Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of Arabidopsis protoplasting and FACS sorting in roots

ABSTRACT: In order to estimate the effects of protoplasting and FACS sorting procedures on salt regulated gene expression we generated expression profiles for whole roots that had been treated with salt for 1 hour and for roots that were protoplasted and FACS sorted after the initial 1 hour salt treatment. Cells are amazingly adept at integrating both external and internal cues to regulate transcriptional states. While internal processes such as differentiation and cell-type specification are generally understood to have an important impact on gene expression, very little is known about how cells utilize these developmental cues to regulate responses to external stimuli. Here we use the response to a well characterized environmental stress, high salinity, to obtain a global view of the role that cell identity plays in guiding transcriptional responses in the root of Arabidopsis. Our analysis is based on three microarray data sets we have generated that explore transcriptional changes spatially among 6 cell layers and 4 longitudinal regions or temporally along 5 time points after salt treatment. We show that the majority of the response to salt stress is cell-type specific resulting in the differential regulation of unique biological functions in subsets of cell layers. To understand the regulatory mechanisms controlling these responses we have analyzed cis-element enrichment in the promoters of salt responsive genes and demonstrate that known stress regulatory elements likely control responses to salt occurring in multiple cell types. Despite the extensive shift in transcriptional state that salt stress elicits, we are able to identify several biological processes that consistently define each cell layer and find that transcriptional regulators of cell-identity tend to exhibit robust cell-type specific expression. Finally, using mutants that disrupt cell-type specification in the epidermis, we reveal cell autonomous and non-autonomous effects when cell identity is altered. Together, these data elucidate a novel intersection between physiology and development and expand our understanding of how transcriptional states are regulated in a multi-cellular context. Experiment Overall Design: To estimate the effect that protoplasting and cell sorting has on the expression of salt regulated genes we prepared samples as in Birnbaum et al. (2005) Nat. Methods, except that all cells were collected after cell sorting. Cells were collected from roots that had been treated with 140mM NaCl for 1hr prior to protoplasting. Whole roots were also collected after a similar treatment regimen with NaCl. Two replicates were performed per condition.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Jose Ramon Dinneny

PROVIDER: E-GEOD-7636 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Cell identity mediates the response of Arabidopsis roots to abiotic stress.

Dinneny José R JR Long Terri A TA Wang Jean Y JY Jung Jee W JW Mace Daniel D Pointer Solomon S Barron Christa C Brady Siobhan M SM Schiefelbein John J Benfey Philip N PN

Science (New York, N.Y.) 20080424 5878

Little is known about the way developmental cues affect how cells interpret their environment. We characterized the transcriptional response to high salinity of different cell layers and developmental stages of the Arabidopsis root and found that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell layers, several of which correspond to observable physiol ...[more]

PMID: 18436742

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Project description:Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Six different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in all radial zones of the root. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to media supplemented with 140 mM NaCl for 1 hour. Cells are amazingly adept at integrating both external and internal cues to regulate transcriptional states. While internal processes such as differentiation and cell-type specification are generally understood to have an important impact on gene expression, very little is known about how cells utilize these developmental cues to regulate responses to external stimuli. Here we use the response to a well characterized environmental stress, high salinity, to obtain a global view of the role that cell identity plays in guiding transcriptional responses in the root of Arabidopsis. Our analysis is based on three microarray data sets we have generated that explore transcriptional changes spatially among 6 cell layers and 4 longitudinal regions or temporally along 5 time points after salt treatment. We show that the majority of the response to salt stress is cell-type specific resulting in the differential regulation of unique biological functions in subsets of cell layers. To understand the regulatory mechanisms controlling these responses we have analyzed cis-element enrichment in the promoters of salt responsive genes and demonstrate that known stress regulatory elements likely control responses to salt occurring in multiple cell types. Despite the extensive shift in transcriptional state that salt stress elicits, we are able to identify several biological processes that consistently define each cell layer and find that transcriptional regulators of cell-identity tend to exhibit robust cell-type specific expression. Finally, using mutants that disrupt cell-type specification in the epidermis, we reveal cell autonomous and non-autonomous effects when cell identity is altered. Together, these data elucidate a novel intersection between physiology and development and expand our understanding of how transcriptional states are regulated in a multi-cellular context. Experiment Overall Design: To gain a genome-scale understanding of the role that developmental processes play in regulating stimulus response, we examined the effect of salt stress on gene expression along the radial axis of the root. Cell identity is the main variable that changes along the radial axis with the epidermis representing the outermost tissue layer and the stele representing the inner most layer. 6 different GFP reporter lines were used to isolate specific populations of cells from the Arabidopsis root using FACS sorting of protoplasted cells. GFP-reporter lines were grown under standard conditions before protoplasting and sorting or they were transfered to media supplemented with 140mM NaCl for 1 hour before hand.

Project description:Cell-type specific transcriptional profiles were generated by FACS (Fluorescence Activated Cell Sorting) sorting of roots that express cell-type specific GFP-reporters. Four different GFP-reporter lines were utilized allowing us to obtain transcriptional profiles for cells in major radial zones of the root. FACS cell populations were isolated from roots grown under standard conditions or roots that had been transfered to media supplemented with 140 mM NaCl for 1 hour, 3 hours, 8 hours, 20 hours, 32 hours and 48 hours. Plant environmental responses involve dynamic changes in growth and signaling, yet little is understood as to how progress through these temporal events is controlled. In this study we explore the phenotypic and transcriptional events involved in the acclimation of the Arabidopsis seedling root to a rapid change in salinity. Using live-imaging analysis, we show that growth is dynamically regulated with a period of growth quiescence followed by growth recovery and homeostasis. Through the development and analysis of a new high-resolution spatiotemporal transcriptional map, we have identified the key hormone signaling pathways that regulate specific transcriptional programs, predict their spatial domain of action and link the activity of these pathways to the control of specific phases of growth control. Through the use of tissue-specific approaches to suppress the ABA pathway, we demonstrate that ABA signaling likely acts in select tissue layers to control spatially localized transcriptional programs and promote growth recovery. In addition to the biological pathways directly affecting growth, we show that salt also controls many tissue-specific and time-point specific transcriptional responses that are expected to modify water transport, Casparian strip formation and protein translation. Together, our data reveal a sophisticated assortment of regulatory programs acting together to coordinate spatially patterned biological changes involved in the immediate and long-term response to a stressful shift in environment. 4 different GFP reporter lines were used to isolate specific populations of cells from the Arabidopsis root using FACS sorting of protoplasted cells. GFP-reporter lines were grown under standard conditions before protoplasting and sorting or they were transfered to media supplemented with 140mM NaCl for a series of time: 1 hour, 3 hours, 8 hours, 20 hours, 32 hours and 48 hours before hand, as well as standard controls for 1 hour and 48 hours. 3 replicates for each condition was used.

Dataset Information

Transcription profiling of Arabidopsis protoplasting and FACS sorting in roots

Publications

Cell identity mediates the response of Arabidopsis roots to abiotic stress.

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