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Next Generation Sequencing of Wild Type and AtSRT1 transgene plants Transcriptomes

ABSTRACT: Next Generation Sequencing of Wild Type and AtSRT1 transgene plants Transcriptomes

PROVIDER: PRJNA412814 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6124090_1.fastq.gz	Fastqsanger.gz
	SRR6124090_2.fastq.gz	Fastqsanger.gz
	SRR6124091_1.fastq.gz	Fastqsanger.gz
	SRR6124091_2.fastq.gz	Fastqsanger.gz
	SRR6124092_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing of Wild Type and AtSRT1 transgene plants Transcriptomes

Project description:To study genome-wide gene expression regulated by AtSRT1, we analyzed transcriptomes of wild type and AtSRT1 RNAi-1 (R) and overexpression OX-SRT1-1(OX) line by RNA-sequencing using the Illumina Hiseq-2000 sequencing system. Three biological replicates for each genotype were tested.The data suggest that AtSRT1 plays an important role in regulation of genes involved in stress responses and in carbon and energy metabolism in Arabidopsis.

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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transgene-derived OsAFB6 overexpression mutant transcriptome profiling (RNA-seq) to microarray Methods: young panicle(<1mm) mRNA profiles of 80 individual plants of OsAFB6 overexpression mutants and the correspondinng negative plants during the same transgenic event as control were generated by deep sequencing, in two replicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we found 59 genes were upregulated and 229 genes were down regulated in OsAFB6 overexpression mutant. Conclusions: Our study represents the first detailed analysis of young panicle transcriptomes of OsAFB6 overexpression mutant, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

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Epigenetic differences between transgenes and endogenous genes promote transgene silencing in plants

Project description:Transgene loci that spontaneously undergo RNA silencing have been instrumental to decipher RNA silencing pathways in plants. In contrast, transgene loci that are stably expressed have been poorly characterized. Here we show that stably expressed transgene loci epigenetically differ from endogenous genes. Impairing the histone H3K4me3 demethylase JMJ14 increases DNA methylation at stably expressed transgene loci but not at endogenous genes, whereas impairing the histone H3K9me2 demethylase IBM1 increases DNA methylation at endogenous genes, but decreases DNA methylation at stably expressed transgene loci. Moreover, impairing IBM1 promotes post-transcriptional gene silencing (PTGS) at stably expressed transgene loci, whereas impairing JMJ14 prevents PTGS induced systemically by grafting onto silenced rootstocks. Given that impairing DNA methylation suppresses the effect of impairing JMJ14 and restores transgene capacity to undergo graft-induced PTGS, we propose that transgene DNA methylation prevents PTGS, likely by limiting the transcription of aberrant RNA by-products that are transformed into dsRNA by cellular RNA-dependent RNA polymerases to activate PTGS.

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