The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation.
Plant homeodomain (PHD) fingers are often present in chromatin-binding proteins and have been shown to bind histone H3 N-terminal tails. Mutations in the autoimmune regulator (AIRE) protein, which harbors two PHD fingers, cause a rare monogenic disease, autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED).
AIRE activates the expression of tissue-specific antigens by directly binding through its first PHD finger (AIRE-PHD1) to histone H3 tails non-methylated at K4 (H3K4me0).
Here, we present the solution structure of AIRE-PHD1 in complex with H3K4me0 peptide and show that AIRE-PHD1 is a highly specialized non-modified histone H3 tail reader, as post-translational modifications of the first 10 histone H3 residues reduce binding affinity.
In particular, H3R2 dimethylation abrogates AIRE-PHD1 binding in vitro and reduces the in vivo activation of AIRE target genes in HEK293 cells.
The observed antagonism by R2 methylation on AIRE-PHD1 binding is unique among the H3K4me0 histone readers and represents the first case of epigenetic negative cross-talk between non-methylated H3K4 and methylated H3R2. Collectively, our results point to a very specific histone code responsible for non-modified H3 tail recognition by AIRE-PHD1 and describe at atomic level one crucial step in the molecular mechanism responsible for antigen expression in the thymus.
Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation.
Modifications on histones control important biological processes through their effects on chromatin structure. Methylation at lysine 4 on histone H3 (H3K4) is found at the 5′ end of active genes and contributes to transcriptional activation by recruiting chromatin-remodeling enzymes.
An adjacent arginine residue (H3R2) is also known to be asymmetrically dimethylated (H3R2me2a) in mammalian cells, but its location within genes and its function in transcription are unknown.
Here we show that H3R2 is also methylated in budding yeast (Saccharomyces cerevisiae), and by using an antibody specific for H3R2me2a in a chromatin immunoprecipitation-on-chip analysis we determine the distribution of this modification on the entire yeast genome.
We find that H3R2me2a is enriched throughout all heterochromatic loci and inactive euchromatic genes and is present at the 3′ end of moderately transcribed genes.
In all cases the pattern of H3R2 methylation is mutually exclusive with the trimethyl form of H3K4 (H3K4me3). We show that methylation at H3R2 abrogates the trimethylation of H3K4 by the Set1 methyltransferase.
The specific effect on H3K4me3 results from the occlusion of Spp1, a Set1 methyltransferase subunit necessary for trimethylation.
Thus, the inability of Spp1 to recognize H3 methylated at R2 prevents Set1 from trimethylating H3K4. These results provide the first mechanistic insight into the function of arginine methylation on chromatin.
Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive.
Eukaryotic genomes are organized into active (euchromatic) and inactive (heterochromatic) chromatin domains. Post-translational modifications of histones (or ‘marks’) are key in defining these functional states, particularly in promoter regions.
Mutual regulatory interactions between these marks–and the enzymes that catalyse them–contribute to the shaping of this epigenetic landscape, in a manner that remains to be fully elucidated.
We previously observed that asymmetric di-methylation of histone H3 arginine 2 (H3R2me2a) counter-correlates with di- and tri- methylation of H3 lysine 4 (H3K4me2, H3K4me3) on human promoters.
Here we show that the arginine methyltransferase PRMT6 catalyses H3R2 di-methylation in vitro and controls global levels of H3R2me2a in vivo.
H3R2 methylation by PRMT6 was prevented by the presence of H3K4me3 on the H3 tail.
Conversely, the H3R2me2a mark prevented methylation of H3K4 as well as binding to the H3 tail by an ASH2/WDR5/MLL-family methyltransferase complex.
Chromatin immunoprecipitation showed that H3R2me2a was distributed within the body and at the 3′ end of human genes, regardless of their transcriptional state, whereas it was selectively and locally depleted from active promoters, coincident with the presence of H3K4me3.
Hence, the mutual antagonism between H3R2 and H3K4 methylation, together with the association of MLL-family complexes with the basal transcription machinery, may contribute to the localized patterns of H3K4 tri-methylation characteristic of transcriptionally poised or active promoters in mammalian genomes.
Genomic Location of PRMT6-Dependent H3R2 Methylation Is Linked to the Transcriptional Outcome of Associated Genes.
Protein arginine methyltransferase 6 (PRMT6) catalyzes asymmetric dimethylation of histone H3 at arginine 2 (H3R2me2a).
This mark has been reported to associate with silent genes.
Here, we use a cell model of neural differentiation, which upon PRMT6 knockout exhibits proliferation and differentiation defects.
Strikingly, we detect PRMT6-dependent H3R2me2a at active genes, both at promoter and enhancer sites.
Loss of H3R2me2a from promoter sites leads to enhanced KMT2A binding and H3K4me3 deposition together with increased target gene transcription, supporting a repressive nature of H3R2me2a.
At enhancers, H3R2me2a peaks co-localize with the active enhancer marks H3K4me1 and H3K27ac. Here, loss of H3R2me2a results in reduced KMT2D binding and H3K4me1/H3K27ac deposition together with decreased transcription of associated genes, indicating that H3R2me2a also exerts activation functions.
Our work suggests that PRMT6 via H3R2me2a interferes with the deposition of adjacent histone marks and modulates the activity of important differentiation-associated genes by opposing transcriptional effects.
The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation.
Plant homeodomain (PHD) fingers are often present in chromatin-binding proteins and have been shown to bind histone H3 N-terminal tails.
Mutations in the autoimmune regulator (AIRE) protein, which harbors two PHD fingers, cause a rare monogenic disease, autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED).
AIRE activates the expression of tissue-specific antigens by directly binding through its first PHD finger (AIRE-PHD1) to histone H3 tails non-methylated at K4 (H3K4me0).
Here, we present the solution structure of AIRE-PHD1 in complex with H3K4me0 peptide and show that AIRE-PHD1 is a highly specialized non-modified histone H3 tail reader, as post-translational modifications of the first 10 histone H3 residues reduce binding affinity. In particular, H3R2 dimethylation abrogates AIRE-PHD1 binding in vitro and reduces the in vivo activation of AIRE target genes in HEK293 cells.
The observed antagonism by R2 methylation on AIRE-PHD1 binding is unique among the H3K4me0 histone readers and represents the first case of epigenetic negative cross-talk between non-methylated H3K4 and methylated H3R2.
Collectively, our results point to a very specific histone code responsible for non-modified H3 tail recognition by AIRE-PHD1 and describe at atomic level one crucial step in the molecular mechanism responsible for antigen expression in the thymus.
Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation.
Modifications on histones control important biological processes through their effects on chromatin structure. