Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

Zhou, Mingqi; Sng, Natasha; LeFrois, Collin; Paul, Anna‐Lisa; Ferl, Robert J.

doi:10.1186/s12864-019-5554-z

Cited by 55 publications

(74 citation statements)

References 110 publications

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“…that is conserved among Arabidopsis cultivars and related species Sugimoto et al, 2014;Ferl et al, 2015;Sng et al, 2018;Choi et al, 2019;Zhou et al, 2019). Our findings were consistent with this trend across genotypes and the skewing mutants based on GO term enrichments associated with the spaceflight response (Figures 6B, 11B).…”

Section: Sku5 Mutation Produces a Dramatic Increase In Differential Gsupporting

confidence: 87%

“…The wild type Wassilewskija (WS) line used in this study was propagated in our laboratory for more than 25 years. This WS line has been used in multiple spaceflight studies (Paul et al, 2012aZhou et al, 2019), and seed samples are available upon request. The ABRC denotes WS as stock CS915.…”

Section: Plant Materials and Plate Setupmentioning

confidence: 99%

“…The Advanced Plant Experiments 03-2 (APEX-03-2) study, also known under NASA Operational Nomenclature as the Transgenic Arabidopsis Gene Expression System -Intracellular Signaling Architecture (TAGES-ISA) study, has been previously described Beisel et al, 2019;Zhou et al, 2019). The SpaceX CRS-5 mission, carrying the dormant, seeded growth plates as part of its cargo, was launched to the International Space Center (ISS) from KSC on January 10, 2015.…”

Section: Spaceflight Experimental Workflowmentioning

confidence: 99%

“…Reactive oxygen species (ROS) signaling and scavenging processes are also common in the spaceflight response, though ROS-associated genes have been observed as both up-and downregulated in spaceflight Abbreviations: d, day; DEG, differentially expressed gene; FLT, spaceflight; GC, ground control; GO, gene ontology; GPI-AP, glycosylphosphatidylinositolanchored protein. (Shagimardanova et al, 2010;Correll et al, 2013;Paul et al, 2013Paul et al, , 2017Kwon et al, 2015;Choi et al, 2019;Zhou et al, 2019). Some stress gene expression changes are also associated with spaceflight-induced changes in the Arabidopsis methylome .…”

Section: Introductionmentioning

confidence: 99%

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Root Skewing-Associated Genes Impact the Spaceflight Response of Arabidopsis thaliana

et al. 2020

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The observation that plant roots skew in microgravity recently refuted the long-held conviction that skewing was a gravity-dependent phenomenon. Further, spaceflight root skewing suggests that specific root morphologies and cell wall remodeling systems may be important aspects of spaceflight physiological adaptation. However, connections between skewing, cell wall modification and spaceflight physiology are currently based on inferences rather than direct tests. Therefore, the Advanced Plant Experiments-03-2 (APEX-03-2) spaceflight study was designed to elucidate the contribution of two skewing-and cell wall-associated genes in Arabidopsis to root behavior and gene expression patterns in spaceflight, to assess whether interruptions of different skewing pathways affect the overall spaceflight-associated process. SPIRAL1 is a skewingrelated protein implicated in directional cell expansion, and functions by regulating cortical microtubule dynamics. SKU5 is skewing-related glycosylphosphatidylinositolanchored protein of the plasma membrane and cell wall implicated in stress response signaling. These two genes function in different cellular pathways that affect skewing on the Earth, and enable a test of the relevance of skewing pathways to spaceflight physiological adaptation. In this study, both sku5 and spr1 mutants showed different skewing behavior and markedly different patterns of gene expression in the spaceflight environment. The spr1 mutant showed fewer differentially expressed genes than its Col-0 wild-type, whereas sku5 showed considerably more than its WS wild-type. Developmental age played a substantial role in spaceflight acclimation in all genotypes, but particularly in sku5 plants, where spaceflight 4d seedlings had almost 10-times as many highly differentially expressed genes as the 8d seedlings. These differences demonstrated that the two skewing pathways represented by SKU5 and SPR1 have unique and opposite contributions to physiological adaptation to spaceflight. The spr1 response is less intense than wild type, suggesting that the loss of SPR1 positively impacts spaceflight adaptation. Conversely, the intensity of the sku5 responses suggests that the loss of SKU5 initiates a much more complex, deeper and more stress related response to spaceflight. This suggests that proper SKU5 function is important to spaceflight adaptation.

