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Multifaceted genome control by Set1 Dependent and Independent of H3K4 methylation and the Set1C/COMPASS complex.

Mikheyeva IV, Grady PJ, Tamburini FB, Lorenz DR, Cam HP - PLoS Genet. (2014)

Bottom Line: Here, we show that the fission yeast Schizosaccharomyces pombe Set1 utilizes distinct domain modules to regulate disparate classes of repetitive elements associated with euchromatin and heterochromatin via H3K4me-dependent and -independent pathways.Intriguingly, we uncover a genome organization role for Set1C and H3K4me in mediating the clustering of Tf2s into Tf bodies by antagonizing the acetyltransferase Mst1-mediated H3K4 acetylation.Our study provides unexpected insights into the regulatory intricacies of a highly conserved chromatin-modifying complex with diverse roles in genome control.

View Article: PubMed Central - PubMed

Affiliation: Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America.

ABSTRACT
Histone modifiers are critical regulators of chromatin-based processes in eukaryotes. The histone methyltransferase Set1, a component of the Set1C/COMPASS complex, catalyzes the methylation at lysine 4 of histone H3 (H3K4me), a hallmark of euchromatin. Here, we show that the fission yeast Schizosaccharomyces pombe Set1 utilizes distinct domain modules to regulate disparate classes of repetitive elements associated with euchromatin and heterochromatin via H3K4me-dependent and -independent pathways. Set1 employs its RNA-binding RRM2 and catalytic SET domains to repress Tf2 retrotransposons and pericentromeric repeats while relying on its H3K4me function to maintain transcriptional repression at the silent mating type (mat) locus and subtelomeric regions. These repressive functions of Set1 correlate with the requirement of Set1C components to maintain repression at the mat locus and subtelomeres while dispensing Set1C in repressing Tf2s and pericentromeric repeats. We show that the contributions of several Set1C subunits to the states of H3K4me diverge considerably from those of Saccharomyces cerevisiae orthologs. Moreover, unlike S. cerevisiae, the regulation of Set1 protein level is not coupled to the status of H3K4me or histone H2B ubiquitination by the HULC complex. Intriguingly, we uncover a genome organization role for Set1C and H3K4me in mediating the clustering of Tf2s into Tf bodies by antagonizing the acetyltransferase Mst1-mediated H3K4 acetylation. Our study provides unexpected insights into the regulatory intricacies of a highly conserved chromatin-modifying complex with diverse roles in genome control.

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Set1 represses Tf2s and heterochromatic loci dependent and independent of Set1C subunits.(A) Set1C components contribute differently to H3K4me. H3K4me1, H3K4me2, and H3K4me3 were analyzed from histone extracts of indicated Set1C mutant strains by western blotting. (B) Set1-mediated repression of Tf2s is little affected in other Set1C mutant strains. (C–E) Set1 represses heterochromatic loci dependent and independent of Set1C. qRT-PCR was performed as in Figure 1 (s.d., error bars; n = 3). Pericentromeric repeat dg (cen), silent mating type cenH (mat), subtelomeric prl70 (subtel).
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pgen-1004740-g003: Set1 represses Tf2s and heterochromatic loci dependent and independent of Set1C subunits.(A) Set1C components contribute differently to H3K4me. H3K4me1, H3K4me2, and H3K4me3 were analyzed from histone extracts of indicated Set1C mutant strains by western blotting. (B) Set1-mediated repression of Tf2s is little affected in other Set1C mutant strains. (C–E) Set1 represses heterochromatic loci dependent and independent of Set1C. qRT-PCR was performed as in Figure 1 (s.d., error bars; n = 3). Pericentromeric repeat dg (cen), silent mating type cenH (mat), subtelomeric prl70 (subtel).

Mentions: The contribution of individual Set1C subunits to H3K4me has been well characterized in S. cerevisiae[8], [9], [10], [38], [39], [40], [41]. However, aside from H3K4me2 [24], the roles of Set1C subunits in S. pombe in H3K4 methylation are not well explored. We therefore assessed the status of H3K4me in cells deficient for individual Set1C components. Cells deficient for set1, swd1 or swd3 exhibit a complete loss of H3K4me (Figures 3A and S3), similar to results observed in S. cerevisiae mutant orthologs [41]. spp1 (spf1) is essential for all three forms of H3K4me in S. pombe. In contrast, the loss of S. cerevisiae SPP1 only diminishes [9], [31] or abolishes H3K4me3 [8]. Loss of swd2, which is lethal in S. cerevisiae[42], abolished H3K4me3 and diminished the levels of H3K4me2 and H3K4me1 in S. pombe. Cells lacking ash2 exhibited relatively intact levels of H3K4me2 and H3K4me1. Although H3K4me3 was detectable within individual cells in the ash2 mutant (Figure S4), we were unable to detect H3K4me3 at bulk histone levels (Figure 3A). In the sdc1 mutant, only H3K4me3 level was slightly diminished, while H3K4me2 and H3K4me1 levels were largely unaffected. These results differ from budding yeast findings, in which loss of ASH2 or SDC1 reduced all three states of H3K4me [9], [10] or completely abolished H3K4me2 [40]. All three forms of H3K4me appeared to be intact in cells deficient for shg1. Collectively, our results show that several components of S. pombe Set1C make different contributions to H3K4me compared to their orthologs in S. cerevisiae.


