A current view on long noncoding RNAs in yeast and filamentous fungi

Abstract

Long noncoding RNAs (lncRNAs) are crucial players in epigenetic regulation. They were initially discovered in human, yet they emerged as common factors involved in a number of central cellular processes in several eukaryotes. For example, in the past decade, research on lncRNAs in yeast has steadily increased. Several examples of lncRNAs were described in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Also, screenings for lncRNAs in ascomycetes were performed and, just recently, the first full characterization of a lncRNA was performed in the filamentous fungus Trichoderma reesei. In this review, we provide a broad overview about currently known fugal lncRNAs. We make an attempt to categorize them according to their functional context, regulatory strategies or special properties. Moreover, the potential of lncRNAs as a biotechnological tool is discussed.

Linking the dynamics of chromatin occupancy and transcription with predictive models

“…We observed two major phenomena consistent with existing studies with respect to antisense transcription. First, as identified in other environmental conditions (Kim et al 2010;Till et al 2018;Wilhelm et al 2008), antisense transcription is induced pervasively in yeast undergoing cadmium stress. The distribution of genes with increased antisense transcripts monotonically skews towards more transcription through the 120-minute time course (Fig.…”

“…The second phenomena we observed pertains to genes whose sense transcription have changed. Previous studies have found that antisense transcription to be associated with both repression or activation of target genes (Kornienko et al 2013;Swamy et al 2014;Till et al 2018;Vance and Ponting 2014). Under cadmium stress, we identi-fied genes whose antisense transcripts increased with decreased sense transcription, such as with MET31 and UTR2, whose overexpression has been linked with endoplasmic reticulum stress (Miller et al 2010) (Supplemental Fig.…”

XRN1‐associated long non‐coding RNAs may contribute to fungal virulence and sexual development in entomopathogenic fungus Cordyceps militaris

“…34 In the past decade, studies of lncRNAs in fungi have steadily increased, such as in yeast, N. crassa, and T. reesei. 15,16,34 However, the characteristics of lncR-NAs in entomopathogenic fungi remain unclear. In this study, we evaluated lncRNAs in the entomopathogenic fungus C. militaris on a genome-wide level.…”

Strategies and Challenges for the Development of Industrial Enzymes Using Fungal Cell Factories

“…Long noncoding RNAs that are involved in gene regulation have been identified in yeast and filamentous fungi (Till et al 2018a). Identification and manipulation of long noncoding RNAs represent another means to engineer filamentous fungi for improved heterologous protein production.…”