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

ABSTRACT: 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.

ORGANISM(S): Zea mays subsp. mays

SUBMITTER: Huan Wang

PROVIDER: E-GEOD-56460 | 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 (paired-end)

Project description: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.

2015-11-25 | E-GEOD-56459 | 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).

2013-03-19 | E-GEOD-43142 | biostudies-arrayexpress

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.

2014-03-01 | E-GEOD-53995 | biostudies-arrayexpress

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

Project description:Aerenchyma is a specialized tissue consisting of longitudinal gas spaces, which enables internal movement of gases (e.g., O2, CO2, ethylene and methane), in plant roots, petioles and stems. Especially, internal transport of oxygen via aerenchyma from shoots to roots is very important for adaptation or survival of plants under waterlogged condition. To identify aerenchyma formation-associated genes expressed in maize root, we used LM combined with a microarray for monitoring genes expressed in root cortical cells under three conditions: under aerobic condition and under waterlogged condition with and without pretreatment with 1-MCP, an inhibitor of ethylene perception. For the waterlogging treatments, the primary root (but not the shoots) was waterlogged. Two and half day-old-seedlings were pre-treated with an inhibitor of ethylene perception 1-methylcyclopropene (1-MCP; 1 ppm) for 12 hours before the waterlogging treatment. Three-day-old seedlings were growing under aerated condition at the same time with other treatments as a control. Total RNA was extracted from root cortex cells from the segment of the primary root, 0.5 cm long: from 1.5 to 2 cm from the junction shoot-root derived from 3-days-old maize seedlings, and subjected to 44k oligo-DNA microarray (1. Aerated vs Hypoxia, 2. Hypoxia+MCP vs Hypoxia) with 3 biological replicates and color swaps.

2010-07-31 | E-GEOD-22943 | biostudies-arrayexpress

MicroRNAs in the development and the environmental responses of the maize root system

Project description:Four sRNA libraries were generated and sequenced from the early developmental stage of primary roots (PRY), the later developmental stage of maize primary roots (PRO), seminal roots (SR), and crown roots (CR). Through integrative analysis, we identified 501 miRNAs (246 conserved and 255 novel ones) and found that the expression patterns of miRNAs differed dramatically in different maize roots. we generated and sequenced four maize small RNA libraries from the early developmental stage of primary roots (PRY), the later developmental stage of maize primary roots (PRO), seminal roots (SR), and crown roots (CR) using Solexa high-throughput sequencing technology

2014-03-01 | E-GEOD-53865 | biostudies-arrayexpress

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

Project description:To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using nondirectional paired-end RNA-seq based on poly(A) selection. Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds.

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

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

Project description:To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using stranded single-end RNA-seq based on poly(A) selection. Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds.

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

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

Project description:In this study, a small RNA library from maize seed 24 hours after imbibition was sequenced by the Solexa technology. A total of 11,338,273 reads were obtained. 1,047,447 total reads representing 431 unique sRNAs matched to known maize miRNAs. Further analysis confirmed the authenticity of 115 known miRNAs belonging to 24 miRNA families and the discovery of 167 novel miRNAs in maize. Both the known and the novel miRNAs were confirmed by sequencing of a second small RNA library constructed the same way as the one used in the first sequencing. We also found 10 miRNAs that had not been reported in maize, but had been reported in other plant species. All novel sequences had not been earlier described in other plant species. In addition, seven miRNA* sequences were also obtained. Putative targets for 106 novel miRNAs were successfully predicted. Our results indicated that miRNA-mediated gene expression regulation is present in maize imbibed seed. This study led to the confirmation of the authenticity of 115 known miRNAs and the discovery of 167 novel miRNAs in maize. Identification of novel miRNAs resulted in significant enrichment of the repertoire of maize miRNAs and provided insights into miRNA regulation of genes expressed in imbibed seed. Discovery of novel miRNAs involved in imbibed maize seed by deep sequencing 2 independent small RNA libraries

2014-03-03 | E-GEOD-27664 | biostudies-arrayexpress

Identification of long ncRNAs using RNA-seq in Arabidopsis

Project description:We profiled Arabidopsis transcriptom using RNA-seq. Each RNA library yielded 223-250 million 101-bp single-end reads (235M on average). Using Tophat and Cufflinks, 30,199~30,650 assembled transcripts were identified in each of 4 samples. Of them, 1340 ones were derived from intergenic regions including 278 long intergenic ncRNAs (LincRNAs). Comparing with the 6,480 lincRNAs we identified by analysis of 200 tiling array data sets, 2,708 lincRNAs were also detected by RNA-seq. Transcriptom profiling in roots, leaves, flowers and siliques.

2012-08-23 | E-GEOD-38612 | biostudies-arrayexpress

Identification of CLF-regulated transcripts using strand-specific RNA-sequencing in Arabidopsis

Project description:CURLY LEAF (CLF), the major histone methyltransferase of Polycomb Repressive Complex 2 (PRC2), modifies trimethylation of histone H3 lysine 27 (H3K27me3) and mediates dynamical chromatin repression in Arabidopsis. Here we used strand specific RNA-sequencing to profile Arabidopsis transcriptomes obtained from roots, shoots, flowers and siliques of Col-0 and clf-28 plants. Our analysis identified a large number of CLF-regulatedd transcripts in Arabidopsis. Transcriptome profiling in roots, shoots, inflorescences and siliques of WT and clf-28 plants with 3 biological replicates.

2016-03-28 | E-GEOD-61545 | biostudies-arrayexpress

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