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ChIP-seq of ASY1 and controls on meiotic-stage floral buds of Arabidopsis

ABSTRACT: ChIP-seq of ASY1 and controls on meiotic-stage floral buds of Arabidopsis

PROVIDER: PRJEB36320 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3829803_1.fastq.gz	Fastqsanger.gz
	ERR3829803_2.fastq.gz	Fastqsanger.gz
	ERR3829804_1.fastq.gz	Fastqsanger.gz
	ERR3829804_2.fastq.gz	Fastqsanger.gz
	ERR3829805_1.fastq.gz	Fastqsanger.gz

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ChIP-seq of ASY1 and controls on meiotic-stage floral buds of Arabidopsis

Project description:ChIP-seq of ASY1 was carried out on meiotic-stage floral buds of Arabidopsis using an a-ASY1 antibody. The experiment aims to determine the genome-wide profile of ASY1. ASY1 is a component of the chromosome axis and is expressed exclusively during meiosis. Two negative controls were used to test the specificity of the ChIP experiment. First, ChIP-seq using the pre-immune on floral buds was carried out. Second, ChIP-seq using an a-ASY1 antibody was performed on leaf tissue where ASY1 is not expressed.

2020-05-18 | E-MTAB-8705 | biostudies-arrayexpress

Meiotic cohesin, chromatin and expression profiling of Arabidopsis thaliana floral buds from wild type and non-CG DNA methylation/H3K9me2 pathway mutant plants (ChIP-seq)

Project description:We generated and sequenced ChIP libraries for the meiotic cohesin subunit REC8 and four histone modifications (H3K4me1, H3K4me2, H3K9me2 and H3K27me1) to investigate their relationships with meiotic chromosome architecture and recombination in Arabidopsis thaliana. REC8 and H3K9me2 ChIP-seq were performed using meiotic-stage floral buds from wild type (Col-0) and non-CG DNA methylation/H3K9me2 pathway mutant (kyp/suvh4 suvh5 suvh6 or cmt3) plants to examine the role of heterochromatin assembly in meiotic cohesin distribution.

2020-01-21 | E-MTAB-7370 | biostudies-arrayexpress

Meiotic cohesin, chromatin and expression profiling of Arabidopsis thaliana floral buds from wild type and non-CG DNA methylation/H3K9me2 pathway mutant plants (RNA-seq)

Project description:To investigate the impact of disruption of the non-CG DNA methylation/H3K9me2 pathway upon transcription in Arabidopsis, we performed RNA-seq using meiotic-stage floral buds from wild type (Col-0) and kyp/suvh4 suvh5 suvh6 mutant plants. This enabled identification of differentially expressed genes and transposable elements (TEs). TEs that were up-regulated in kyp/suvh4 suvh5 suvh6 relative to wild type were evaluated for over-representation of elements within each TE family.

2020-01-21 | E-MTAB-7371 | biostudies-arrayexpress

Affinity proteomics targeting the meiotic chromosome axis protein, ASY1, from Brassica oleracea.

Project description:Meiosis is a highly complex process that underpins recombination in sexually reproducing organisms. Recent genomics studies suggest that up to several thousand genes/proteins contribute to the meiotic pathway, yet relatively few have been functionally characterised. Our understanding of the physical interactions between meiotic proteins and how the meiotic machinery interacts with other components of the cell is also limited. In this study, we used affinity proteomics targeting the meiotic chromosome axis protein, ASY1, to enrich for axis-associated proteins in Brassica oleracea anthers or meiocytes in prophase I of meiosis. LC-MS/MS analysis identified 540 proteins which co-immunoprecipitated with ASY1 in a sample-specific manner. These correspond to 485 Arabidopsis orthologues, 90% of which form a coherent predicted protein-protein interaction network which includes known and novel meiotic proteins, based on mutant analysis, but also proteins more usually associated with other cellular processes including replication and proteolysis. Our data provided new insights into the role of the chromosome axis in plant meiosis. We identified a novel axis-associated protein and showed that during prophase I, ASY1 and its interacting partner, ASY3, are extensively phosphorylated. Further studies targeting other meiotic proteins may ultimately enable the construction of a comprehensive meiosis protein-protein interaction network for higher plants.

