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

Abstract

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 2,709 genes were differentially expressed between 37 degrees C, the optimum temperature for growth, and 28 degrees 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.

Characterization of Natural Antisense Transcript, Sclerotia Development and Secondary Metabolism by Strand-Specific RNA Sequencing of Aspergillus flavus

“…In all, 1124 and 839 NATs were identified in the AflavusCA43_M and AflavusCA43_S samples, respectively ( Table S7 ). This is many more compared to A. flavus NATs on the basis of EST data (352, 2.8%) and Cryptococcus neoformans NATs (53, 0.8%) [25]. The number of RNA-seq-based A. flavus NATs is in the same range as S. cerevisiae (1103, 16.7%) [46].…”

“…Natural antisense transcripts (NATs), a subset of non-coding RNAs (ncRNAs), are endogenous RNA molecules transcribed from the opposite DNA strand and can be complementary to the sense RNA through base pairing [23]–[25]. Expressed sequence tag (EST) sequencing, tiling microarrays, SAGE libraries, asymmetric strand-specific analysis of gene expression and global run-on sequencing (GRO-seq) could be used to identify NATs [26].…”

“…NATs have been found in a divergent group of fungi, including the ascomycetes Saccharomyces cerevisiae , Candida albicans , A. flavus , Magnaporthe oryzae, Tuber melanosporum and Schizosaccharomyces pombe, and the basidiomycetes Cryptococcus neoformans , Ustilago maydis and Schizophyllum commune [28]. There are two distinct drawbacks in the study of A. flavus NATs, however; first, there were only 352 NATs (2.8% of the total open reading frames (ORFs)) found in A. flavus by analyzing ∼23,000 A. flavus cDNAs from cells grown under different nutritional conditions [25], while this number soars to 16.7–85.2% in comprehensively analyzed transcriptomes such as S. cerevisiae (16.7%), C. albicans (40.0%) and S. pombe (85.2%) [28]. Second, the biological function of NATs in A. flavus remained elusive due to the limited amount of NATs detected [42].…”

Genetic regulation of aflatoxin biosynthesis: From gene to genome

“…Recently, a global analysis of NAT expression in A. flavus during its colonization of maize seeds incubated at 28 or 37°C identified 32 of 352 putative cis NATs whose expression was directly or inversely correlated with expression of their respective sense gene (Smith et al, 2008). The expression of one of these NATs was inversely correlated with the expression of aflD.…”

<i>Aspergillus flavus</i> Secondary Metabolites: More than Just Aflatoxins

“…Microarray technology was among early approaches characterizing A. flavus gene function 42) , natural antisense transcripts 43) , and secondary metabolism, with an initial focus on AF regulation [44][45][46][47][48] . Subsequent to this, the examination of other SM gene clusters using customized microarrays were reported 8,29,49,50) .…”