Natural antisense transcripts in fungi

Donaldson, Michael E.; Saville, Barry J.

doi:10.1111/j.1365-2958.2012.08125.x

Cited by 65 publications

(84 citation statements)

References 83 publications

(160 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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 are involved in transcriptional and post-transcriptional gene regulation by RNA interference (RNAi) [27], [28], chromatin-level gene silencing [23], [26], [29]–[31], chromatin remodeling [28], [32] and local chromatin modifications [33]–[35]. Global analysis of NATs has been done for mammals [23], insects [36], worms [37] and plants [38], [39].…”

Section: Introductionmentioning

confidence: 99%

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

Zhou

Yin

et al. 2014

PLoS ONE

View full text Add to dashboard Cite

Aspergillus flavus has received much attention owing to its severe impact on agriculture and fermented products induced by aflatoxin. Sclerotia morphogenesis is an important process related to A. flavus reproduction and aflatoxin biosynthesis. In order to obtain an extensive transcriptome profile of A. flavus and provide a comprehensive understanding of these physiological processes, the isolated mRNA of A. flavus CA43 cultures was subjected to high-throughput strand-specific RNA sequencing (ssRNA-seq). Our ssRNA-seq data profiled widespread transcription across the A. flavus genome, quantified vast transcripts (73% of total genes) and annotated precise transcript structures, including untranslated regions, upstream open reading frames (ORFs), alternative splicing variants and novel transcripts. We propose natural antisense transcripts in A. flavus might regulate gene expression mainly on the post-transcriptional level. This regulation might be relevant to tune biological processes such as aflatoxin biosynthesis and sclerotia development. Gene Ontology annotation of differentially expressed genes between the mycelia and sclerotia cultures indicated sclerotia development was related closely to A. flavus reproduction. Additionally, we have established the transcriptional profile of aflatoxin biosynthesis and its regulation model. We identified potential genes linking sclerotia development and aflatoxin biosynthesis. These genes could be used as targets for controlled regulation of aflatoxigenic strains of A. flavus.

show abstract

Section: Introductionmentioning

confidence: 99%

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

Zhou

Yin

et al. 2014

PLoS ONE

View full text Add to dashboard Cite

show abstract

“…This also may generate overlapping transcripts for epigenetic regulation. A role for the latter is demonstrated in fungi and metazoans (16), and it would be interesting to see if this also holds true for oomycetes.…”

mentioning

confidence: 99%

Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution

Judelson

2012

Eukaryot Cell

View full text Add to dashboard Cite

The eukaryotic microbes known as oomycetes are common inhabitants of terrestrial and aquatic environments and include saprophytes and pathogens. Lifestyles of the pathogens extend from biotrophy to necrotrophy, obligate to facultative pathogenesis, and narrow to broad host ranges on plants or animals. Sequencing of several pathogens has revealed striking variation in genome size and content, a plastic set of genes related to pathogenesis, and adaptations associated with obligate biotrophy. Features of genome evolution include repeat-driven expansions, deletions, gene fusions, and horizontal gene transfer in a landscape organized into gene-dense and gene-sparse sectors and influenced by transposable elements. Gene expression profiles are also highly dynamic throughout oomycete life cycles, with transcriptional polymorphisms as well as differences in protein sequence contributing to variation. The genome projects have set the foundation for functional studies and should spur the sequencing of additional species, including more diverse pathogens and nonpathogens.

show abstract

“…These siRNAs have not been identified in fungi as yet, and we thus refrain from their discussion in this article. Long ncRNAs (lncRNAs) have been identified in all eukaryotic cells including fungi (Engström et al 2006;Katayama et al 2005;Wang et al 2005;Donaldson and Saville 2012). Some of them are components of the ribosome (5.8S, 18S, and 26S rRNA), but a subset of lncRNAs is the so-called natural antisense transcripts (NATs) whose sequence is complementary to other RNAs.…”

Section: Rna Interferencementioning

confidence: 98%

“…Their action appears to involve formation of doublestranded RNA, transcriptional interference, and chromatin remodeling. In fungi, they were shown to be involved in the regulation of mating and meiosis, cell aging, carbon metabolism, circadian rhythm, and plant pathogenesis (reviewed by Donaldson and Saville 2012).…”

Section: Rna Interferencementioning

confidence: 99%

Epigenetics as an emerging tool for improvement of fungal strains used in biotechnology

Aghcheh

Kubicek

2015

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

Filamentous fungi are today a major source of industrial biotechnology for the production of primary and secondary metabolites, as well as enzymes and recombinant proteins. All of them have undergone extensive improvement strain programs, initially by classical mutagenesis and later on by genetic manipulation. Thereby, strategies to overcome rate-limiting or yield-reducing reactions included manipulating the expression of individual genes, their regulatory genes, and also their function. Yet, research of the last decade clearly showed that cells can also undergo heritable changes in gene expression that do not involve changes in the underlying DNA sequences (=epigenetics). This involves three levels of regulation: (i) DNA methylation, (ii) chromatin remodeling by histone modification, and (iii) RNA interference. The demonstration of the occurrence of these processes in fungal model organisms such as Aspergillus nidulans and Neurospora crassa has stimulated its recent investigation as a tool for strain improvement in industrially used fungi. This review describes the progress that has thereby been obtained.

show abstract

Natural antisense transcripts in fungi

Cited by 65 publications

References 83 publications

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

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

Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution

Epigenetics as an emerging tool for improvement of fungal strains used in biotechnology

Contact Info

Product

Resources

About