The Double-Bromodomain Proteins Bdf1 and Bdf2 Modulate Chromatin Structure to Regulate S-Phase Stress Response in Schizosaccharomyces pombe

Abstract

Bromodomain proteins bind acetylated histones to regulate transcription. Emerging evidence suggests that histone acetylation plays an important role in DNA replication and repair, although its precise mechanisms are not well understood. Here we report studies of two double bromodomain-containing proteins, Bdf1 and Bdf2, in fission yeast. Loss of Bdf1 or Bdf2 led to a reduction in the level of histone H4 acetylation. Both bdf1Δ and bdf2Δ cells showed sensitivity to DNA damaging agents, including camptothecin, that cause replication fork breakage. Consistently, Bdf1 and Bdf2 were important for recovery of broken replication forks and suppression of DNA damage. Surprisingly, deletion of bdf1 or bdf2 partially suppressed sensitivity of various checkpoint mutants including swi1Δ, mrc1Δ, cds1Δ, crb2Δ, chk1Δ, and rad3Δ, to hydroxyurea, a compound that stalls replication forks and activates the Cds1-dependent S-phase checkpoint. This suppression was not due to reactivation of Cds1. Instead, we found that bdf2 deletion alleviates DNA damage accumulation caused by defects in the DNA replication checkpoint. We also show that hydroxyurea sensitivity of mrc1Δ and swi1Δ was suppressed by mutations in histone H4 acetyltransferase subunits or histone H4. These results suggest that the double bromodomain-containing proteins modulate chromatin structure to coordinate DNA replication and S-phase stress response.

Histone H4 acetylation required for chromatin decompaction during DNA replication

“…As it is known that Mst1 catalyzes histone H4 acetylation in S. pombe 20 , we examined the acetylation of lysine residues (K5, K8, K12, and K16) of histone H4 during meiosis. Acetylation of histone H3-K56, which was reported as a replication-coupled histone modification 17 , was used as a positive control.…”

NuA4 Initiates Dynamic Histone H4 Acetylation to Promote High-Fidelity Sister Chromatid Recombination at Postreplication Gaps

“…Also, similar to H4 acetylation mutants, expansions in both the rsc1Δ and rsc2Δ mutants were suppressed in the absence of Rad5 (Table S1), supporting that these remodelers play a role in the PRR template switch pathway. Strains mutant for Esa1, Rsc1, Rsc2, and Bdf1 have all been shown to be MMS-sensitive, with esa1 and rsc2 mutants showing the greatest sensitivity (Bird et al, 2002; Oum et al, 2011; Garabedian et al, 2012). …”

Epe1 recruits BET family bromodomain protein Bdf2 to establish heterochromatin boundaries

“…S1). Our screen identified epe1D, which is known to be required for boundary function (Ayoub et al 2003;Zofall and Grewal 2006;Trewick et al 2007), as well as an uncharacterized null mutant of SPAC631.02, which has been named bdf2 + (Garabedian et al 2012) and nrc1 + in PomBase. The Bdf2 protein contains two bromodomains and is homologous to the mammalian bromodomain and extraterminal (BET) family of double bromodomain proteins (Supplemental Fig.…”

“…It is also possible that Bdf2 regulates transcription of other factors involved in heterochromatin boundary functions, and it would be interesting to determine the role of Bdf2 in regulating gene expression at euchromatic regions in the future. Bdf2 has also been shown to regulate DNA damage response, which is attributed to its effect on regulating global H4 acetylation levels (Garabedian et al 2012). …”