Assessing chromatin accessibility in maize with ATAC-seq
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ABSTRACT:
PROVIDER: PRJNA493188 | ENA |
REPOSITORIES: ENA
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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
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
Project description:Assessing chromatin accessibility in WT and STAT4-/- ILC1s
| PRJNA548943 | ENA
Project description:Chromatin accessibility profiling by ATAC-seq
| PRJNA780405 | ENA
Project description:Analysis of chromatin accessibility in primary GCTB samples with ATAC-seq
2020-08-31 | E-MTAB-9512 | biostudies-arrayexpress
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).
2019-06-17 | GSE132769 | GEO
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.
2022-09-30 | E-MTAB-12076 | biostudies-arrayexpress
Project description:chromatin accessibility (ATAC-seq) experiment. HeLa cells were primed with IFNγ for 24 hours, followed by IFNγ washout. After 48h, naïve and primed cells were induced by IFNγ for 1h and 3h. Cells were harvested at indicated time points and processed for ATAC-seq.
2023-05-06 | E-MTAB-12624 | biostudies-arrayexpress
Project description:Regulation of gene expression is linked to the organization of the genome. With age, chromatin alterations occur on all levels of genome organization, accompanied by changes in the gene expression profile. However, little is known about the changes on the level of transcriptional regulation. Here, we used a multi-omics approach and integrated ATAC-, RNA- and NET-seq to identify age-related changes in the chromatin landscape of murine liver and to investigate how these are linked to transcriptional regulation. We provide the first systematic inventory of the connection between aging, chromatin accessibility and transcriptional regulation in a whole tissue. Aging in murine liver is characterized by an increase in chromatin accessibility at promoter regions, but not in an increase of transcriptional output. Instead, aging is accompanied by a decrease of promoter-proximal pausing of RNA polymerase II (Pol II). We propose that these changes in transcriptional regulation are due to a reduced stability of the pausing complex and may represent a mechanism to compensate for the age-related increase in chromatin accessibility in order to prevent aberrant transcription.
2022-09-15 | PXD034564 | Pride
Project description:Role of TBP in chromatin accessibility (ATAC-seq)
| PRJNA475872 | ENA