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Zea mays

ABSTRACT: Analysis of transcriptomes from filling endosperms of zmnac128 zmnac130 mutants

PROVIDER: PRJNA1057451 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27378290_1.fastq.gz	Fastqsanger.gz
	SRR27378290_2.fastq.gz	Fastqsanger.gz
	SRR27378291_1.fastq.gz	Fastqsanger.gz
	SRR27378291_2.fastq.gz	Fastqsanger.gz
	SRR27378292_1.fastq.gz	Fastqsanger.gz

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Zea mays Epigenomics

Project description:RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2.

2014-12-05 | E-MTAB-4191 | biostudies-arrayexpress

Nascent transcription defined by RNA polymerase IV in Zea mays

Project description:Maize RNA Polymerase D1 (RPD1), the largest subunit of RNA polymerase IV (Pol IV), is required for normal plant development, repression of transposable elements (TEs), and for the regulation of specific alleles associated with TEs. Here, we define the nascent transcriptomes of rpd1 mutant and wild-type (WT) seedlings using global run-on sequencing (GRO-seq) to identify the broader targets of RPD1-based transcriptional regulation. Surprisingly, although TE-like sequences comprise >85% of the maize genome, most TEs are not transcribed at the seedling stage, even in rpd1 mutants. Profile comparisons identify the global set of genes and TEs whose transcription is altered in the absence of RPD1, in some cases in antisense orientation. These results indicate that maize Pol IV specifies Pol II-based transcriptional regulation for certain regions of the maize genome.

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RNA-Seq mapping enabled quantitative analysis of gene expression differences between normal and ded1-ref in Zea mays (Maize)

Project description:The goals of this study are to compare NGS-derived transcriptomes (RNA-Seq) derived from ded1-ref mutant and normal maize endosperm tissue. Homozygous ded1-ref mutants exhibit a seed defect. Maize Ded1 encodes a transcription factor. This study characterizes DEGs between ded1-ref and normal endosperm and serves to identify direct target genes together with DAP-seq data.

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Zea mays Transcriptome or Gene expression

Project description:To discover the transcriptional dynamics during seed germination we have obtained the time course transcriptomes for embryonic shoot apical meristem (SAM) every six hours, starting from dry seeds to hour 72 (3 days).

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Zea mays Transcriptome or Gene expression

Project description:In this study the transcriptomes of 2cm-long primary roots (without apical 5mm) of wildtype and rum1 mutant seedlings were compared to identify genes directly or indirectly regulated by RUM1. Besides the RUM1-dependent gene network, novel functions of RUM1 were revealed.

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Zea mays Transcriptome or Gene expression

Project description:Alternative splicing (AS) is an important regulatory mechanism that greatly contributes to eukaryotic transcriptome diversity. A substantial amount of evidence has demonstrated that AS complexity is relevant to eukaryotic evolution, development, adaptation, and complexity. In this study, six teosinte and ten maize transcriptomes were sequenced to analyze AS changes and signatures of selection in maize domestication and improvement.

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Zea mays

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes for Wild Type and Mutants including opaque2, PbfRNAi and PbfRNAi o2 in Maize (Zea mays)

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Zea mays cultivar:B73

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Zea mays Transcriptome or Gene expression

Project description:Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cultivated worldwide and its productivity is closely linked to the amount of fertilizer used. A survey of the transcriptomes of shoot and root tissues of a maize hybrid line and its two parental inbred lines grown under sufficient and limiting N conditions by mRNA-Seq has been conducted to have a better understanding of how different maize genotypes respond to N limitation.

2014-01-09 | E-MTAB-4410 | biostudies-arrayexpress

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