environmental conditions1,2,3. Light and the circadian clock interact to consolidate the phase of hypocotyl cell elongation to peak at dawn under diurnal cycles in Arabidopsis thaliana4,5,6,7. Here we identify a protein complex (called the evening complex)—composed of the proteins encoded by EARLY FLOWERING 3 (ELF3), ELF4 and the transcription-factor-encoding gene LUX ARRHYTHMO (LUX; also known as PHYTOCLOCK 1)—that directly regulates plant growth8,9,10,11,12. ELF3 is both necessary and sufficient to form a complex between ELF4 and LUX, and the complex is diurnally regulated, peaking at dusk. ELF3, ELF4 and LUX are required for the proper expression of the growth-promoting transcription factors encoded by PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF5 (also known as PHYTOCHROME INTERACTING FACTOR 3-LIKE 6) under diurnal conditions4,6,13. LUX targets the complex to the promoters of PIF4 and PIF5 in vivo. Mutations in PIF4 and/or PIF5 are epistatic to the loss of the ELF4–ELF3–LUX complex, suggesting that regulation of PIF4 and PIF5 is a crucial function of the complex. Therefore, the evening complex underlies the molecular basis for circadian gating of hypocotyl growth in the early evening.

/pdf/the-elf4-elf3-lux-complex-links-the-circadian-clock-to-4vqdo56vny.pdf

The ELF4–ELF3–LUX complex links the circadian clock to diurnal control of hypocotyl growth

As nonmotile organisms, plants must rapidly adapt to ever-changing environmental conditions, including those caused by daily light/dark cycles. One important mechanism for anticipating and preparing for such predictable changes is the circadian clock. Nearly all organisms have circadian oscillators that, when they are in phase with the Earth's rotation, provide a competitive advantage. In order to understand how circadian clocks benefit plants, it is necessary to identify the pathways and processes that are clock controlled. We have integrated information from multiple circadian microarray experiments performed on Arabidopsis thaliana in order to better estimate the fraction of the plant transcriptome that is circadian regulated. Analyzing the promoters of clock-controlled genes, we identified circadian clock regulatory elements correlated with phase-specific transcript accumulation. We have also identified several physiological pathways enriched for clock-regulated changes in transcript abundance, suggesting they may be modulated by the circadian clock. Our analysis suggests that transcript abundance of roughly one-third of expressed A. thaliana genes is circadian regulated. We found four promoter elements, enriched in the promoters of genes with four discrete phases, which may contribute to the time-of-day specific changes in the transcript abundance of these genes. Clock-regulated genes are over-represented among all of the classical plant hormone and multiple stress response pathways, suggesting that all of these pathways are influenced by the circadian clock. Further exploration of the links between the clock and these pathways will lead to a better understanding of how the circadian clock affects plant growth and leads to improved fitness.

/pdf/global-transcriptome-analysis-reveals-circadian-regulation-1fyrkryvpl.pdf

Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development.

The circadian clock regulates diverse aspects of plant growth and development and promotes plant fitness. Molecular identification of clock components, primarily in Arabidopsis, has led to recent rapid progress in our understanding of the clock mechanism in higher plants. Using mathematical modeling and experimental approaches, workers in the field have developed a model of the clock that incorporates both transcriptional and posttranscriptional regulation of clock genes. This cell-autonomous clock, or oscillator, generates rhythmic outputs that can be monitored at the cellular and whole-organism level. The clock not only confers daily rhythms in growth and metabolism, but also interacts with signaling pathways involved in plant responses to the environment. Future work will lead to a better understanding of how the clock and other signaling networks are integrated to provide plants with an adaptive advantage.

/pdf/the-circadian-system-in-higher-plants-45w0pcu6x7.pdf

The Circadian System in Higher Plants

Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation

/pdf/network-discovery-pipeline-elucidates-conserved-time-of-day-38gv4cwyo3.pdf

Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.

Background 
WHITE COLLAR-1 (WC-1) mediates interactions between the circadian clock and the environment by acting as both a core clock component and as a blue light photoreceptor in Neurospora crassa. Loss of the amino-terminal polyglutamine (NpolyQ) domain in WC-1 results in an arrhythmic circadian clock; this data is consistent with this simple sequence repeat (SSR) being essential for clock function.
Methodology/Principal Findings 
Since SSRs are often polymorphic in length across natural populations, we reasoned that investigating natural variation of the WC-1 NpolyQ may provide insight into its role in the circadian clock. We observed significant phenotypic variation in the period, phase and temperature compensation of circadian regulated asexual conidiation across 143 N. crassa accessions. In addition to the NpolyQ, we identified two other simple sequence repeats in WC-1. The sizes of all three WC-1 SSRs correlated with polymorphisms in other clock genes, latitude and circadian period length. Furthermore, in a cross between two N. crassa accessions, the WC-1 NpolyQ co-segregated with period length.
Conclusions/Significance 
Natural variation of the WC-1 NpolyQ suggests a mechanism by which period length can be varied and selected for by the local environment that does not deleteriously affect WC-1 activity. Understanding natural variation in the N. crassa circadian clock will facilitate an understanding of how fungi exploit their environments.

/pdf/simple-sequence-repeats-provide-a-substrate-for-phenotypic-1w2mc4cg94.pdf

Simple sequence repeats provide a substrate for phenotypic variation in the Neurospora crassa circadian clock.

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Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.

Simple sequence repeats provide a substrate for phenotypic variation in the Neurospora crassa circadian clock.