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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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Set1C and H3K4me are required for the integrity of Tf bodies.(A, B) Declustering of Tf2s in (A) set1 mutant with defects in H3K4me and (B) Set1C mutants. Fluorescence in situ hybridization (FISH) analysis was performed using a FISH probe corresponding to the ∼3.6 kb coding region of Tf2 elements. Representative FISH images from indicated strains (top panels). Quantitative FISH analysis of observed Tf2 foci/cell in indicated strains (bar graph; bottom panels). Number of cells analyzed per strain (n). Except for sdc1Δ, Tf2 declustering in all mutant strains compared to WT was significant (p<0.005, chi-square test).
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pgen-1004740-g005: Set1C and H3K4me are required for the integrity of Tf bodies.(A, B) Declustering of Tf2s in (A) set1 mutant with defects in H3K4me and (B) Set1C mutants. Fluorescence in situ hybridization (FISH) analysis was performed using a FISH probe corresponding to the ∼3.6 kb coding region of Tf2 elements. Representative FISH images from indicated strains (top panels). Quantitative FISH analysis of observed Tf2 foci/cell in indicated strains (bar graph; bottom panels). Number of cells analyzed per strain (n). Except for sdc1Δ, Tf2 declustering in all mutant strains compared to WT was significant (p<0.005, chi-square test).

Mentions: We have previously identified a novel role for Set1 in the nuclear organization of Tf2s into Tf bodies [27]. To dissect potential mechanisms underlying Set1-mediated clustering of Tf2s, we performed fluorescence in situ hybridization (FISH) analysis to monitor the status of Tf bodies in various set1 mutants. In contrast to wildtype cells with intact Tf bodies, set1 mutants lacking the RRM1, nSET, SET or pSET domain exhibited defects in Tf bodies to the same extent as set1Δ (Figure 5A). Because H3K4me is severely compromised in these set1 mutants (see Figure 1B and. S1), H3K4me might be required to maintain the integrity of Tf bodies. Indeed, Tf2 elements were observed to decluster in the set1FH3K4me- cells which lack H3K4me altogether. In the set1 mutant containing the RRM2 deletion, which resulted in intermediately increased levels of Tf2 expression (see Figure 1C), the integrity of Tf bodies was modestly affected. These results suggest that Set1 relies on disparate domains and possibly different catalytic activities (see discussion below) to exert control over different aspects of Tf2 regulation.


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)

Set1C and H3K4me are required for the integrity of Tf bodies.(A, B) Declustering of Tf2s in (A) set1 mutant with defects in H3K4me and (B) Set1C mutants. Fluorescence in situ hybridization (FISH) analysis was performed using a FISH probe corresponding to the ∼3.6 kb coding region of Tf2 elements. Representative FISH images from indicated strains (top panels). Quantitative FISH analysis of observed Tf2 foci/cell in indicated strains (bar graph; bottom panels). Number of cells analyzed per strain (n). Except for sdc1Δ, Tf2 declustering in all mutant strains compared to WT was significant (p<0.005, chi-square test).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4214589&req=5

pgen-1004740-g005: Set1C and H3K4me are required for the integrity of Tf bodies.(A, B) Declustering of Tf2s in (A) set1 mutant with defects in H3K4me and (B) Set1C mutants. Fluorescence in situ hybridization (FISH) analysis was performed using a FISH probe corresponding to the ∼3.6 kb coding region of Tf2 elements. Representative FISH images from indicated strains (top panels). Quantitative FISH analysis of observed Tf2 foci/cell in indicated strains (bar graph; bottom panels). Number of cells analyzed per strain (n). Except for sdc1Δ, Tf2 declustering in all mutant strains compared to WT was significant (p<0.005, chi-square test).
Mentions: We have previously identified a novel role for Set1 in the nuclear organization of Tf2s into Tf bodies [27]. To dissect potential mechanisms underlying Set1-mediated clustering of Tf2s, we performed fluorescence in situ hybridization (FISH) analysis to monitor the status of Tf bodies in various set1 mutants. In contrast to wildtype cells with intact Tf bodies, set1 mutants lacking the RRM1, nSET, SET or pSET domain exhibited defects in Tf bodies to the same extent as set1Δ (Figure 5A). Because H3K4me is severely compromised in these set1 mutants (see Figure 1B and. S1), H3K4me might be required to maintain the integrity of Tf bodies. Indeed, Tf2 elements were observed to decluster in the set1FH3K4me- cells which lack H3K4me altogether. In the set1 mutant containing the RRM2 deletion, which resulted in intermediately increased levels of Tf2 expression (see Figure 1C), the integrity of Tf bodies was modestly affected. These results suggest that Set1 relies on disparate domains and possibly different catalytic activities (see discussion below) to exert control over different aspects of Tf2 regulation.

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
Related in: MedlinePlus