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

Numerous long noncoding RNAs (lncRNAs) are generated in response to external stimuli, but the scope and functions of such activity are not known. Here, we provide insight into how the transcription of lncRNAs are connected to DNA damage response by identifying a lncRNA ZFAS1, which is required for cell cycle arrest, transcription regulation and DNA repair. Mechanistically, ZFAS1 facilitates the changing hyperphosphorylated forms of the large subunit of RNAPII around transcription initiation sites by directly targeting the regulated genes. We revealed extensive transcription shutdown and concomitant stimulated engagement of RNAPII-Ser2P are crucial for repair and cell survival upon genotoxic stress. Finally, ZFAS1 knockout in mice dampened transcription-coupled nucleotide excision repair (TC-NER) and led to kidney dysplasia. Our study extends the understanding of lncRNAs in DNA damage repair (DDR) and implies a protective role of lncRNA against DDR-deficient developmental disorders. Overall design: WT and ZFAS1-knockdown MRC5 cells were treated with DRB (100 µM, 3.5 hrs), followed by 10 J/m2 UV-C irradiation or left untreated. Cells were washed with PBS to remove DRB immediately after UV-C treatment and incubated for 10 or 40 minutes, followed by cell lysis and nuclei isolation. Nuclei were subjected to GRO-Seq.