2017-11-01 | PXD006042 | Pride

LC-MSMS of Arabidopsis thaliana flower bud samples (TurboID-based proximity labeling of meiotic chromosome axes)

Project description:The meiotic chromosome axis is a proteinaceous structure along which sister chromatids are arranged in a loop-base array during meiotic prophase I. In diverse species including plants, chromosome axis components have been shown to be critical for synapsis and meiotic recombination and hence essential for assuring the fidelity of meiosis. In Arabidopsis thaliana, the limited number of meiotic cells embedded in floral organs constrains proteomic approaches for the identification of new axis components. Therefore, we employed TurboID (TbID) based proximity labeling (PL) in meiotic cells of A. thaliana. The two axis proteins ASY1 and ASY3 were selected and ASY1-TbID and ASY3-TbID transgenic plants were generated to enable specific targeted biotin labeling of meiotic chromosome axis. ASY1-eYFP and nucTbID (TbID driven by UBQ10 promoter) were generated and used as controls. These lines were either treated or not with exogenous biotin followed by streptavidin affinity-purification coupled with mass spectrometry to identify their proximate candidate proteins. By stringent filtering a final candidates list was established which covered most of the known meiotic chromosome axis-related proteins and new proteins without a reported meiotic function. Functional validation of selected candidates and comparison with ASY1 AP-MS data (in Brassica oleracea) suggest the TbID based PL is a robust tool for identification of proximate proteins in meiotic cells of A. thaliana.

2023-03-08 | PXD034241 | Pride

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Project description:We performed ChIP-seq for the meiotic strand exchange protein DMC1, which marks an early stage in the meiotic recombination pathway, and the chromosome axis protein ASY1, which promotes interhomolog synapsis and recombination in plants, using tissue collected from immature pre-emergence spikes from wild type bread wheat cultivar Chinese Spring plants. To investigate connections between meiotic recombination and chromatin states in wheat, we also performed ChIP-seq for euchromatic (H3K4me3) and constitutive heterochromatic (H3K9me2 and H3K27me1) marks, and mapped genome-wide nucleosome occupancy via micrococcal nuclease sequencing (MNase-seq) using leaf tissue from Chinese Spring.

2021-07-07 | E-MTAB-9632 | biostudies-arrayexpress

Genome-wide profiling of the meiotic recombinase DMC1, the chromosome axis protein ASY1 and chromatin states in hexaploid wheat (MNase-seq)

2021-07-07 | E-MTAB-9633 | biostudies-arrayexpress

Comparison of male and female floral organs

Project description:We conducted micro-array analysis to quantify the global transcriptome variations in floral organs of a male and female tree allowing for identification of sex-linked transcripts. We used RNA samples from male floral buds in August and female floral buds in Spetemeber. Bud scale were removed. While the sampling time differed, the developmental stage of the floral organs was similar between the male and female.

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Meiotic recombination initiation hotspots in Arabidopsis genes and transposons (H3K4m3 ChIP-seq)

Project description:To investigate the relationship between meiotic recombination initiation and H3K4m3 in Arabidopsis, we generated and sequenced H3K4m3 ChIP libraries from meiotic stage floral buds in wild type, arp6 and met1. To produce high-resolution of H3K4m3 mapping, we used micrococcal nuclease (MNase) to digest chromatins that were cross-linked by formaldehyde for ChIP. This experiment provides for H3K4m3 maps with the resolution of mononucleosomal DNA level (~150 bp).

2017-06-05 | E-MTAB-5048 | biostudies-arrayexpress

Expression data from Arabidopsis wild type and cdm1 young floral buds

Project description:We used microarray analysis to examine transcriptomic changes in cdm1 mutant, identifying genes potentially regulated by CDM1 by comparing gene expression between cdm1 and wild type young floral buds. Among 375 genes that showed differential expression (P-value <0.05) with >1.5-fold changes between wild type and cdm1, 185 genes were down-regulated by 1.5 to 7.10-folds, whereas 190 genes were up-regulated by 1.5 to 5.82-folds. Wild type and cdm1 young floral buds were used to isolate total RNA, with two biological replicates for each. Microarray analysis was performed using 500ng of total RNA per sample as described in the Genechip Expression Analysis Technical Manual.

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