lncRNA-ZFAS1, an emerging gate-keeper in DNA damage-dependent transcriptional regulation [ZFAS1-mRNA-seq]

The hereditary information encoded in DNA sequence is intrinsically susceptible to alterations, being continually threatened by a variety of genotoxic perturbations. To safeguard the stability of the genome, eukaryotic cells have evolved a set of sophisticated surveillance system that controls several aspects of the cellular response, including the detection of DNA lesions, a temporary cell cycle arrest, regulation of transcription, and the repair of the damaged DNA. However, it is still poorly understood how the DNA damage checkpoints and stalled RNAPII molecules convert a very limited amount of molecular-level information (even a single DNA lesion) in the context of an otherwise genome into regulation that halts and resumes the cell-cycle engine in a coordinated way. In this study, we reveal a map of extensive lncRNA transcription during DDR by using synchronized cells, leading to the unexpected identification of a poorly characterized mammalian lncRNA-ZFAS1. We describe that ZFAS1 functions as a key player of cellular response to DNA damage in both human and rodent cells by fine tuning RNAPII kinetics, suggesting a lncRNA-dependent transcriptional regulatory axis that maintains genomic stability upon DNA damage in mammalian cells. Overall design: To study the effect of ZFAS1 lncRNA on mature RNA synthesis upon DNA damage, we knocked down ZFAS1 in MRC5_VA cells by using lentiviral shRNA plasmids targeting two distinct regions of ZFAS1. Cells were UV irradiated and recovered for the indicated time intervals (3 h and 24 h), total RNA was extracted from the three cell lines (empty vector, ZFAS1-sh1, and ZFAS1-sh2). We then performed gene expression profiling analysis using data obtained from RNA-seq of 9 samples.