Restriction of histone gene transcription to S phase by phosphorylation of a chromatin boundary protein

Abstract

The cell cycle-regulated expression of core histone genes is required for DNA replication and proper cell cycle progression in eukaryotic cells. Although some factors involved in histone gene transcription are known, the molecular mechanisms that ensure proper induction of histone gene expression during S phase remain enigmatic. Here we demonstrate that S-phase transcription of the model histone gene HTA1 in yeast is regulated by a novel attach-release mechanism involving phosphorylation of the conserved chromatin boundary protein Yta7 by both cyclin-dependent kinase 1 (Cdk1) and casein kinase 2 (CK2). Outside S phase, integrity of the AAA-ATPase domain is required for Yta7 boundary function, as defined by correct positioning of the histone chaperone Rtt106 and the chromatin remodeling complex RSC. Conversely, in S phase, Yta7 is hyperphosphorylated, causing its release from HTA1 chromatin and productive transcription. Most importantly, abrogation of Yta7 phosphorylation results in constitutive attachment of Yta7 to HTA1 chromatin, preventing efficient transcription post-recruitment of RNA polymerase II (RNAPII). Our study identified the chromatin boundary protein Yta7 as a key regulator that links S-phase kinases with RNAPII function at cell cycle-regulated histone gene promoters.

Cell cycle-regulated oscillator coordinates core histone gene transcription through histone acetylation

“…1A) (11). Consistent with an important function for the Spt10-HIR interaction on chromatin, we observed a strong reduction in the recruitment of both negative regulators of histone gene expression-HIR, Rtt106, Asf1, and RSC-as well as activators of histone transcription-SWI/SNF and Yta7-to the HTA1-HTB1 promoter in an SPT10 deletion strain (Fig.…”

“…To explore the mechanism of Spt10-dependent activation of histone gene transcription, we first used affinity purification and mass spectrometry to discover proteins associated with Spt10. Specifically, we used a tandem affinity purification (TAP)-tagged version of Spt10 expressed either at its endogenous locus or from an inducible promoter (GAL1-10) and a modified chromatin immunoprecipitation (mChIP) protocol to identify proteins associated with Spt10 on chromatin (8,11,26). We discovered interactions between Spt10 and all HIR subunits (Hir1, Hir2, Hir3, and Hpc2), RSC, as well as most subunits of SWI/SNF (Fig.…”

“…Because we detected all four HIR subunits in our mChIP of Spt10-TAP, we next used chromatin immunoprecipitation (ChIP) to test whether SPT10 is required for recruitment of HIR (Hir1-TAP), the HIR-dependent regulators RSC (Rsc8-TAP), SWI/SNF (Snf6), Rtt106-TAP, and Asf1-TAP, and the transcriptional activator Yta7 (Yta7-TAP) (8,11,13) to the promoter region of HTA1-HTB1 (Fig. 1A) (11).…”

“…HTA2-HTB2, the fourth histone gene pair, does not have a NEG region and is regulated in a HIR-independent manner. At HIR-dependent promoters, HIR recruits other histone chaperones, Asf1 and Rtt106, as well as the chromatin boundary protein Yta7 (8,9) and the remodel structure of chromatin (RSC) ATP-dependent chromatin-remodeling complex (10), which together assemble repressive chromatin, blocking recruitment of RNAPII (11,12). In S phase, this repressive chromatin is overcome, allowing recruitment of RNAPII and activation of transcription.…”

“…In S phase, this repressive chromatin is overcome, allowing recruitment of RNAPII and activation of transcription. After recruitment of RNAPII, the AAA-ATPase Yta7 is important for efficient transcript elongation by evicting histones H3-H4 (11)(12)(13). Other chromatin remodelers also have roles in histone gene activation, including the SWI/SNF chromatin-remodeling complex, which activates NEG-dependent histone genes (14), and the histone-acetyltransferase (HAT) complex Rtt109-Vps75 (8).…”