Unknown,Transcriptomics,Genomics,Proteomics

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Methylation mimic mutations of progesterone receptor AF1 impair gene-specific regulation through stabilized chromatin interactions

ABSTRACT: ChIP-seq analysis was conducted to determine the genome-wide binding profiles of PRB, PRB-FFF, and PRB-QQQ cell lines following R5020 treatment compared to vehicle (ETOH). We propose a tripartite model in which transient and calibrated interactions among AF1, AF2, and coregulators are essential for productive enhancer function and dynamic cycling of the transcription complex. We hypothesize that the PRB-FFF mutation leads to more stable interactions, resulting in prolonged enhancer occupancy and a slower transcription rate.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Homo sapiens

SUBMITTER: Qian Yee Woo

PROVIDER: E-MTAB-15999 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

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Methylation mimic mutations of progesterone receptor AF1 impair gene-specific regulation through stabilized chromatin interactions

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