Two-Color Cell Array Screen Reveals Interdependent Roles for Histone Chaperones and a Chromatin Boundary Regulator in Histone Gene Repression

Rtt106 recruitment to the histone promoters almost completely depends on Asf1, HIR and acetylation of histone H3 at K56 (H3K56Ac), and is limited by Yta7.

“Rtt106 recruitment to the histone promoters almost completely depends on Asf1, HIR and acetylation of histone H3 at K56 (H3K56Ac), and is limited by Yta7, a bromodomain- and AAA-ATPase domain-containing boundary protein31,32,35.”

Outside S phase, Rtt106 forms a repressive complex together with other histone chaperones HIR and Asf1 to recruit RSC to the histone promoters.

“Outside S phase, Rtt106 forms a repressive complex together with other histone chaperones HIR and Asf1 to recruit RSC (Remodel the Structure of Chromatin), an essential ATP-dependent chromatin-remodelling complex, to the histone promoters31–33.”

Rtt106 localises at the promoters of three out of four histone gene pairs (HTA1-HTB1, HHT1-HHF1 and HHT2-HHF2, but not HTA2-HTB2) and restricts their transcription to S phase.

“Rtt106 localises at the promoters of three out of four histone gene pairs (HTA1-HTB1, HHT1-HHF1 and HHT2-HHF2, but not HTA2-HTB2), and restricts their transcription to S phase, when new histone supply is required to package newly synthesised DNA31,32.”

Yta7 limits Rtt106 binding at the PDRE-containing promoters.

“We further observed that Yta7, a boundary protein that restricts Rtt106 binding at the histone promoters31,32 (Fig. 2b, yta7Δ), limits Rtt106 binding also at the PDRE-containing promoters, as loss of Yta7 increased Rtt106 binding (Fig. 2a, yta7Δ).”

The difference in histone gene effects may reflect the fact that we prepared RNA from asynchronous cells rather than cells at specific cell-cycle stages.

“This difference may reflect the fact that we prepared RNA from asynchronous cells rather than cells at specific cell-cycle stages31,32.”

In our experiments, only HHF1 mRNA was significantly increased in rtt106Δ, unlike previous reports which found additional histone genes affected.

“Regarding histone gene expression, in our experiments only HHF1 mRNA was significantly increased in rtt106Δ (Fig. 3a and Supplementary Data 3), unlike previous reports which found additional histone genes affected31,32.”

At the histone promoters, RTT106 deletion causes further reduction of nucleosome occupancy.

“At the histone promoters, RTT106 deletion causes further reduction of nucleosome occupancy as reported previously31 (Fig. 2g, Type B, compare green dashed line with solid line).”

The HIR histone chaperone contributes to Rtt106 recruitment to PDRE-containing promoters.

“We observed that the HIR histone chaperone, a crucial factor for recruitment of Rtt106 to the HTA1-HTB1 promoter31,32 (Fig. 2b, hir1Δ), contributes to Rtt106 recruitment to PDRE-containing promoters, since the loss of the HIR subunit Hir1 caused a reduction of Rtt106 binding (Fig. 2a, hir1Δ).”

Rtt106 localises at the promoter of the histone gene pair HTA1-HTB1 in S. cerevisiae.

“As expected31,32, Rtt106 localised at the promoter of the histone gene pair HTA1-HTB1 (Fig. 1a).”