Abstract
Epigenetic modifications can maintain or alter the inherent symmetry of the nucleosome. However, the mechanisms that deposit and/or propagate symmetry or asymmetry are not understood. Here we report that yeast Set1C/ COMPASS (complex of proteins associated with Set1) is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. Mutation of the dimer interface to make Set1C monomeric abolished H3K4me3 on most promoters. The most active promoters, particularly those involved in the oxidative phase of the yeast metabolic cycle, displayed H3K4me2, which is normally excluded from active promoters, and a subset of these also displayed H3K4me3. In wild-type yeast, deletion of the sole H3K4 demethylase, Jhd2, has no effect. However, in monomeric Set1C yeast, Jhd2 deletion increased H3K4me3 levels on the H3K4me2 promoters. Notably, the association of Set1C with the elongating polymerase was not perturbed by monomerization. These results imply that symmetrical H3K4 methylation is an embedded consequence of Set1C dimerism and that Jhd2 demethylates asymmetric H3K4me3. Consequently, rather than methylation and demethylation acting in opposition as logic would suggest, a dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. This presents a new paradigm for the establishment of epigenetic detail.
| Original language | English |
|---|---|
| Pages (from-to) | 550-564 |
| Number of pages | 15 |
| Journal | Genes & development |
| Volume | 33 |
| Issue number | 9-10 |
| DOIs | |
| Publication status | Published - 1 May 2019 |
| Externally published | Yes |
Keywords
- Chromatin
- Epigenetics
- Histone demethylation
- Histone methylation
- Promoter architecture
Cite this
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The set1 complex is dimeric and acts with jhd2 demethylation to convey symmetrical h3k4 trimethylation. / Choudhury, Rupam; Singh, Sukhdeep; Arumugam, Senthil; Roguev, Assen; Francis Stewart, A.
In: Genes & development, Vol. 33, No. 9-10, 01.05.2019, p. 550-564.Research output: Contribution to journal › Article › Research › peer-review
TY - JOUR
T1 - The set1 complex is dimeric and acts with jhd2 demethylation to convey symmetrical h3k4 trimethylation
AU - Choudhury, Rupam
AU - Singh, Sukhdeep
AU - Arumugam, Senthil
AU - Roguev, Assen
AU - Francis Stewart, A.
PY - 2019/5/1
Y1 - 2019/5/1
N2 - Epigenetic modifications can maintain or alter the inherent symmetry of the nucleosome. However, the mechanisms that deposit and/or propagate symmetry or asymmetry are not understood. Here we report that yeast Set1C/ COMPASS (complex of proteins associated with Set1) is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. Mutation of the dimer interface to make Set1C monomeric abolished H3K4me3 on most promoters. The most active promoters, particularly those involved in the oxidative phase of the yeast metabolic cycle, displayed H3K4me2, which is normally excluded from active promoters, and a subset of these also displayed H3K4me3. In wild-type yeast, deletion of the sole H3K4 demethylase, Jhd2, has no effect. However, in monomeric Set1C yeast, Jhd2 deletion increased H3K4me3 levels on the H3K4me2 promoters. Notably, the association of Set1C with the elongating polymerase was not perturbed by monomerization. These results imply that symmetrical H3K4 methylation is an embedded consequence of Set1C dimerism and that Jhd2 demethylates asymmetric H3K4me3. Consequently, rather than methylation and demethylation acting in opposition as logic would suggest, a dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. This presents a new paradigm for the establishment of epigenetic detail.
AB - Epigenetic modifications can maintain or alter the inherent symmetry of the nucleosome. However, the mechanisms that deposit and/or propagate symmetry or asymmetry are not understood. Here we report that yeast Set1C/ COMPASS (complex of proteins associated with Set1) is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. Mutation of the dimer interface to make Set1C monomeric abolished H3K4me3 on most promoters. The most active promoters, particularly those involved in the oxidative phase of the yeast metabolic cycle, displayed H3K4me2, which is normally excluded from active promoters, and a subset of these also displayed H3K4me3. In wild-type yeast, deletion of the sole H3K4 demethylase, Jhd2, has no effect. However, in monomeric Set1C yeast, Jhd2 deletion increased H3K4me3 levels on the H3K4me2 promoters. Notably, the association of Set1C with the elongating polymerase was not perturbed by monomerization. These results imply that symmetrical H3K4 methylation is an embedded consequence of Set1C dimerism and that Jhd2 demethylates asymmetric H3K4me3. Consequently, rather than methylation and demethylation acting in opposition as logic would suggest, a dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. This presents a new paradigm for the establishment of epigenetic detail.
KW - Chromatin
KW - Epigenetics
KW - Histone demethylation
KW - Histone methylation
KW - Promoter architecture
UR - http://www.scopus.com/inward/record.url?scp=85065532928&partnerID=8YFLogxK
U2 - 10.1101/gad.322222.118
DO - 10.1101/gad.322222.118
M3 - Article
C2 - 30842216
AN - SCOPUS:85065532928
VL - 33
SP - 550
EP - 564
JO - Genes and Development
JF - Genes and Development
SN - 0890-9369
IS - 9-10
ER -