Transcriptional networks — crops, clocks, and abiotic stress

Gehan, Malia; Greenham, Kathleen; Mockler, Todd C.; McClung, C. Robertson

doi:10.1016/j.pbi.2015.01.004

Cited by 72 publications

(54 citation statements)

References 92 publications

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“…In this work, phylogenomic and transcriptomic data integration and analysis have been performed by gene co-expression networks construction (Romero-Campero et al, 2013; Gehan et al, 2015; Ruprecht et al, 2017) and a novel algorithm for the identification of potential orthologues called Multiple Best Bi-directional Hit (MBBH). Using clustering techniques, specific gene clusters or modules that showed a rhythmic daily regulation have been identified.…”

Section: Introductionmentioning

confidence: 99%

Evolution of Daily Gene Co-expression Patterns from Algae to Plants

et al. 2017

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Daily rhythms play a key role in transcriptome regulation in plants and microalgae orchestrating responses that, among other processes, anticipate light transitions that are essential for their metabolism and development. The recent accumulation of genome-wide transcriptomic data generated under alternating light:dark periods from plants and microalgae has made possible integrative and comparative analysis that could contribute to shed light on the evolution of daily rhythms in the green lineage. In this work, RNA-seq and microarray data generated over 24 h periods in different light regimes from the eudicot Arabidopsis thaliana and the microalgae Chlamydomonas reinhardtii and Ostreococcus tauri have been integrated and analyzed using gene co-expression networks. This analysis revealed a reduction in the size of the daily rhythmic transcriptome from around 90% in Ostreococcus, being heavily influenced by light transitions, to around 40% in Arabidopsis, where a certain independence from light transitions can be observed. A novel Multiple Bidirectional Best Hit (MBBH) algorithm was applied to associate single genes with a family of potential orthologues from evolutionary distant species. Gene duplication, amplification and divergence of rhythmic expression profiles seems to have played a central role in the evolution of gene families in the green lineage such as Pseudo Response Regulators (PRRs), CONSTANS-Likes (COLs), and DNA-binding with One Finger (DOFs). Gene clustering and functional enrichment have been used to identify groups of genes with similar rhythmic gene expression patterns. The comparison of gene clusters between species based on potential orthologous relationships has unveiled a low to moderate level of conservation of daily rhythmic expression patterns. However, a strikingly high conservation was found for the gene clusters exhibiting their highest and/or lowest expression value during the light transitions.

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Section: Introductionmentioning

confidence: 99%

Evolution of Daily Gene Co-expression Patterns from Algae to Plants

et al. 2017

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“…The circadian clock was estimated to control a large proportion ∼25% of the of the transcriptome under constant conditions which is comparable to estimates for the proportion of circadian transcripts in Arabidopsis, rice ( Oryza sativa ) and poplar ( Populus trichocarpa ) (Filichkin et al 2011, Covington et al 2008, Michael et al 2008, Gehan et al 2015). Despite the strong control of the clock on transcript oscillations under LL, day-night cues had a major influence on shaping expression patterns of circadian transcripts under diel conditions.…”

Section: Discussionmentioning

confidence: 52%

Differential effects of day-night cues and the circadian clock on the barley transcriptome

