Gene regulatory circuitry of plant–environment interactions: scaling from cells to the field

Bailey-Serres, 2019, Genetic strategies for improving crop yields, Nature, 575, 109, 10.1038/s41586-019-1679-0 Lee, 2017, Lighting the shadows: methods that expose nuclear and cytoplasmic gene regulatory control, Curr Opin Biotechnol, 49, 29, 10.1016/j.copbio.2017.07.010 Zander, 2020, Integrated multi-omics framework of the plant response to jasmonic acid, Nat Plants, 6, 290, 10.1038/s41477-020-0605-7 Bailey-Serres, 2013, Microgenomics: genome-scale, cell-specific monitoring of multiple gene regulation tiers, Annu Rev Plant Biol, 64, 293, 10.1146/annurev-arplant-050312-120035 Tripathi, 2021, Single cell gene regulatory networks in plants: opportunities for enhancing climate change stress resilience, Plant Cell Environ, 10.1111/pce.14012 Shojaee, 2021, Potentials of single-cell genomics in deciphering cellular phenotypes, Curr Opin Plant Biol, 63, 102059, 10.1016/j.pbi.2021.102059 Farmer, 2021, Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level, Mol Plant, 14, 372, 10.1016/j.molp.2021.01.001 Lee, 2019, Integrative analysis from the epigenome to translatome uncovers patterns of dominant nuclear regulation during transient stress, Plant Cell, 31, 2573 Fröschel, 2021, Plant roots employ cell-layer-specific programs to respond to pathogenic and beneficial microbes, Cell Host Microbe, 29, 299, 10.1016/j.chom.2020.11.014 Missra, 2015, The circadian clock modulates global daily cycles of mRNA ribosome loading, Plant Cell, 27, 2582, 10.1105/tpc.15.00546 Bonnot, 2021, Time of day prioritizes the pool of translating mRNAs in response to heat stress, Plant Cell, 10.1093/plcell/koab113 Sun, 2019, Global heat stress on health, wildfires, and agricultural crops under different levels of climate warming, Environ Int, 128, 125, 10.1016/j.envint.2019.04.025 Donat, 2012, The shifting probability distribution of global daytime and night-time temperatures, Geophys Res Lett, 39, 10.1029/2012GL052459 Sillmann, 2013, Climate extremes indices in the CMIP5 multimodel ensemble: Part 2. Future climate projections, J Geophys Res, 118, 2473, 10.1002/jgrd.50188 Bussemaker, 2001, Regulatory element detection using correlation with expression, Nat Genet, 27, 167, 10.1038/84792 Schacht, 2014, Estimating the activity of transcription factors by the effect on their target genes, Bioinformatics, 30, i401, 10.1093/bioinformatics/btu446 Reynoso, 2019, Evolutionary flexibility in flooding response circuitry in angiosperms, Science, 365, 1291, 10.1126/science.aax8862 Obertello, 2015, Cross-species network analysis uncovers conserved nitrogen-regulated network modules in rice, Plant Physiol, 168, 1830, 10.1104/pp.114.255877 García de la Torre, 2021, Wide cross-species RNA-Seq comparison reveals convergent molecular mechanisms involved in nickel hyperaccumulation across dicotyledons, New Phytol, 229, 994, 10.1111/nph.16775 Meng, 2021, Predicting transcriptional responses to cold stress across plant species, Proc Natl Acad Sci U S A, 118 van Veen, 2013, Two Rumex species from contrasting hydrological niches regulate flooding tolerance through distinct mechanisms, Plant Cell, 25, 4691, 10.1105/tpc.113.119016 Rich, 2021, Lipid exchanges drove the evolution of mutualism during plant terrestrialization, Science, 372, 864, 10.1126/science.abg0929 Dinneny, 2008, Cell identity mediates the response of Arabidopsis roots to abiotic stress, Science, 320, 942, 10.1126/science.1153795 Mustroph, 2009, Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis, Proc Natl Acad Sci U S A, 106, 18843, 10.1073/pnas.0906131106 Wendrich, 2020, Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions, Science, 370 Tian, 2021, Photoperiod-responsive changes in chromatin accessibility in phloem companion and epidermis cells of Arabidopsis leaves, Plant Cell, 33, 475, 10.1093/plcell/koaa043 Marand, 2021, A cis-regulatory atlas in maize at single-cell resolution, Cell, 10.1016/j.cell.2021.04.014 Kajala, 2021, Innovation, conservation, and repurposing of gene function in root cell type development, Cell, 10.1016/j.cell.2021.04.024 Edwards, 2019, Soil domestication by rice cultivation results in plant-soil feedback through shifts in soil microbiota, Genome Biol, 20, 221, 10.1186/s13059-019-1825-x Li, 2019, Legacy of land use history determines reprogramming of plant physiology by soil microbiome, ISME J, 13, 738, 10.1038/s41396-018-0300-0 Hu, 2018, Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota, Nat Commun, 9, 2738, 10.1038/s41467-018-05122-7 Varoquaux, 2019, Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses, Proc Natl Acad Sci U S A, 10.1073/pnas.1907500116 Quiroga, 2017, Enhanced drought stress tolerance by the arbuscular mycorrhizal symbiosis in a drought-sensitive maize cultivar is related to a broader and differential regulation of host plant aquaporins than in a drought-tolerant cultivar, Front Plant Sci, 8, 1056, 10.3389/fpls.2017.01056 Chareesri, 2020, Increased arbuscular mycorrhizal