Casein Kinase 2 Mediated Phosphorylation of Spt6 Modulates Histone dynamics and Regulates Spurious Transcription (RNA-Seq)

CK2 is an essential protein kinase implicated in various cellular processes. In this study, we address a potential role of this kinase in chromatin modulations associated with transcription. We found that CK2 depletion from yeast cells leads to replication-independent increase of histone H3K56 acetylation and global activation of H3 turnover in coding regions. This suggests a positive role of CK2 in maintenance/recycling of the histone H3/H4 tetramers during transcription. Interestingly, strand-specific RNA-seq analyses show that CK2 inhibits global cryptic promoters driving both sense and antisense transcription. This further indicates a role of CK2 in the modulation of chromatin during transcription. Next, we showed that CK2 interacts with the major histone chaperone Spt6, and phosphorylates it in vivo and in vitro. CK2 phosphorylation of Spt6 is required for its cellular levels, for the suppression of histone H3 turnover and for the inhibition of spurious transcription. Finally, we show that CK2 and Spt6 phosphorylation sites are important to various transcriptional responses suggesting that cryptic intragenic and antisense transcript production may have an impact on cell adaptation to environmental cues. Altogether, our data indicate that CK2 mediated phosphorylation of Spt6 regulates chromatin dynamics associated with transcription, and prevents aberrant transcription. Cells from CK2ts and spt6-7SA mutant strains and a WT strain were grown in YPD to an OD600 of 0.5 at 30°C and shifted to 39°C for 2h before RNA extraction. Total RNA was extracted using the hot-phenol method. Prior to library preparation, total RNA was depleted for ribosomal RNA using the Ribo-zero Gold yeast kit (Epicentre-Illumina). RNA-seq experiments were performed following TruSeq stranded total RNA illumina protocol and Illumina next generation sequencing was performed as 50 base pairs single-end reads on an Illumina Hi-Seq2000 (McGill University and Génome Québec Innovation Centre, Montréal, Canada). The sequenced reads from each sample were preprocessed with Trimmomatic (Bolger et al., 2014) and aligned with bwa (Li et al., 2009) to S.cerevisiae genome assembly R64-1-1 (GCA_000146045.2) and the numbers of reads for each exon annotated in Ensembl Release 77 was calculated for both the sense and antisense strands using SAMtools.