RT Journal Article SR Electronic T1 Real-time in vivo Global Transcriptional Dynamics During Plasmodium falciparum Blood-stage Development JF bioRxiv FD Cold Spring Harbor Laboratory SP 265975 DO 10.1101/265975 A1 Heather J. Painter A1 Neo Christopher Chung A1 Aswathy Sebastian A1 Istvan Albert A1 John D. Storey A1 Manuel LlinĂ¡s YR 2018 UL http://biorxiv.org/content/early/2018/02/14/265975.abstract AB Genome-wide analysis of transcription in the human malaria parasite Plasmodium falciparum has revealed robust variation in steady-state mRNA abundance throughout the 48-hour intraerythrocytic developmental cycle (IDC) suggesting that this process is highly dynamic and tightly regulated. However, the precise timing of mRNA transcription and decay remains poorly understood due to the utilization of methods that only measure total RNA and cannot differentiate between newly transcribed, decaying and stable cellular RNAs. Here we utilize rapid 4-thiouracil (4-TU) incorporation via pyrimidine salvage to specifically label, capture and quantify newly-synthesized P. falciparum RNA transcripts at every hour throughout the IDC following erythrocyte invasion. This high resolution global analysis of the transcriptome captures the timing and rate of transcription for each newly synthesized mRNA in vivo, revealing active transcription throughout all stages of the IDC. To determine the fraction of active transcription and/or transcript stabilization contributing to the total mRNA abundance at each timepoint we have generated a statistical model to fit the data for each gene which reveals varying degrees of transcription and stabilization for each mRNA corresponding to developmental transitions and independent of abundance profile. Finally, our results provide new insight into co-regulation of mRNAs throughout the IDC through regulatory DNA sequence motifs associated with these processes, thereby expanding our understanding of P. falciparum mRNA dynamics.