fungal colonization reduces yield loss of rice (Oryza sativa L.) under drought, Mycorrhiza, 30, 315, 10.1007/s00572-020-00953-z Xu, 2018, Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria, Proc Natl Acad Sci U S A, 115, E4284, 10.1073/pnas.1717308115 Groen, 2020, The strength and pattern of natural selection on gene expression in rice, Nature, 578, 572, 10.1038/s41586-020-1997-2 Baxter, 2008, The leaf ionome as a multivariable system to detect a plant's physiological status, Proc Natl Acad Sci U S A, 105, 12081, 10.1073/pnas.0804175105 Gruber, 2013, Plasticity of the Arabidopsis root system under nutrient deficiencies, Plant Physiol, 163, 161, 10.1104/pp.113.218453 Müller, 2015, Iron-dependent callose deposition adjusts root meristem maintenance to phosphate availability, Dev Cell, 33, 216, 10.1016/j.devcel.2015.02.007 Korshunova, 1999, The IRT1 protein from Arabidopsis thaliana is a metal transporter with a broad substrate range, Plant Mol Biol, 40, 37, 10.1023/A:1026438615520 Barberon, 2016, Adaptation of root function by nutrient-induced plasticity of endodermal differentiation, Cell, 164, 447, 10.1016/j.cell.2015.12.021 Güsewell, 2004, P ratios in terrestrial plants: variation and functional significance, New Phytol, 164, 243, 10.1111/j.1469-8137.2004.01192.x Hu, 2019, Nitrate-NRT1.1B-SPX4 cascade integrates nitrogen and phosphorus signalling networks in plants, Nat Plants, 5, 401, 10.1038/s41477-019-0384-1 Medici, 2019, Identification of molecular integrators shows that nitrogen actively controls the phosphate starvation response in plants, Plant Cell, 31, 1171, 10.1105/tpc.18.00656 Humbert, 2013, Genome-wide expression profiling of maize in response to individual and combined water and nitrogen stresses, BMC Genom, 14, 3, 10.1186/1471-2164-14-3 Swift, 2019, Water impacts nutrient dose responses genome-wide to affect crop production, Nat Commun, 10, 1374, 10.1038/s41467-019-09287-7 Zhu, 2020, Applications of CRISPR-Cas in agriculture and plant biotechnology, Nat Rev Mol Cell Biol, 21, 661, 10.1038/s41580-020-00288-9 Rodriques, 2019, Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution, Science, 363, 1463, 10.1126/science.aaw1219 Fawkner-Corbett, 2021, Spatiotemporal analysis of human intestinal development at single-cell resolution, Cell, 184, 810, 10.1016/j.cell.2020.12.016 Slavov, 2020, Unpicking the proteome in single cells, Science, 367, 512, 10.1126/science.aaz6695 Raj, 2008, Nature, nurture, or chance: stochastic gene expression and its consequences, Cell, 135, 216, 10.1016/j.cell.2008.09.050 Wimmers, 2018, Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells, Nat Commun, 9, 3317, 10.1038/s41467-018-05784-3 Jariani, 2020, A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast, Elife, 9, 10.7554/eLife.55320 Mair, 2019, Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID, Elife, 8, 10.7554/eLife.47864 Ricci, 2019, Widespread long-range cis-regulatory elements in the maize genome, Nat Plants, 5, 1237, 10.1038/s41477-019-0547-0 Walley, 2016, Integration of omic networks in a developmental atlas of maize, Science, 353, 814, 10.1126/science.aag1125 Cruz, 2020, Using single-plant-omics in the field to link maize genes to functions and phenotypes, Mol Syst Biol, 16, 10.15252/msb.20209667 Liang, 2021, Reorganization of the 3D chromatin architecture of rice genomes during heat stress, BMC Biol, 19, 53, 10.1186/s12915-021-00996-4 Wilkins, 2016, EGRINs (environmental gene regulatory influence networks) in rice that function in the response to water deficit, high temperature, and agricultural environments, Plant Cell, 28, 2365, 10.1105/tpc.16.00158 Plessis, 2015, Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions, Elife, 4, 10.7554/eLife.08411 Zeng, 2019, Cold stress induces enhanced chromatin accessibility and bivalent histone modifications H3K4me3 and H3K27me3 of active genes in potato, Genome Biol, 20, 123, 10.1186/s13059-019-1731-2 Chantarachot T, Sorenson RS, Hummel M, Ke H, Kettenburg AT, Chen D, Aiyetiwa K, Dehesh K, Eulgem T, Sieburth LE, et al.: DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs associated with innate immunity and growth inhibition. [date unknown], https://doi.org/10.1101/772087. Xu, 2017, Global translational reprogramming is a fundamental layer of immune regulation in plants, Nature, 545, 487, 10.1038/nature22371 Xu, 2017, uORF-mediated translation allows engineered plant disease resistance without fitness costs, Nature, 545, 491, 10.1038/nature22372 Zhang, 2021, Single-cell transcriptome atlas and chromatin accessibility landscape reveal differentiation trajectories in the rice root, Nat Commun, 12, 2053, 10.1038/s41467-021-22352-4 Traubenik, 2020, Reprogramming of root cells during nitrogen-fixing symbiosis involves dynamic polysome association of coding and noncoding RNAs, Plant Cell, 32, 352, 10.1105/tpc.19.00647 Li, 2016, High-resolution expression map of the Arabidopsis root reveals alternative splicing and lincRNA regulation, Dev Cell, 39, 508, 10.1016/j.devcel.2016.10.012