Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications [ChIP-seq]

The genetic information encoded in DNA is framed by additional layers of information, referred to as the epigenome. Epigenetic marks such as DNA methylation, histone modifications and histone variants are concentrated on specific genomic sites as means to instruct, but also sometimes as a consequence of, gene expression. How this information is maintained, notably in the face of transcription, is not understood. Here we show that the histone chaperones FACT and Spt6 are required for maintaining proper localization of several histone modifications including H3K4me1,2,3, H3K36me3, H3K79me3, H3K14ac, H3K18ac and H2Bub in Saccharomyces cerevisiae. In the absence of functional FACT or Spt6, transcription generates massive nucleosome loss which is partially compensated by increased histone assembly by histone chaperones such as Asf1 and HIR. Because re-incorporation of histones by these histone chaperones in not coupled to transcription, the modified histones are randomly incorporated, leading to scrambling of the epigenetic information. Hence, our work highlights the importance of local nucleosome recycling by FACT and Spt6 during transcription in the maintenance of a proper epigenetic landscape. Occupancy profiling by ChIP-seq of histone modifications H3K4me3 and H3K56ac as well as histones H4 and H3 in wild-type (WT) and temperature-sensitive mutants for the histone chaperones FACT and Spt6 (spt16-197 and spt6-1004 respectively) in yeast Saccharomyces cerevisiae, in duplicate, for a total of 12 Input DNA and 24 ChIP samples. For all samples, a fixed amount of crosslinked S. pombe cells (representing 10% of the S. cerevisiae cells) was added to the S. cerevisiae cells prior to cell lysis. This spike-in control was used to normalise samples.