Mechanisms for the inheritance of chromatin states

Abstract

Studies in eukaryotes ranging from yeast to mammals indicate that specific chromatin structures can be inherited following DNA replication via mechanisms acting in cis. Both the initial establishment of such chromatin structures and their inheritance require sequence-dependent specificity factors and changes in histone posttranslational modifications. Here I propose models for the maintenance of epigenetic information in which DNA silencers or nascent RNA scaffolds act as sensors that work cooperatively with parentally inherited histones to re-establish chromatin states following DNA replication.

Figure 1. Re-establishment of Epigenetic States from Parental Histone Modifications

During chromatin replication, parental histones and their posttranslational modifications are retained and randomly associate with the newly synthesized daughter DNA strands. The modifications of parental histones are proposed to be copied onto newly deposited histones by chromatin modification complexes that contain a subunit that recognizes the modification on the parental histone and another subunit that is an enzyme that catalyzes the same modification on an adjacent nucleosome. Note that distribution of histones to daughter DNA strands is random. For simplicity, equally spaced nucleosomes are depicted.

Figure 2. Assembly of Silent Chromatin in Budding Yeast

(A, Top) At the silent mating loci in Saccharomyces cerevisiae, silencers (DNA regions composed of binding sites) for the origin recognition complex (ORC), Rap1, and Abf1 recruit the Sir1, Sir2, Sir3, and Sir4 proteins through multiple weak interactions. Sir2 uses NAD to deacetylate histone H4 lysine 16 (H4K16), releasing O-acetyl-ADP-ribose (AAR), which binds to one of the Sir proteins and induces a conformational change in the SIR complex that may result in a tighter interaction between Sir3 and Sir4, and Sir3 and the nucleosome. (A, Bottom) H4K16 deacetylation promotes binding of Sir3, and sequential cycles of deacetylation and Sir3 binding to deacetylated nucleosomes are proposed to mediate the spreading of the SIR complex away from the silencer. The interaction of Sir3 with Sir4 is also required for spreading. (B) Insertion of the ADE2 gene near a yeast telomere results in stochastic spreading of telomeric heterochromatin into the ADE2 gene. The resulting ON and OFF states appear as white and red sectors, respectively, in the yeast colony on the right and indicate mitotically stable epigenetic states. (C) Switches in expression state, ON or OFF, are stable for more than 20 generations, indicating an epigenetic memory during cell divisions after the switch.

Figure 3. Heterochromatin Assembly at Pericentromeric DNA Repeats in Fission Yeast

In Schizosaccharomyces pombe, the small-interfering RNA (siRNA)-programmed RITS (RNA-induced initiator of transcriptional silencing) complex targets a nascent noncoding RNA, transcribed from pericentromeric (cen) DNA repeats by base-pairing interactions. The RITS complex recruits the RNA-dependent RNA polymerase complex (RDRC) and the Dicer (Dcr1) ribonuclease, which generate additional siRNAs. RITS also directly recruits the CLRC complex, containing the Clr4/Suv39h H3 lysine 9 (H3K9) methyl-transferase. The methylation of H3K9 (red) allows efficient association of RITS with chromatin.

Figure 4. Specificity Factors and Histone Modifications Cooperatively Recruit Silencing Complexes

(A) During replication of S. cerevisiae silent chromatin, the silent state is efficiently re-established because the SIR complex is recruited through cooperative interactions with both deacetylated parental histones and silencer-binding factors (SBF). (B) In contrast, during replication of the epigenetic ON state, even though the silencer is present, the interactions between the SIR complex and silencer-binding proteins are too weak to efficiently re-establish silencing. The ON state is therefore stable for many generations. Note that epigenetic variegation in budding yeast silent mating-type loci is only observed in cells containing weak silencers or lacking Sir1. (C) In S. pombe pericentromeric heterochromatin, small-interfering RNAs (siRNAs) take the place of DNA-binding proteins. During replication of heterochromatin, the silent state is efficiently re-established because the RITS complex can bind cooperatively via siRNA-mediated base pairing and association with H3K9 methylation. RITS-mediated recruitment of CLRC then results in methylation of newly deposited histones and re-establishment of silencing. During replication of active chromatin (not shown), although siRNAs may be present, the RITS complex binds inefficiently and silencing is not re-established. In these models, the silencer and the noncoding RNA scaffold act as sensors for chromatin modification states, while the modifications are carriers of epigenetic information.

Figure 5. Recruitment of the Drosophila PRC1 and PRC2 Complexes

Multiple weak interactions with factors associated with Polycomb response elements (PREs) contribute to the recruitment of the Drosophila PRC1 and PRC2 complexes. The PRE contains binding sites for several site-specific DNA-binding proteins and is transcribed by RNA polymerase II (pol II) to give rise to noncoding RNA, which may participate in recruitment. Also depicted are GAGA factor (homolog of mammalian GAGA-related factors), Dsp1 (homolog of mammalian HMGB2), Spps (an Sp1/KLF transcription factor), Zeste (a Drosophila-specific transcription factor), and the Pho-repressive complex (PhoRC). H3K27 trimethylation and H3K9/H4K20 monomethylation (red) bind to the Pc and Eed subunits of the PRC1/2 and the dSfmbt subunit of the PhoRC, respectively.