Abstract
The SWR1 chromatin remodeling complex, which deposits the histone variant H2A.Z into nucleosomes, has been well characterized in yeast and animals, but its composition in plants has remained uncertain. We used the conserved SWR1 subunit ACTIN RELATED PROTEIN 6 (ARP6) as bait in tandem affinity purification experiments to isolate associated proteins from Arabidopsis thaliana. We identified all 11 subunits found in yeast SWR1 and the homologous mammalian SRCAP complexes, demonstrating that this complex is conserved in plants. We also identified several additional proteins not previously associated with SWR1, including Methyl-CpG-BINDING DOMAIN 9 (MBD9) and three members of the Alfin1-like protein family, all of which have been shown to bind modified histone tails. Since mbd9 mutant plants were phenotypically similar to arp6 mutants, we explored a potential role for MBD9 in H2A.Z deposition. We found that MBD9 is required for proper H2A.Z incorporation at thousands of discrete sites, which represent a subset of the genomic regions normally enriched with H2A.Z. We also discovered that MBD9 preferentially interacts with acetylated histone H4 peptides, as well as those carrying mono- or dimethylated H3 lysine 4, or dimethylated H3 arginine 2 or 8. Considering that MBD9-dependent H2A.Z sites show a distinct histone modification profile, we propose that MBD9 recognizes particular nucleosome modifications via its PHD- and Bromo-domains and thereby guides SWR1 to these sites for H2A.Z deposition. Our data establish the SWR1 complex as being conserved across eukaryotes and suggest that MBD9 may be involved in targeting the complex to specific genomic sites through nucleosomal interactions. The finding that MBD9 does not appear to be a core subunit of the Arabidopsis SWR1 complex, along with the synergistic phenotype of arp6;mbd9 double mutants, suggests that MBD9 also has important roles beyond H2A.Z deposition.
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Claims 10
Claim · model-written summary
The purified Arabidopsis complex contained all 11 subunits known from yeast SWR1 and mammalian SRCAP.
- Taxon
- Arabidopsis
Arabidopsist0 - Outcome
- all 11 subunitse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We identified all 11 subunits found in yeast SWR1 and the homologous mammalian SRCAP complexes”
t0“Arabidopsis genome”
Claim · model-written summary
The complex also contained MBD9 and three Alfin1-like family proteins.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- several additional proteins not previously associated with SWR1e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We also identified several additional proteins not previously associated with SWR1, including Methyl-CpG-BINDING DOMAIN 9 (MBD9) and three members of the Alfin1-like protein family”
t0“Arabidopsis genome”
Claim · model-written summary
mbd9 mutant plants resembled arp6 mutants phenotypically.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- phenotypically similare0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“mbd9 mutant plants were phenotypically similar to arp6 mutants”
t0“Arabidopsis genome”
Claim · model-written summary
MBD9 was needed for proper H2A.Z incorporation at thousands of discrete sites.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- MBD9e0
- Outcome
- proper H2A.Z incorporation at thousands of discrete sitese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“MBD9 is required for proper H2A.Z incorporation at thousands of discrete sites”
t0“Arabidopsis genome”
Claim · model-written summary
MBD9 preferentially interacted with acetylated H4 peptides and H3 peptides with specified methylation.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- MBD9e0
- Outcome
- preferentially interacts with acetylated histone H4 peptidese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“MBD9 preferentially interacts with acetylated histone H4 peptides, as well as those carrying mono- or dimethylated H3 lysine 4, or dimethylated H3 arginine 2 or 8”
t0“Arabidopsis genome”
Claim · model-written summary
MBD9-dependent H2A.Z sites had a distinct histone modification profile.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- distinct histone modification profilee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“MBD9-dependent H2A.Z sites show a distinct histone modification profile”
t0“Arabidopsis genome”
Claim · model-written summary
MBD9 is proposed to recognize nucleosome modifications and guide SWR1 to H2A.Z deposition sites.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- MBD9e0
- Outcome
- guides SWR1 to these sites for H2A.Z depositione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we propose that MBD9 recognizes particular nucleosome modifications via its PHD- and Bromo-domains and thereby guides SWR1 to these sites for H2A.Z deposition”
t0“Arabidopsis genome”
Claim · model-written summary
MBD9 did not appear to be a core Arabidopsis SWR1 subunit.
- Taxon
- ArabidopsisArabidopsise0
- Gene
- MBD9e0
- Outcome
- does not appear to be a core subunite0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“MBD9 does not appear to be a core subunit of the Arabidopsis SWR1 complex”
Claim · model-written summary
The arp6;mbd9 double mutant displayed a synergistic phenotype.
- Taxon
- ArabidopsisArabidopsist0
- Outcome
- synergistic phenotypee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“synergistic phenotype of arp6;mbd9 double mutants”
t0“Arabidopsis genome”
Claim · model-written summary
The authors infer that MBD9 also has roles beyond H2A.Z deposition.
- Taxon
- ArabidopsisArabidopsist0
- Gene
- MBD9e0
- Outcome
- important roles beyond H2A.Z depositione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“MBD9 also has important roles beyond H2A.Z deposition”
t0“Arabidopsis genome”