This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

No abstract

DNA damage response significantly affects transcription. UV exposure of mammalian cells elicits global transcriptional shutdown orchestrated by an essentially enigmatic mechanism. We show here that a brief treatment of budding yeast with hydroxyurea, 4‐nitroquinoline 1‐oxide, or bleocin causes significant reduction in newly synthesized RNAs produced by all three RNA polymerases. This effect is not restricted to S phase and is suppressed by inactivation of checkpoint kinases MEC1 and RAD53, as well as by inactivation of histone chaperones ASF1 and RTT106. In addition, the genotoxic stress leads to removal of TATA‐binding protein from promoters of genes transcribed by all three RNA polymerases and removal of RNA Pol I and RNA Pol II from the corresponding genes. The effect of genotoxic stress on the stability of preinitiation complexes (PICs) does not seem to be significantly suppressed by ASF1, RAD53, or MEC1 inactivation. Together, our data suggest that genotoxic stress affects stability of PICs and production of new RNAs by at least partly independent mechanisms.

In addition to DNA damage checkpoint (DDC), eukaryotic cells have also DNA replication checkpoint (DRC) that is distinct from the DDC and specifically signals slowly progressing or arrested replication forks. We have showed previously that DDC activates respiration to increase ATP production and to elevate dNTP levels, which are required for efficient DNA repair and cell survival upon DNA damage. The underlying mechanism involves DNA damage‐induced downregulation of histone expression and altered chromatin structure, leading to increased transcription of genes encoding enzymes of tricarboxylic acid cycle, electron transport chain (ETC), and oxidative phosphorylation. Here we show that similarly to DDC, activation of DRC also induces respiration. However, unlike DDC, DRC does not affect histone gene expression and chromatin structure. DRC induces respiration by inducing transcription of RNR1‐4, upregulating synthesis of dNTPs, and elevating mtDNA copy number. Fitness of rrm3∆ and sgs1∆, mutants with defects in DNA replication, requires checkpoint kinase Dun1, but does not require ETC and oxidative metabolism. However, in the absence of Dun1, ETC is required for viability of rrm3Δ and sgs1Δ cells. In addition, inactivation of ETC in dun1Δ cells results in a synthetic growth defect. Together, our data show that when Dun1p function is compromised, rrm3Δand sgs1Δ cells depend on oxidative metabolism.