Dataset Information

Spatiotemporal regulation of enhancers during cardiogenesis.

ABSTRACT: With the advance in chromatin immunoprecipitation followed by high-throughput sequencing, there has been a dramatic increase in our understanding of distal enhancer function. In the developing heart, the identification and characterisation of such enhancers have deepened our knowledge of the mechanisms of transcriptional regulation that drives cardiac differentiation. With next-generation sequencing techniques becoming widely accessible, the quantity of data describing the genome-wide distribution of cardiac-specific transcription factor and chromatin modifiers has rapidly increased and it is now becoming clear that the usage of enhancers is highly dynamic and complex, both during the development and in the adult. The identification of those enhancers has revealed new insights into the transcriptional mechanisms of how tissue-specific gene expression patterns are established, maintained, and change dynamically during development and upon physiological stress.

SUBMITTER: Dupays L

PROVIDER: S-EPMC5219004 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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Spatiotemporal regulation of enhancers during cardiogenesis.

Dupays Laurent L Mohun Timothy T

Cellular and molecular life sciences : CMLS 20160806 2

With the advance in chromatin immunoprecipitation followed by high-throughput sequencing, there has been a dramatic increase in our understanding of distal enhancer function. In the developing heart, the identification and characterisation of such enhancers have deepened our knowledge of the mechanisms of transcriptional regulation that drives cardiac differentiation. With next-generation sequencing techniques becoming widely accessible, the quantity of data describing the genome-wide distributi ...[more]

PMID: 27497925

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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. 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

Spatiotemporal regulation of enhancers during cardiogenesis.

Publications

Spatiotemporal regulation of enhancers during cardiogenesis.

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