Cellular fractionation reveals transcriptome responses of human fibroblasts to UV-C irradiation

The response to DNA damage intersects with many other physiological processes in the cells, including initiation of DNA repair, regulation of transcription and translation, chromatin remodeling, and the cell cycle regulation to contend with the challenge. Transcription shutdown is not simply a consequence of the physical arrest of RNA polymerase II by DNA lesions, but also could be elicited by signaling in trans. While to date many of the specific molecular events are not fully elucidated. What is the signal that operates in trans to slow transcriptional elongation globally? Which factors are required for transcription restart after DNA repair? How is TC-NER controlled by the multifaceted transcriptional response? In this study, we sought to map the transcription restart and isolate the set of lncRNAs that are likely to function at the chromatin interface by using biochemical fractionation of the cellular compartment coupled to RNA-seq. Overall design: MRC5_VA cells were either left untreated as control or treated with 10 J/m2 of UV-C irradiation, followed by recovery for 30 minutes, 3 or 24 hours. Cellular fractionation was performed to isolate total RNA from cytoplasm and chromatin extracts.