(228cs) Antisense RNA Exclusively Regulate Key Genes in Anaerobic Fungi

Anaerobic fungi resident in the digestive tracts of large mammalian herbivores degrade crude plant material through the expression and regulation of powerful cellulolytic enzymes. These enzymes are strongly expressed on demand with specific activities tuned to the architecture of the available substrates. Thus, elucidating the specific regulatory patterns of these genes may reveal more efficient strategies of converting complex plant materials to the simple sugars needed for microbial biofuel production. Here, we use strand-specific RNASeq and genomics to examine the transcriptional regulatory patterns of 3 non-model species of anaerobic fungi: Anaeromyces robustus, Neocallimastix californiae, and Piromyces finnis. In this work, we sequenced the genomes of these organisms and collected their transcriptomes when grown on a collection of monosaccharides, disaccharides, oligosaccharides, and complex plant material. Mapping these transcripts to the genome revealed that non-coding antisense RNA formed up to 30% of the transcriptome. These antisense RNA target genes involved in a number of cellular processes, including lignocellulose hydrolysis. Antisense RNA arose early in gut fungal genomes with transcripts targeting genes involved in RNA processing and protein expression sharing a common ancestor across all three fungal genera. Similarly, antisense RNA is critical to the regulation of genes involved in protein expression, and DNA replication and repair as revealed by their functional enrichment in fungal genomes and convergent evolution. More importantly, antisense regulation is not redundant â?? genes targeted by antisense RNA differentially expressed under various substrates are typically not transcriptionally regulated. That is, seemingly constitutive genes were, in fact, regulated exclusively via antisense RNA. Collectively, this work demonstrates the central nature of antisense RNA regulation in anaerobic fungi and highlights the importance of antisense RNA in understanding gene regulation.