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Section: Sku5 Mutation Produces a Dramatic Increase In Differential Gsupporting

confidence: 87%

Section: Plant Materials and Plate Setupmentioning

confidence: 99%

Section: Spaceflight Experimental Workflowmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Root Skewing-Associated Genes Impact the Spaceflight Response of Arabidopsis thaliana

et al. 2020

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“…These studies are now generating extensive characterizations of the responses of diverse plant species to spaceflight. As part of the output from this research, there is an ever-increasing set of genome-scale analyses that range from transcriptomics [e.g., (Kwon et al, 2015;Johnson et al, 2017;Paul et al, 2017;Choi et al, 2019;Herranz et al, 2019;Vandenbrink et al, 2019)] and proteomics [e.g., (Mazars et al, 2014;Ferl et al, 2015;Basu et al, 2017)] to epigenomics [e.g., (Zhou et al, 2019)]. These datasets help catalog the plant response to growing in space.…”

Section: Introductionmentioning

confidence: 99%

Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments

et al. 2020

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Recent advances in the routine access to space along with increasing opportunities to perform plant growth experiments on board the International Space Station have led to an ever-increasing body of transcriptomic, proteomic, and epigenomic data from plants experiencing spaceflight. These datasets hold great promise to help understand how plant biology reacts to this unique environment. However, analyses that mine across such expanses of data are often complex to implement, being impeded by the sheer number of potential comparisons that are possible. Complexities in how the output of these multiple parallel analyses can be presented to the researcher in an accessible and intuitive form provides further barriers to such research. Recent developments in computational systems biology have led to rapid advances in interactive data visualization environments designed to perform just such tasks. However, to date none of these tools have been tailored to the analysis of the broad-ranging plant biology spaceflight data. We have therefore developed the Test Of Arabidopsis Space Transcriptome (TOAST) database (https://astrobiology. botany.wisc.edu/astrobotany-toast) to address this gap in our capabilities. TOAST is a relational database that uses the Qlik database management software to link plant biology, spaceflight-related omics datasets, and their associated metadata. This environment helps visualize relationships across multiple levels of experiments in an easy to use gene-centric platform. TOAST draws on data from The US National Aeronautics and Space Administration's (NASA's) GeneLab and other data repositories and also connects results to a suite of web-based analytical tools to facilitate further investigation of responses to spaceflight and related stresses. The TOAST graphical user interface allows for quick comparisons between plant spaceflight experiments using real-time, gene-specific queries, or by using functional gene ontology, Kyoto Encyclopedia of Genes and Genomes pathway, or other filtering systems to explore genetic networks of interest. Testing of the database shows that TOAST confirms patterns of gene expression already highlighted in the literature, such as revealing the modulation of oxidative stressrelated responses across multiple plant spaceflight experiments. However, this data

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Plant Space Biology in the Genomics Age

Meyers

Wyatt

2022

Annual Plant Reviews Online

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Advances in molecular technologies have ushered in a new age of understanding across all disciplines of biology. Research in plant biology has capitalised on these novel capabilities, unlocking new understanding of how plants respond to a myriad of conditions. Plant growth in spaceflight environments represents a decades‐long endeavour, but the past 20 years have produced a wealth of data aimed toward understanding gravitational biology and informing the optimisation of plant growth for long‐duration spaceflight missions. The spaceflight environment subjects plants to low gravity and ionising radiation, which have a variety of downstream impacts on plant growth and well‐being. Omics technologies have revealed a perplexing web of stress responses to spaceflight, and optimally growing plants in these environments requires characterising the mechanistic origins of those responses. Here, we review the plant omics data gathered to date from spaceflight experiments and highlight trends and future directions as we move forward into a new age of discovery.

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Epigenomics in an extraterrestrial environment: organ-specific alteration of DNA methylation and gene expression elicited by spaceflight in Arabidopsis thaliana

Cited by 55 publications

References 110 publications

Root Skewing-Associated Genes Impact the Spaceflight Response of Arabidopsis thaliana

Root Skewing-Associated Genes Impact the Spaceflight Response of Arabidopsis thaliana

Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments

Plant Space Biology in the Genomics Age

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