Heterochromatin formation involves changes in histone modifications over multiple cell generations

Abstract

Stable, epigenetic inactivation of gene expression by silencing complexes involves a specialized heterochromatin structure, but the kinetics and pathway by which euchromatin is converted to the stable heterochromatin state are poorly understood. Induction of heterochromatin in Saccharomyces cerevisiae by expression of the silencing protein Sir3 results in rapid loss of histone acetylation, whereas removal of euchromatic histone methylation occurs gradually through several cell generations. Unexpectedly, Sir3 binding and the degree of transcriptional repression gradually increase for 3-5 cell generations, even though the intracellular level of Sir3 remains constant. Strains lacking Sas2 histone acetylase or the histone methylases that modify lysines 4 (Set1) or 79 (Dot1) of H3 display accelerated Sir3 accumulation at HMR or its spreading away from the telomere, suggesting that these histone modifications exert distinct inhibitory effects on heterochromatin formation. These findings suggest an ordered pathway of heterochromatin assembly, consisting of an early phase, driven by active enzymatic removal of histone acetylation and resulting in incomplete transcriptional silencing, followed by a slower maturation phase, in which gradual loss of histone methylation enhances Sir association and silencing. Thus, the transition between euchromatin and heterochromatin is gradual and requires multiple cell division cycles.

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

“…4). The absence of Set1, however, did not impact on PHO84 mRNA levels in aged cells, suggesting that Set1 is required at early stages and that additional chromatinmodifying activities may take over to silence PHO84 in aging cells (Katan-Khaykovich and Struhl 2005). The same phenotypes were observed in the H3K4A mutant.…”

Symmetry, asymmetry, and kinetics of silencing establishment in Saccharomyces cerevisiae revealed by single-cell optical assays

“…HML and HMR loci are constitutively repressed in wild-type cells. However, conditional alleles of the SIR genes have led to a greater understanding of heterochromatin establishment, loss, and maintenance (5)(6)(7)(8)(9). Investigating the dynamics of transitions between heterochromatin and euchromatin in mutants with altered chromatin structure should reveal how chromatin modifications impact the formation of these two states.…”

“…When silent chromatin is formed, the levels of H4 K16 acetylation decline across the HMR locus followed soon after by a decline in H3 K4 methylation and H3 K79 methylation (8). Interestingly, the removal of methylation at these positions by deletion of the genes encoding their methyltransferases allows silencing to establish more rapidly as measured either by the association of Sir proteins with chromatin or by phenotypic changes (8,22). Thus, the removal of methyl marks seems to be an integral step in silent chromatin formation rather than a passive consequence of silencing.…”

“…Silencing establishment is thought to occur in multiple steps with Sir proteins initially recruited to the silencers flanking HML and HMR and subsequently enriched throughout the silenced loci (3,8,10). The apparent spreading of Sir proteins from silencers requires Sir2-dependent deacetylation of the critical histone residue H4 K16 and possibly other acetylated lysines as well (3,(11)(12)(13)(14).…”

Chromatin computation: Epigenetic inheritance as a pattern reconstruction problem

“…Furthermore, it has been reported repeatedly that particular epigenetic modifications can be gradually changed over generations through a number of different settings. In particular, these include the progressive reduction of higher histone methylation levels to lower methylation forms (Katan-Khaykovich and Struhl, 2005), epigenetic reprogramming (Jeong et al, 2007;Katz et al, 2009), epigenetic silencing / heterochromatin formation (Mutskov and Felsenfeld, 2003;Millar and Grunstein, 2006), and transcription-coupled histone modifications (Tippmann et al, 2012). Furthermore, histone modification gradients for a number of different modifications have been observed along a particular genomic region (for a review, see Henikoff and Shilatifard, 2011).…”