The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA112843 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
2009-03-25 | GSE12594 | GEO
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 3 samples (reps) for each temperature treatment were analyzed with a total of 6 samples.
2010-06-21 | E-GEOD-12594 | biostudies-arrayexpress
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 detect the expression levels of these NAT pairs, we designed an Agilent custom array, ATH NAT array, and analyzed RNA samples from Arabidopsis inflorescences, leaves and roots, with 3 biological replicates each.
2013-12-23 | GSE49381 | GEO
Project description:Here we demonstrate a natural antisense transcript of notch-1 that interacts with the sense transcript and regulates its availability and pace of G1 phase of cell cycle.
2021-03-03 | GSE168092 | GEO
Project description:The Affymetrix GeneChip Wheat Genome Array currently provides the most comprehensive coverage of the wheat genome for a microarray. In addition to using this resource for transcript expression studies and hybridization-based DNA marker discovery, we endeavored to use the GeneChip to discover the expression of natural antisense transcript (NAT) pairs. By using alternative target preparation schemes, both the sense- and antisense-strand derived transcripts were labeled and hybridized to the Wheat GeneChip. To enable maximum discovery, five different tissue types were selected for assay, and the wheat cultivar ‘Chinese Spring’ was used considering that most of the GeneChip probe sequences were based on sequencing of this genome. [PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tristan Coram. The equivalent experiment is TA21 at PLEXdb.]
2009-06-11 | GSE12528 | GEO
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 detect the expression levels of these NAT pairs, we designed an Agilent custom array, ATH NAT array, and analyzed RNA samples from Arabidopsis inflorescences, leaves and roots, with 3 biological replicates each. Expression levels of cis-NAT pairs were investigated in WT inflorescences, leaves and roots with 3 biological replicates.
2013-12-23 | E-GEOD-49381 | biostudies-arrayexpress
Project description:A natural antisense transcript of notch-1 regulates cell cycle
| PRJNA706012 | ENA
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. 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.
2013-12-23 | E-GEOD-49382 | biostudies-arrayexpress
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
Project description:To better understand the effect of temperature on mycotoxin biosynthesis, RNA-Seq technology was used to profile the Aspergillus flavus transcriptome under different temperature conditions. This approachallowed us to quantify transcript abundance for over 80% of fungal genes including 1,153 genes that were differentially expressed at 30°C and 37°C. Wleven of the 55 secondary metabolite clusters were up-regulated at the lower temperature, including aflatoxin biosynthesis genes, which were among the most highly up-expressed genes. On average, transcript abundance for the 30 aflatoxin biosynthesis genes was 3,300 times greater at 30°C as compared to 37°C. The results are consistent with the view that high temperature negatively affects aflatoxin production by turning down transcription of the two key transcriptional regulators, aflR and aflS. Subtle changes in the expression levels of aflS to aflR appear to control transcription activation of the aflatoxin cluster.
2011-06-16 | GSE30031 | GEO