Müller

Mombaerts

Pankin

et al. 2019

Preprint

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the original research project. L.M.M. and M.K. designed the 22 experiments. L.M.M. carried out the experiments and analysed the RNA-sequencing data. L.M. 23 calculated LTI models with the help of J.G. and A.W. A.P. contributed to the bioinformatic 24 analyses. L.M.M., L.M., A.W., A.P. and M.K. wrote the manuscript.25 26 Abstract 32The circadian clock is a complex transcriptional network that regulates gene expression in 33 anticipation of the day-night cycle and controls agronomic traits in plants. However, in crops, 34 information on the effects of the internal clock and day-night cues on the transcriptome is 35 limited. We analysed the diel and circadian leaf transcriptomes in the barley cultivar Bowman 36 and derived introgression lines carrying mutations in EARLY FLOWERING 3 (ELF3), LUX1, 37 and EARLY MATURITY 7 (EAM7). Mutations in ELF3 and LUX1 abolished circadian 38 transcriptome oscillations under constant conditions, whereas eam7 maintained oscillations of 39 ≈30% of the circadian transcriptome. However, day-night cues fully restored transcript 40 oscillations in all three mutants and thus compensated for a disrupted oscillator in the arrhythmic 41 barley clock mutants elf3 and lux1. Nevertheless, elf3 but not lux1 affected the phase of the diel 42 oscillating transcriptome and thus the integration of external cues into the clock. Using 43 dynamical modelling, we predicted a structure of the barley circadian oscillator and interactions 44 of its individual components with day-night cues. Our findings provide a valuable resource for 45 exploring the function and output targets of the circadian clock and for further investigations into 46 the diel and circadian control of the barley transcriptome.47 48 49 Keywords: 50 Circadian clock, transcriptional networks, EARLY FLOWERING 3 (ELF3), LUX1, EARLY 51 MATURITY 7 (EAM7), linear systems identification, transcriptome regulation, barley 52 53 109accelerates flowering by abolishing sensitivity to the photoperiod (Gallagher et al., 1991). We 110 used the RNAseq time-course data to analyse the effects of barley clock genes on diel and 111 circadian transcriptome oscillations including changes in phase and period under constant 112 conditions and light and dark cycles. Dynamical modelling allowed us to predict a molecular 113 5 structure of the barley circadian oscillator and to uncover how circadian oscillator components 114 interact with day/night cues to regulate the global transcriptome in barley. 115 6 Results 116 Diel and circadian oscillations of the barley transcriptome 117 We analysed the diel and circadian global leaf transcriptome of the barley cultivar Bowman and 118 the derived introgression lines carrying mutations in HvELF3 (BW290), HvLUX1 (BW284) and 119 HvEAM7 (BW287). Plants were grown under cycles of 12h light and 12 h night (LD) and the 120 second leaf of replicate plants was harvested every four hours over 24h. Additional samples were 121 taken in a 2h interval at dusk in all genotypes and additionally at dawn in Bowman 122 (Supplem...

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“…Circadian clocks are found in organisms that live exposed to daily light/dark cycles and allow them to predict and adapt to changes in their environment. In photosynthetic organisms, these clocks modulate photosynthetic capacity, growth, development, and responses to biotic and abiotic stimuli, and have been shown to be necessary for optimal growth and survival (Ouyang et al, 1998;Dodd et al, 2004;Woelfle et al, 2004;Yerushalmi et al, 2011;Gehan et al, 2015); however, some cyanobacteria and plant species apparently lack self-sustained rhythms (Holtzendorff et al, 2008;Gyllenstrand et al, 2014). Although evidence of rhythmic behavior has been detected in a large number of species in different taxa, a good understanding of the molecular components of circadian oscillators is only available for a few species of bacteria (Cohen and Golden, 2015), archeoplastida (green algae and plants) ( Noordally and Millar, 2015;Linde et al, 2017) and opisthokonts (animals and fungi) (Crane and Young, 2014;Dunlap and Loros, 2017).…”

Section: Introductionmentioning

confidence: 99%

Identification of circadian rhythms in Nannochloropsis species using bioluminescence reporter lines

et al. 2019

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Utilization of microalgae has been hampered by limited tools for creating loss-of-function mutants. Furthermore, modified strains for deployment into the field must be free of antibiotic resistance genes and face fewer regulatory hurdles if they are transgene free. The oleaginous microalga, Nannochloropsis oceanica CCMP1779, is an emerging model for microalgal lipid metabolism. We present a one-vector episomal CRISPR/Cas9 system for N. oceanica that enables the generation of marker-free mutant lines. The CEN/ARS6 region from Saccharomyces cerevisiae was included in the vector to facilitate its maintenance as circular extrachromosal DNA. The vector utilizes a bidirectional promoter to produce both Cas9 and a ribozyme flanked sgRNA. This system efficiently generates targeted mutations, and allows the loss of episomal DNA after the removal of selection pressure, resulting in marker-free non-transgenic engineered lines. To test this system, we disrupted the nitrate reductase gene (NR) and subsequently removed the CRISPR episome to generate non-transgenic marker-free nitrate reductase knockout lines (NR-KO).

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Transcriptional networks — crops, clocks, and abiotic stress

Cited by 72 publications

References 92 publications

Evolution of Daily Gene Co-expression Patterns from Algae to Plants

Evolution of Daily Gene Co-expression Patterns from Algae to Plants

Differential effects of day-night cues and the circadian clock on the barley transcriptome

Identification of circadian rhythms in Nannochloropsis species using bioluminescence reporter lines

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