The regional sequestration of heterochromatin structural proteins is critical to form and maintain silent chromatin

Abstract

Budding yeast Saccharomyces cerevisiae and fission yeast Schizosaccharomyces pombe are good models for heterochromatin study. In S. pombe, H3K9 methylation and Swi6, an ortholog of mammalian HP1, lead to heterochromatin formation. However, S. cerevisiae does not have known epigenetic silencing markers and instead has Sir proteins to regulate silent chromatin formation. Although S. cerevisiae and S. pombe form and maintain heterochromatin via mechanisms that appear to be fundamentally different, they share important common features in the heterochromatin structural proteins. Heterochromatin loci are localized at the nuclear periphery by binding to perinuclear membrane proteins, thereby producing distinct heterochromatin foci, which sequester heterochromatin structural proteins. In this review, we discuss the nuclear peripheral anchoring of heterochromatin foci and its functional relevance to heterochromatin formation and maintenance.

Keywords: Heterochromatin structural proteins; SIR complex; Saccharomyces cerevisiae; Schizosaccharomyces pombe; Swi6.

Fig. 1

Heterochromatin formation in Saccharomyces cerevisiae. A Heterochromatin formation in silent mating-type loci of S. cerevisiae. At budding yeast chromosome III, two silent mating-type loci—HMLα and HMRa—surround the mating-type (MAT) locus. Each homothallic mating (HM) locus is surrounded by two proto-silencers, E and I, which nucleate the heterochromatin assembly. Silencer elements are bound by Orc1, Rap1, and Abf1. Orc1 interacts with Sir1 and Abf1 interacts with Sir3. Through the self-reinforcing mechanism of the SIR complex composed of Sir2, Sir3, and Sir4, silent chromatin is formed at HM loci. B Heterochromatin formation in telomeres of S. cerevisiae. Telomeres consist of TG_1-3 repeat regions and chromosomal ends. Chromosomal ends are bound by yKu70/80 heterodimeric complexes. Telomeric repeats contain multiple Rap1 binding sites and the SIR complex is recruited to telomeric repeats through Rap1. Rif1 competes with Sir4 for binding to Rap1. The yKu complex regulates this competition process for Sir4 recruitment and SIR complex assembly. C Heterochromatin formation in rDNA repeats of S. cerevisiae. Approximately 100 to 200 rDNA repeats are positioned at chromosome XII. Each repeat consists of the 35S pre-rRNA gene and 5S rRNA gene which are separated by intergenic spacer 1(IGS1). IGS2 is located upstream of the 5S rRNA gene. A replication fork barrier (RFB) site is positioned within IGS1 and the binding site for Fob1. The binding of Fob1 into RFB sites causes recombination of rDNA repeats, which should be prevented by the binding of additional proteins. Net1 tethers to Fob1 and recruits Cdc14 and Sir2 into rDNA loci, thereby forming the regulator of nucleolar silencing and telophase exit (RENT) complex. Tof2 binds to Fob1, leading to the recruitment of two cohibin complex components, Lrs4 and Csm1, for Sir2-independent rDNA silencing. Lrs4/Csm1 interacts with Heh1/Nur1 (two nuclear membrane proteins)

Fig. 2

Heterochromatin formation in Schizosaccharomyces pombe. A Heterochromatin formation in centromeres. In centromeres, centromeric repeats (cnt) are surrounded by two innermost repeats (imr) regions with inverted orientation. Outer repeat (otr) elements are positioned further outside, and they consist of dg/dh repeat elements. dg/dh repeats nucleate heterochromatin in an RNAi-dependent manner. Once nucleated, heterochromatin is spread through the H3K9me-Swi6-dependent self-reinforcing mechanism up to its encounter with boundary elements including tRNA gene clusters. B Heterochromatin formation in silent mating-type loci. The mating-type is determined by the MAT1 gene; two mating-type determining regions, mat2P and mat3M, which contain information on both mating types, are maintained in silent chromatin. CenH regions show high homology to centromeric dg/dh repeats and function as RNAi-dependent nucleation centers. The REIII element is the binding site for Atf1/Pcr1, constituting an RNAi-independent heterochromatin nucleation site. Once nucleated, heterochromatin is spread up to its encounter with boundary elements, IR (inverted repeats)-L and IR-R. C Heterochromatin formation in telomeres. Telomeres are composed of double-stranded telomeric DNA repeats and single-stranded overhangs at chromosomal ends. Telomeric DNA repeats and immediately adjacent telomere-associated sequences (TAS) are RNAi-independent heterochromatin nucleation sites. Regions more distal to chromosomal ends contain multiple CenH-like sequences, functioning as RNAi-dependent heterochromatin nucleation sites (e.g., centromeres and silent mating-type loci). The shelterin complex consists of Tpz1/Pot1 subcomplexes bound to single-stranded overhangs and the double-stranded telomeric repeat-binding protein Taz1 connected by Rap1 and Poz1. The shelterin component Ccq1 recruits Clr4 for H3K9 methylation and subsequent Swi6-dependent heterochromatin formation. Additionally, Ccq1 leads to SHREC recruitment for transcriptional gene silencing. There is no known boundary element at telomeres; therefore, telomeres contain a long transition zone showing a gradual decrease in the heterochromatin domain

Fig. 3

Regional sequestration of heterochromatin structural proteins at nuclear periphery. A Perinuclear anchoring of heterochromatin structural proteins in S. cerevisiae. Budding yeast silent chromatin loci, such as telomeres, HM loci and rDNA repeats are anchored to the nuclear periphery through interaction with inner nuclear membrane proteins (INMPs) and nucleoporins. At rDNA repeats, Net1 sequesters Sir2 and Cdc14 specifically during the S-phase for RENT complex formation. rDNA repeats are anchored to the nuclear periphery through interaction between INMPs Heh1/Nur1 and the cohibin components Lrs4/Csm1. Telomeric repeats are anchored to the nuclear periphery by binding to the INMP Mps3 or nucleoporin Nup170. The yKu70/80 heterodimeric complex combines with telomerase to bind to Mps3. Sir4 interacts with Mps3. Sir4 binds to Nup170 and forms a distinct complex with SUMO E3 ligase Siz2 and nuclear periphery protein Esc1. At HM loci, HML is linked to HMR via a long-range interaction. HML and HMR loci are clustered with the telomeres of chromosome III. HMR locus is anchored to nuclear periphery through Sir4-dependent manner. B Perinuclear anchoring of heterochromatin structural proteins in S. pombe. At fission yeast silent mating-type loci, the Rix1 complex (RIXC) binds to the silent chromatin domain and the boundary and nuclear rim protein Amo1 interacts with RIXC at the silent chromatin boundary for the anchoring of silent mating-type loci at the nuclear periphery. They construct concentrated foci of Swi6 and the FACT components Spt16 and Pob3 for heterochromatin maintenance and inheritance. Centromeric regions are anchored to the nuclear periphery through Lem2/Nur1. The nucleoporin components Npp106 and Nup211 lead to the nuclear periphery anchoring and silent chromatin formation of centromeres and telomeres