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Transcriptome profiling of noncoding RNAs in maize (paired-end)

ABSTRACT: To identificate long noncoding RNAs in maize, we profiled transcriptome of shoots and roots using non-directional paired-end RNA-seq based on poly(A) selection. Transcriptom profiling in maize shoots and roots.

ORGANISM(S): Zea mays subsp. mays

SUBMITTER: Huan Wang

PROVIDER: E-GEOD-56459 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits.

Wang Huan H Niu Qi-Wen QW Wu Hui-Wen HW Liu Jun J Ye Jian J Yu Niu N Chua Nam-Hai NH

The Plant journal : for cell and molecular biology 20151001 2

Long non-coding RNAs (lncRNAs) have recently been found to widely exist in eukaryotes and play important roles in key biological processes. To extend our knowledge of lncRNAs in crop plants we performed both non-directional and strand-specific RNA-sequencing experiments to profile non-coding transcriptomes of various rice and maize organs at different developmental stages. Analysis of more than 3 billion reads identified 22 334 long intergenic non-coding RNAs (lincRNAs) and 6673 pairs of sense a ...[more]

PMID: 26387578

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Transcriptome profiling of noncoding RNAs in maize (single-end)

Project description:To identificate long noncoding RNAs in maize, we profiled transcriptome of shoots and roots using stranded single-end RNA-seq based on poly(A) selection. Transcriptom profiling in maize shoots and roots.

2015-11-25 | E-GEOD-56460 | biostudies-arrayexpress

Conservation and Divergence of Transcriptomic and Epigenomic Variations in Maize Hybrids

Project description:The complexity of the maize (Zea mays) genome makes it an ideal system for the study of both genetics and epigenetics. Here, we generated the integrated maps of transcriptomes and epigenomes of shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different tissues and different genotypes. We observed that whereas histone modifications vary both between tissues and between genotypes, DNA methylation patterns are more distinguishable between genotypes than between tissues. Histone modifications were associated with transcriptomic divergence between tissues and between hybrids and parents. Further, we show that genes up-regulated in both shoots and roots of hybrids were significantly enriched in the nucleosome assembly pathway. Interestingly, 22- and 24-nt siRNAs were shown to be derived from distinct transposable elements (TEs), and for different TEs in both shoots and roots, the differences in siRNA activity between hybrids and patents were primarily driven by different siRNA species. Together, our results suggest that despite of the variations in specific genes or genomic loci, similar mechanisms may account for the genome-wide epigenetic regulation of gene activity and transposon stability in different tissues of maize hybrids. Genome-wide integrated maps of mRNA and small RNA (sRNA) transcriptomes, DNA methylomes and genome-wide distribution of three representative histone modifications (H3K4me3, H3K9ac and H3K36me3) in the shoots and roots of 14 day old seedlings of two maize inbred lines (B73 and Mo17) and their reciprocal hybrids (B73 x Mo17 and Mo17 x B73).

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The distinct transcription patterns correlate with the differential growth responses to salt stress in maize roots

Project description:We found that primary root (PR) is more resistant to salt stress compared with crown roots (CR) and seminal roots (SR). To understand better salt stress responses in maize roots, six RNA libraries were generated and sequenced from primary root (PR), primary roots under salt stress (PR-salt) , seminal roots (SR), seminal roots under salt stress (SR-salt), crown roots (CR), and crown roots under salt stress (CR-salt). Through integrative analysis, we identified 444 genes regulated by salt stress in maize roots, and found that the expression patterns of some genes and enzymes involved in important pathway under salt stress, such as reactive oxygen species scavenging, plant hormone signal perception and transduction, and compatible solutes synthesis differed dramatically in different maize roots. 16 of differentially expressed genes were selected for further validation with quantitative real time RT-PCR (qRT-PCR).We demonstrate that the expression patterns of differentially expressed genes are highly diversified in different maize roots. The differentially expressed genes are correlated with the differential growth responses to salt stress in maize roots. Our studies provide deeper insight into the molecular mechanisms about the differential growth responses of different root types in response to environmental stimuli in planta. Examination of three root types of maize under salt treatment for understanding the different responding mechenism to salt stress.

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Identification of genes expressed in maize root cortical cells during lysigenous aerenchyma formation using laser microdissection and a microarray

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Transcriptome profiling of various organs at different developmental stages in rice (paired-end)

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2015-11-25 | E-GEOD-56462 | biostudies-arrayexpress

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2015-11-25 | E-GEOD-56463 | biostudies-arrayexpress

Identification and Characterization of Maize MicroRNAs Involved in the Very Early Stage of Seed Germination

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