Multifaceted genome control by Set1 Dependent and Independent of H3K4 methylation and the Set1C/COMPASS complex.

Mikheyeva IV, Grady PJ, Tamburini FB, Lorenz DR, Cam HP - PLoS Genet. (2014)

Set1 represses Tf2s and heterochromatic loci dependent and independent of Set1C subunits.(A) Set1C components contribute differently to H3K4me. H3K4me1, H3K4me2, and H3K4me3 were analyzed from histone extracts of indicated Set1C mutant strains by western blotting. (B) Set1-mediated repression of Tf2s is little affected in other Set1C mutant strains. (C–E) Set1 represses heterochromatic loci dependent and independent of Set1C. qRT-PCR was performed as in Figure 1 (s.d., error bars; n = 3). Pericentromeric repeat dg (cen), silent mating type cenH (mat), subtelomeric prl70 (subtel).
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pgen-1004740-g003: Set1 represses Tf2s and heterochromatic loci dependent and independent of Set1C subunits.(A) Set1C components contribute differently to H3K4me. H3K4me1, H3K4me2, and H3K4me3 were analyzed from histone extracts of indicated Set1C mutant strains by western blotting. (B) Set1-mediated repression of Tf2s is little affected in other Set1C mutant strains. (C–E) Set1 represses heterochromatic loci dependent and independent of Set1C. qRT-PCR was performed as in Figure 1 (s.d., error bars; n = 3). Pericentromeric repeat dg (cen), silent mating type cenH (mat), subtelomeric prl70 (subtel).
Mentions: The contribution of individual Set1C subunits to H3K4me has been well characterized in S. cerevisiae[8], [9], [10], [38], [39], [40], [41]. However, aside from H3K4me2 [24], the roles of Set1C subunits in S. pombe in H3K4 methylation are not well explored. We therefore assessed the status of H3K4me in cells deficient for individual Set1C components. Cells deficient for set1, swd1 or swd3 exhibit a complete loss of H3K4me (Figures 3A and S3), similar to results observed in S. cerevisiae mutant orthologs [41]. spp1 (spf1) is essential for all three forms of H3K4me in S. pombe. In contrast, the loss of S. cerevisiae SPP1 only diminishes [9], [31] or abolishes H3K4me3 [8]. Loss of swd2, which is lethal in S. cerevisiae[42], abolished H3K4me3 and diminished the levels of H3K4me2 and H3K4me1 in S. pombe. Cells lacking ash2 exhibited relatively intact levels of H3K4me2 and H3K4me1. Although H3K4me3 was detectable within individual cells in the ash2 mutant (Figure S4), we were unable to detect H3K4me3 at bulk histone levels (Figure 3A). In the sdc1 mutant, only H3K4me3 level was slightly diminished, while H3K4me2 and H3K4me1 levels were largely unaffected. These results differ from budding yeast findings, in which loss of ASH2 or SDC1 reduced all three states of H3K4me [9], [10] or completely abolished H3K4me2 [40]. All three forms of H3K4me appeared to be intact in cells deficient for shg1. Collectively, our results show that several components of S. pombe Set1C make different contributions to H3K4me compared to their orthologs in S. cerevisiae.

Bottom Line: Here, we show that the fission yeast Schizosaccharomyces pombe Set1 utilizes distinct domain modules to regulate disparate classes of repetitive elements associated with euchromatin and heterochromatin via H3K4me-dependent and -independent pathways.Intriguingly, we uncover a genome organization role for Set1C and H3K4me in mediating the clustering of Tf2s into Tf bodies by antagonizing the acetyltransferase Mst1-mediated H3K4 acetylation.Our study provides unexpected insights into the regulatory intricacies of a highly conserved chromatin-modifying complex with diverse roles in genome control.

View Article: PubMed Central - PubMed

Affiliation: Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America.

ABSTRACT
Histone modifiers are critical regulators of chromatin-based processes in eukaryotes. The histone methyltransferase Set1, a component of the Set1C/COMPASS complex, catalyzes the methylation at lysine 4 of histone H3 (H3K4me), a hallmark of euchromatin. Here, we show that the fission yeast Schizosaccharomyces pombe Set1 utilizes distinct domain modules to regulate disparate classes of repetitive elements associated with euchromatin and heterochromatin via H3K4me-dependent and -independent pathways. Set1 employs its RNA-binding RRM2 and catalytic SET domains to repress Tf2 retrotransposons and pericentromeric repeats while relying on its H3K4me function to maintain transcriptional repression at the silent mating type (mat) locus and subtelomeric regions. These repressive functions of Set1 correlate with the requirement of Set1C components to maintain repression at the mat locus and subtelomeres while dispensing Set1C in repressing Tf2s and pericentromeric repeats. We show that the contributions of several Set1C subunits to the states of H3K4me diverge considerably from those of Saccharomyces cerevisiae orthologs. Moreover, unlike S. cerevisiae, the regulation of Set1 protein level is not coupled to the status of H3K4me or histone H2B ubiquitination by the HULC complex. Intriguingly, we uncover a genome organization role for Set1C and H3K4me in mediating the clustering of Tf2s into Tf bodies by antagonizing the acetyltransferase Mst1-mediated H3K4 acetylation. Our study provides unexpected insights into the regulatory intricacies of a highly conserved chromatin-modifying complex with diverse roles in genome control.

Show MeSH