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Abscisic acid transcriptional response of the maize epigenetic mutant, mop1-1

ABSTRACT: Abscisic acid transcriptional response of the maize epigenetic mutant, mop1-1

PROVIDER: PRJNA546250 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9200720_1.fastq.gz	Fastqsanger.gz
	SRR9200720_2.fastq.gz	Fastqsanger.gz
	SRR9200711_1.fastq.gz	Fastqsanger.gz
	SRR9200711_2.fastq.gz	Fastqsanger.gz
	SRR9200721_1.fastq.gz	Fastqsanger.gz

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Abscisic acid transcriptional response of the maize epigenetic mutant, mop1-1

Project description:MOP1-dependent and ABA-responsive pathways act within complex, connected transcriptional regulatory networks to mediate tissue-specific growth and responses to abiotic stress in maize Purpose: To identify genome-wide ABA-induced, MOP1-dependent and independent transcriptional responses Methods: mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings were subjected to ABA and MS treatments for 8 hours. The trimmed sequence reads were analyzed at the gene level using HISAT2, stringite, and edgeR. Results: we mapped ~23 million, 150 bp, paired-end sequence reads per sample to the B73 version 4 maize genome and identified 3,242 genes in four pairwise-comparisons to be differentially expressed genes (DEGs) with a fold change ≥2 and FDR <0.05, 1,561 DEGs were found to be unique to one genotype/treatment comparison. Conclusions: Our study represents the first analysis of ABA in maize seedlings in the RdDM (mop1-1) mutant, with biological replicates, and generated by RNA-seq technology. We identified common targets of MOP1 and ABA transcriptional regulation.

2020-03-22 | GSE132167 | GEO

Small RNA SBS signatures identified from maize using Illumina's SBS technology

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Abscisic acid effect on wild type and the abh1 mutant

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Comparative transcriptome analysis of abscisic acid (ABA) deficient mutant (vp5) and normal maize (Vp5) embryos during seed maturation

Project description:Comparative transcriptome analysis of abscisic acid (ABA) deficient mutant (vp5) and normal maize (Vp5) embryos during seed maturation

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Small RNA SBS signatures identified from maize using Illumina's SBS technology

Project description:Most endogenous siRNAs in Arabidopsis are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. Recent work has demonstrated that the maize MEDIATOR OF PARAMUTATION1 (mop1) gene is a predicted ortholog of the Arabidopsis RDR2 gene. The mop1 gene is required for establishment of paramutation and maintenance of transcriptional silencing of transposons and transgenes, suggesting the potential involvement of small RNAs. We analyzed small RNAs in wildtype maize and in the isogenic mop1-1 loss-of-function mutant using Illumina’s sequencing-by-synthesis (SBS) technology, which allowed us to characterize the complement of maize small RNAs to considerable depth. Similar to rdr2 in Arabidopsis, in mop1-1, the 24 nt (nucleotide) endogenous heterochromatic short-interfering siRNAs were dramatically reduced resulting in an enrichment of miRNAs and trans-acting siRNAs (ta-siRNAs). In contrast to the Arabidopsis rdr2 mutant, the mop1-1 plants retained a highly abundant heterochromatic ~22 nt class of small RNAs. These data suggest that maize, unlike Arabidopsis, has a second mechanism for heterochromatic siRNA production. The enrichment of miRNAs and loss of 24 nt heterochromatic siRNAs in mop1-1 should be advantageous for miRNA discovery as the maize genome becomes more fully sequenced. This library was derived from maize variety K55 wild-type and mop1 mutant. Immature ears were harvested from plants grown outdoors in Tuscon, AZ. The material was harvested from plants 68 days after germination, with the floral tissue including young tassels 2-3 cm long. Total RNA was isolated using a standard TRIZOL-based method and the small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by sequencing with Illumina's SBS method. The adapter sequences were removed, and the abundance of each distinct small RNA was determined. Raw data are unavailable from Illumina

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mop1 reshapes maize recombination landscape by modulating DNA methylation at MITEs with open chromatin

Project description:Meiotic recombination ensures genetic diversity and proper chromosome segregation, but its regulation remains not yet completely understood in many species. Here, we investigate the role of Mediator of paramutation1 (Mop1), a key component of the RNA-directed DNA methylation pathway, in reshaping the recombination landscape in maize. Using high-resolution crossover (CO) mapping, we show that mop1 mutants exhibit sex-specific effects on recombination, with CO numbers significantly reduced in male meiosis but unchanged in females. Sequence analysis of CO-associated motifs reveals increased enrichment of A/T polymer motifs in female mop1 and decreased enrichment of C/G motifs in male mop1 mutants, suggesting a transition to open chromatin states at these regions. Furthermore, we demonstrate that mop1 preferentially introduces new CO sites in females within regions of higher genetic diversity, particularly near miniature inverted-repeat transposable elements (MITEs). Epigenomic profiling reveals that mop1 significantly reduces CHH methylation at MITEs near genes. MITEs that overlap with differentially methylated regions (DMRs) and CO sites exhibit higher levels of histone marks associated with open chromatin, such as H2A.Z and histone acetylation, compared to MITEs outside DMRs or COs. However, the removal of CHH methylation in mop1 at MITEs that introduce COs does not alter the expression of flanking genes. Together, these results highlight the critical role of MOP1 in regulating meiotic recombination by modulating DNA methylation and chromatin states at transposable elements, providing new insights into the epigenetic regulation of meiotic recombination.

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Project description:Transcriptome of chemical-treated plants were investigated for the evaluation of ABA derivatives. Abscisic acid and its derivatives up-regulated mainly abiotic stress responsive genes.

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Comparative transcriptome analysis of abscisic acid (ABA) deficient mutant (vp5) and normal maize (Vp5) embryos during seed maturation

Project description:Identification of key genes and pathways regulated by phytohormone ABA during maize seed maturation, using the ABA synthesis-deficient mutant (vp5) and regular maize (Vp5) developing embryos.

2021-12-02 | E-MTAB-11224 | biostudies-arrayexpress

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