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Dynamic changes of Arabidopsis cis-NAT pairs during de-etiolation

ABSTRACT: We systematically identified long noncoding natural antisense transcripts (lncNATs), defined as lncRNAs transcribed from the opposite DNA strand of coding or noncoding genes. We identified in total 37,238 sense-antisense transcript pairs and found 70% mRNAs are associated with antisense transcripts in Arabidopsis. To investigate the role of NATs in response to white light treatment, we designed an Agilent custom array, ATH NAT array, and analyzed WT seedlings grown in the dark (0h) and seedlings undergoing de-etiolation in continuous white light for 1h and 6h. To obtain information on organ-specific transcriptome profiles, we further dissected seedlings into cotyledons, hypocotyls and roots. We examined the abundance of NATs in etiolated seedlings and seedlings undergoing de-etiolation in continuous white light for 1/6h. Seedlings were further dissected into cotyledons, hypocotyls and roots. RNAs from 3 biological replicates of each of the 3 organs were separately hybridized to ATH NAT arrays to profile light-regulated NAT pairs.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Huan Wang

PROVIDER: E-GEOD-49382 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Dynamic changes of Arabidopsis cis-NAT pairs during de-etiolation

Project description:We systematically identified long noncoding natural antisense transcripts (lncNATs), defined as lncRNAs transcribed from the opposite DNA strand of coding or noncoding genes. We identified in total 37,238 sense-antisense transcript pairs and found 70% mRNAs are associated with antisense transcripts in Arabidopsis. To investigate the role of NATs in response to white light treatment, we designed an Agilent custom array, ATH NAT array, and analyzed WT seedlings grown in the dark (0h) and seedlings undergoing de-etiolation in continuous white light for 1h and 6h. To obtain information on organ-specific transcriptome profiles, we further dissected seedlings into cotyledons, hypocotyls and roots.

2013-12-23 | GSE49382 | GEO

Expression Profiling of Arabidopsis Long Noncoding RNAs Under Continuous Light Condition

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Expression data from Arabidopsis during de-etiolation

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Project description:This microarray experiment serves to identify the genes in the Arabidopsis genome that are regulated by carbon and light signaling interactions in 7 day dark grown seedlings. The expression profile of wild-type will be compared to the cli186 mutant, a mutant defective in carbon and light signaling. Plants of both the wild-type and cli186 genotypes are treated with the following light (L) and carbon (C) treatments: -C-L, +C-L, +C+L, -C+L. Comparison of the expression profiles under all treatments will help to identify genes that are misregulated in carbon and/or light treatments in the cli186 mutant.

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The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus

Project description:Naturally occurring Antisense Transcripts (NATs) compose an emerging group of regulatory RNAs. These regulatory elements appear in all organisms examined, but little is known about global expression of NATs in fungi. Analysis of currently available EST sequences suggests that 352 cis NATs are present in Aspergillus flavus. An Affymetrix GeneChip® microarray containing probes for these cis NATs, as well as all predicted genes in A. flavus, allowed a whole genome expression analysis of these elements in response to two ecologically important temperatures for the fungus. RNA expression analysis showed that 32 NATs and 2709 genes were differentially expressed between 37°C, the optimum temperature for growth, and 28°C, the conducive temperature for the biosynthesis of aflatoxin (AF) and many other secondary metabolites. These NATs correspond to sense genes with diverse functions including transcription initiation, carbohydrate processing and binding, temperature sensitive morphogenesis, and secondary metabolism. This is the first report of a whole genome transcriptional analysis of NAT expression in a fungus and shows that although less than 10% of putative NATs are differentially expressed in response to temperature, some of the NAT-cis gene interactions are likely to be important. Keywords: temperature response

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The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus

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2019-03-28 | GSE115584 | GEO

Light releases the TCP4-SAUR16/50 transcription module from the repression of PIF3 to facilitate cotyledon opening during de-etiolation [ChIP-Seq]

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Photomorphogenesis of Arabidopsis seedlings is accompanied by complex alternative splicing alterations

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