| Summary: | Carotenoid biosynthesis in the fungus <i>Fusarium fujikuroi</i> is regulated by environmental factors, with light being the main stimulating signal. The CarS RING-finger protein plays an important role in the downregulation of structural genes of the carotenoid pathway. A recent transcriptomic analysis on the effect of <i>carS</i> mutation identified a gene for a long non-coding RNA (lncRNA) upstream of <i>carS</i>, called <i>carP</i>, the deletion of which results in increased <i>carS</i> mRNA levels and lack of carotenoid production. We have investigated the function of <i>carP</i> by studying the transcriptomic effect of its deletion and the phenotypes resulting from the reintroduction of <i>carP</i> to a deletion strain. The RNA-seq data showed that the loss of <i>carP</i> affected the mRNA levels of hundreds of genes, especially after illumination. Many of these changes appeared to be cascade effects as a result of changes in <i>carS</i> expression, as suggested by the comparison with differentially expressed genes in a <i>carS</i> mutant. Carotenoid production only recovered when <i>carP</i> was integrated upstream of <i>carS</i>, but not at other genomic locations, indicating a <i>cis</i>-acting mechanism on <i>carS</i>. However, some genes hardly affected by CarS were strongly upregulated in the <i>carP</i> mutant, indicating that <i>carP</i> may have other regulatory functions as an independent regulatory element.
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