Landscape and metabolism of cryptic unstable transcripts in human malaria parasites

The highly tight regulation of gene expression plays a critical role in the development and pathogenesis of human malaria parasites Plasmodium falciparum throughout the complex life cycle. Accumulated experimental data reveals nascent transcripts and non-coding RNAs have been involved in the regulation of virulence gene expression, suggesting a hidden transcriptome composed of nascent message RNAs and non-coding cryptic unstable transcripts (CUTs) contributes to post-transcriptional regulation (PTR) of gene expression in this pathogen. Nevertheless, the source, dynamic transcription, metabolism and related biological functions of CUTs are still poorly investigated. Here we performed dynamic nascent RNA profiling by ribosome RNA-depleted and strand-specific RNA sequencing in 48-hour intraerythrocytic developmental cycle (IDC). Our data revealed the dynamics of post- transcriptionally regulated genes, and genome-wide sources of 2252 CUTs, mostly originating from intergenic regions and untranslated regions of annotated genes including var gene family. By utilizing transposase accessible chromatin sequencing (ATAC-seq) combined with chromatin immunoprecipitation sequencing (ChIP-seq) data, we systematically defined the local euchromatin-like environment where those newly identified CUTs originated, and revealed a significantly positive correlation between CUTs and corresponding mRNA abundance. Finally, we showed the cooperation of RNA exosome catalytic subunit PfDis3 and its cofactor PfMtr4 played a major role in CUTs degradation. Collectively, this study provides new insight into the potential regulatory functions of short-lived CUTs, which would contribute to our understanding of the complex mechanism of gene expression in P. falciparum.