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. 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.