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FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) analysis of chromatin accessibility in kidney bean under drought stress

ABSTRACT: FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) analysis of chromatin accessibility in kidney bean under drought stress

PROVIDER: PRJNA777286 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16706100_1.fastq.gz	Fastqsanger.gz
	SRR16706100_2.fastq.gz	Fastqsanger.gz
	SRR16706101_1.fastq.gz	Fastqsanger.gz
	SRR16706101_2.fastq.gz	Fastqsanger.gz
	SRR16706102_1.fastq.gz	Fastqsanger.gz

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FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) analysis of chromatin accessibility in kidney bean under drought stress

Project description:Purpose: To identify nucleosome-depleted regions in response to drought in the kidney bean, a genome-wide chromatin profiling strategy was implemented. A better understanding of these OCRs (Open chromatin regions) will be useful in exploring potential genomic regions for crop improvement. Results: Using a comprehensive FAIRE-Seq approach, nucleosome-free chromatin regions were explored in kidney bean (Phaseolus vulgaris. L) in response to both drought and rewatering stress. In all samples, FAIRE peaks (>50%) were enriched in the promoter regions. The drought samples showed peaks very distinct from control and rewatered samples, which showed peaks predominantly at the transcription start site (TSS). Drought and heat-responsive genes and transcription factors were identified within the flanking region of differential peaks. When drought was compared to control, it showed upregulated differential peaks primarily in the promoter and distal intergenic regions. Conclusion: By analyzing FAIRE we are able to identify distinct genomic regions corresponding to droughts and controls. Upstream regions of genes play a significant role in drought stress response. Our data suggest that promoter regions of >2 kb, downstream regions of <= 300, and distant regulatory regions are predominant during the upregulation of drought stress. It would also be helpful to note that genomic regions vary in response to drought, and distal intergenic regions may also be involved in drought responses. Understanding plant genomes and epigenomics could help us develop varieties that can withstand extreme weather conditions.

2023-11-08 | GSE187025 | GEO

Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) sequencing of msh1 memory line

Project description:Col-0 wild type and msh1 memory line were grown, crosslinked and chromatin isolated as described in (Omidbakhshfard et al., 2014). Briefly, plants were germinated in MS media at 24°C, 12 hr light and 12 hr dark cycle for 14 days and crosslinked with formaldehyde. DNA was sonicated to get a size range of 250-800bp. Samples were divided equally into two lots and one was used directly for FAIRE experiments while the other lot was decrossed-linked and compared with the crosslinked samples to confirm he FAIRE treatment. FAIRE analysis was carried out on crosslinked sampes of wild ype and msh1 memory line.

2019-05-18 | GSE114664 | GEO

Formaldehyde-assisted isolation of regulatory elements with next generation sequencing (FAIRE-seq) in primary human macrophages and foam cells

Project description:We report the open chromatin landscape in primary human macrophages and foam cells using FAIRE-seq CD14+ monocytes were isolated from the blood of 3 healthy volunteers. Monocytes were differentiated into macrophages by culture for 7 days with 50ng/ml macrophage colony stimulating factor and then treated for 48 hours with either oxidized low density lipoprotein (oxLDL) to induce foam cell formation or with a control buffer that lacked oxLDL. The resulting six samples were then subjected to FAIRE-seq using an established protocol (Simon JM, Giresi PG, Davis IJ, Lieb JD. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature protocols 2012;7:256-67).

2015-04-08 | E-GEOD-54971 | biostudies-arrayexpress

Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) sequencing of msh1 memory line

Project description:Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) sequencing of msh1 memory line

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Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) Analysis Uncovers Broad Changes in Chromatin Structure Resulting from Hexavalent Chromium Exposure

Project description:The ability of chromatin to switch back and forth from open euchromatin to closed heterochromatin is vital for transcriptional regulation and genomic stability, and subject to disruption by exposure to environmental agents such as hexavalent chromium. Cr(VI) exposure can cause chromosomal disruption through formation of Cr-DNA adducts, free radical-induced DNA damage, and DNA-Cr-protein and DNA-Cr-DNA cross-links, all of which may disrupt chromatin remodeling mechanisms responsible for maintenance or controlled modification of epigenetic homeostasis. In addition, dose-response analyses have shown that acute exposures to high-concentrations of Cr(VI) and chronic exposures to low-concentrations of the same agent lead to significantly different transcriptomic and genomic stability outcomes. To investigate how transcriptional responses to chromium exposure might correlate to structural changes in chromatin, we have used whole genome Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) analysis coupled with deep sequencing to identify regions of the genome that switch from open to closed chromatin or vice versa in response to exposure to varying Cr(VI) concentrations. We find that the switch affects gene expression levels in the target areas that vary depending on Cr(VI) concentration. At either Cr(VI) concentration, chromatin domains surrounding binding sites for AP-1 transcription factors become significantly open, treatment whereas BACH2 and CTCF binding sites are open solely at the low and high concentrations, respectively. Our results suggest that FAIRE may be a useful technique to map chromatin elements targeted by DNA damaging agents for which there is no prior knowledge of their specificity, and to identify subsequent transcriptomic changes induced by those agents.

2014-04-10 | GSE56636 | GEO

FAIRE-seq

Project description:Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) in U2OS cells detected by SOLiD sequencing

2011-11-03 | E-MTAB-584 | biostudies-arrayexpress

FAIRE-chip in MCF7 and LNCaP

Project description:The compaction degree of chromatin is intimately related to its functionality and active cis-regulatory elements typically exist within open chromatin regions depleted in nucleosomes (Heintzman et al. 2007; Boyle et al. 2008). These domains can be identified using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) that allows for enrichment of nucleosome-depleted genomic regions when cross-linked chromatin is subjected to phenol-chloroform extraction (Nagy et al. 2003; Hogan et al. 2006) Here, chromatin structure was analyzed in MCF7 and LNCaP cells using Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) (Nagy et al. 2003; Hogan et al. 2006) Keywords: FAIRE-chip

2009-01-07 | GSE11579 | GEO