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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 localization at euchromatic and heterochromatic targets is largely unaffected by certain domain deletions or H3K4me status.Enrichment of Set1 was determined by chromatin immunoprecipitation (ChIP) followed by quantitative PCR (qPCR) using primers targeting (A) the highly expressed actin gene (act1) promoter, (B) the 5′ end of Tf2 open reading frames, (C) the pericentromeric dg repeat of chromosome II (cen), (D) the silent mating type cenH (mat), and (E) the chromosome I subtelomeric prl70 (subtel). Mock denotes untagged wildtype Set1 strains. Percent enrichment of target amplification compared to input (whole cell extract) was calculated using the 2−ΔΔCt method following normalization by primers targeting mitochondrial DNA (see Materials and Methods). (s.d., error bars; n = 2 biological×2 qPCR replicates).
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pgen-1004740-g002: Set1 localization at euchromatic and heterochromatic targets is largely unaffected by certain domain deletions or H3K4me status.Enrichment of Set1 was determined by chromatin immunoprecipitation (ChIP) followed by quantitative PCR (qPCR) using primers targeting (A) the highly expressed actin gene (act1) promoter, (B) the 5′ end of Tf2 open reading frames, (C) the pericentromeric dg repeat of chromosome II (cen), (D) the silent mating type cenH (mat), and (E) the chromosome I subtelomeric prl70 (subtel). Mock denotes untagged wildtype Set1 strains. Percent enrichment of target amplification compared to input (whole cell extract) was calculated using the 2−ΔΔCt method following normalization by primers targeting mitochondrial DNA (see Materials and Methods). (s.d., error bars; n = 2 biological×2 qPCR replicates).

Mentions: We have previously shown that Set1 localizes at Tf2s[27]. Whether Set1 localizes at heterochromatic repeats is not known. We utilized chromatin immunoprecipitation (ChIP) to monitor Set1 enrichment at known euchromatin and heterochromatin targets in set1 mutant strains. In strains deficient in either the RRM1 or nSET domain, there was reduced Set1 enrichment at the housekeeping actin gene act1 and Tf2s (Figures 2A and 2B). Loss of the RRM2, SET domain or H3K4me function did not appear to hamper Set1 localization at these elements. Surprisingly, we detected Set1 localization at pericentromeric repeats (Figure 2C). Unlike the two examined euchromatic targets (i.e., act1 and Tf2s), Set1 localization at pericentromeric repeats was generally not affected in strains deficient in any one of the domains. We did not detect Set1 enrichment at the mat locus or subtelomeric repeats either in wildtype or domain mutants (Figures 2D and 2E). These results suggest that the absence of H3K4me does not adversely affect Set1 localization at certain euchromatic and heterochromatic targets and that H3K4me-dependent repression might not require stable interaction of Set1 with its target loci.


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 localization at euchromatic and heterochromatic targets is largely unaffected by certain domain deletions or H3K4me status.Enrichment of Set1 was determined by chromatin immunoprecipitation (ChIP) followed by quantitative PCR (qPCR) using primers targeting (A) the highly expressed actin gene (act1) promoter, (B) the 5′ end of Tf2 open reading frames, (C) the pericentromeric dg repeat of chromosome II (cen), (D) the silent mating type cenH (mat), and (E) the chromosome I subtelomeric prl70 (subtel). Mock denotes untagged wildtype Set1 strains. Percent enrichment of target amplification compared to input (whole cell extract) was calculated using the 2−ΔΔCt method following normalization by primers targeting mitochondrial DNA (see Materials and Methods). (s.d., error bars; n = 2 biological×2 qPCR replicates).
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4214589&req=5

pgen-1004740-g002: Set1 localization at euchromatic and heterochromatic targets is largely unaffected by certain domain deletions or H3K4me status.Enrichment of Set1 was determined by chromatin immunoprecipitation (ChIP) followed by quantitative PCR (qPCR) using primers targeting (A) the highly expressed actin gene (act1) promoter, (B) the 5′ end of Tf2 open reading frames, (C) the pericentromeric dg repeat of chromosome II (cen), (D) the silent mating type cenH (mat), and (E) the chromosome I subtelomeric prl70 (subtel). Mock denotes untagged wildtype Set1 strains. Percent enrichment of target amplification compared to input (whole cell extract) was calculated using the 2−ΔΔCt method following normalization by primers targeting mitochondrial DNA (see Materials and Methods). (s.d., error bars; n = 2 biological×2 qPCR replicates).
Mentions: We have previously shown that Set1 localizes at Tf2s[27]. Whether Set1 localizes at heterochromatic repeats is not known. We utilized chromatin immunoprecipitation (ChIP) to monitor Set1 enrichment at known euchromatin and heterochromatin targets in set1 mutant strains. In strains deficient in either the RRM1 or nSET domain, there was reduced Set1 enrichment at the housekeeping actin gene act1 and Tf2s (Figures 2A and 2B). Loss of the RRM2, SET domain or H3K4me function did not appear to hamper Set1 localization at these elements. Surprisingly, we detected Set1 localization at pericentromeric repeats (Figure 2C). Unlike the two examined euchromatic targets (i.e., act1 and Tf2s), Set1 localization at pericentromeric repeats was generally not affected in strains deficient in any one of the domains. We did not detect Set1 enrichment at the mat locus or subtelomeric repeats either in wildtype or domain mutants (Figures 2D and 2E). These results suggest that the absence of H3K4me does not adversely affect Set1 localization at certain euchromatic and heterochromatic targets and that H3K4me-dependent repression might not require stable interaction of Set1 with its target loci.

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