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Assessing chromatin accessibility in maize with ATAC-seq

ABSTRACT: Assessing chromatin accessibility in maize with ATAC-seq

PROVIDER: PRJNA493188 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7904001_1.fastq.gz	Fastqsanger.gz
	SRR7904001_2.fastq.gz	Fastqsanger.gz
	SRR7904002_1.fastq.gz	Fastqsanger.gz
	SRR7904002_2.fastq.gz	Fastqsanger.gz
	SRR7904003_1.fastq.gz	Fastqsanger.gz

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Assessing chromatin accessibility in maize using ATAC-seq

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Assessing chromatin accessibility in maize using ATAC-seq

Project description:The depiction of maize chromatin architecture using Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) provides great opportunities to investigate cis-regulatory elements, which is crucial for crop improvement. We demonstrate a streamlined ATAC-seq protocol for maize in which nuclei purification can be achieved without cell sorting, and using only a standard bench-top centrifuge. Our protocol, coupled with the bioinformatic analysis, provides a precise and efficient assessment of the maize chromatin landscape.

2024-01-10 | GSE252638 | GEO

Assessing chromatin accessibility in maize with ATAC-seq

Project description:Maize (Zea mays) is one of the most important crop in the world. Better understanding the maize chromatin architecture points to novel approaches to improve crop yield. Here, we describe the first ATAC-seq protocol to assess the maize genome. Fresh leaf tissue was gently chopped by a blade to release intact nuclei which later were fractionated using Percoll-sucrose gradient. The isolated nuclei were treated with a transposase that fragments and tags the genome; these fragments were subjected to two rounds of PCR to generate the ATAC-seq library. In the first round of PCR, these fragments were amplified with 5 cycles and sequencing barcodes were added. A fraction of the first PCR product was subjected to qPCR to determine the optimal amplification cycle number in the second round of PCR. The library quality can be assessed by a Bioanalyzer prior to sequencing. The distinct bands indicated good quality. After sequencing, the computational analysis of fragment size distribution may show patterns of periodicity that is a characteristic to ATAC-seq libraries. In our preliminary analysis, we found that 85% percent of the identified regions deviate from closed regions previously identified by MNase-seq, suggesting that the ATAC-seq library preparation procedure described here is effective in identifying open chromatin regions of the maize genome.

2019-01-23 | GSE120491 | GEO

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Project description:STAT4 dynamically interacts with the genomic landscape and functions in modulating chromatin accessibility to influence gene expression. We aimed to evaluate the impact of STAT4 on chromatin accessibility of colonic lamina propria ILC1s. To address this aim, we sorted ILC1s from the colonic LP of unmanipulated C57BL/6 and STAT4-/- mice and performed the assay for transposase-accessible chromatin using sequencing (ATAC-seq).

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SNP effect on chromatin accessibility (ATAC-Seq)

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ATAC-seq experiment at four time points in HEK293 and hESC cells, assessing the time-resolved response on chromatin accessibility upon Wnt/β-catenin signaling activation

Project description:Wnt/β-catenin signaling is a highly organized biochemical cascade that triggers a gene expression program in the signal-receiving cell. The Wnt/β-catenin -driven transcriptional response is involved in virtually all cellular processes during development, homeostasis, and its deregulation causes human disease. However, outstanding questions remain unanswered. Among these, one regards how the Wnt/β-catenin cascade modulates the chromatin behavior: to date, there exists no comprehensive genome-wide annotation of changing chromatin patterns upon Wnt pathway activation. This is important, as shifts in chromatin patterns might underlie how different cells promote diverging gene expression programs in response to Wnt. To address this question, we characterized how Wnt/β-catenin signaling shapes the genome-wide chromatin accessibility landscape in two human cell types, human embryonic kidney cells 293T (HEK293T) and human embryonic stem cells (hESCs), over time. To this end, we treated HEK293T and hESCs with the GSK3 inhibitor/Wnt activator CHIR99021 (10 mM) for 3 days and assessed chromatin accessibility via ATAC-sequencing 4 hours, 24 hours and 3 days after the onset of the stimulation. We found that hESCs respond to Wnt/β-catenin activation by progressively shaping their chromatin accessibility profile in a manner that is consistent with their gradual acquisition of a mesodermal identity: differentiation genes loci open over time, while pluripotency ones close. We refer to this genomic response as plastic. On the other hand, HEK293T, which are known to be highly responsive to Wnt activation, appear more resistant to a long-term Wnt/β-catenin-driven change in cell identity. In this context, the chromatin displays a temporary opening of relevant regions at 4 hours after stimulation, followed by a re-establishment of its pre-stimulation state: we define this transient response as elastic.

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