Expression dynamics of periodic transcripts during cancer cell cycle progression and their correlation with anticancer drug sensitivity

Cell cycle is the center of cellular activities and is orchestrated by complex regulatory mechanisms, among which transcriptional regulation is one of the most important parts. Alternative splicing dramatically expands the regulatory network by producing transcript isoforms of genes to exquisitely control the cell cycle. However, the patterns of transcript isoform expression in the cell cycle are unclear. Therapies targeting cell cycle checkpoints are commonly used as anticancer therapies, but none of them were designed and have been evaluated at alternative splicing transcripts level. To explore alternative splicing patterns during cell cycle progression, we performed sequential transcriptomic assays following cell cycle synchronization in breast cancer MDA-MB-231 cell lines, used flow cytometry and reference cell cycle transcripts to confirm the cell cycle phases of samples. Overall design: MDA-MB-231 cells were harvested at 0, 3, 4.5, 6, 7, 9, 10, 11.5, 13, and 16 hr after G1/S phase release. For M phase arrest, when MDA-MB-231 cells were released from G1/S phase, 1 µg/ml nocodazole was added, and after 10 hr, they were supplemented with 5 µg/ml actinomycin D.