A structural model of elongating RNA polymerase II (cyan) in the act of transcribing a gene. The DNA strands are yellow and green, respectively, while the newly synthesized RNA is red.

Jesper Svejstrup Transcription during DNA damage

Bulky DNA lesions not only block the progress of RNAPII locally, but also affect transcription genome-wide so that even genes that are not damaged temporarily cease to be expressed.

The mechanisms and factors that underlie the more general, DNA damaged-induced repression of gene expression, and its eventual re-start, are still very poorly understood.

In order to uncover factors with a role in the transcription-related DNA damage response, we carried out several general and more specific proteomic screens, as well as a functional genomics screen.

The proteomic screens all made use of quantitative SILAC proteomics, enabling us to distinguish between ‘constitutive’ and UV-induced interactors of RNAPII and CSB, respectively. As well as the well-known TC-NER factors, this multi-omic approach has uncovered numerous new factors that had not previously been connected to the transcription-related DNA damage response, many of which we are presently investigating in detail.

Discovery of new factors via the multi-omic approach is complemented by genome-wide deep sequencing techniques such as ChIP-Seq, RNA-Seq, CLIP-Seq, 4SU-Seq and DRB/GRO-Seq to investigate the role of these new factors in the transcriptional response to UV-induced DNA damage at the genome-wide level.

Because UV-damage has turned out to trigger a dramatic change in mRNA splicing, termination, and RNA biology in general, much of our present focus has shifted more and towards RNA biology, including the function of stable RNAs.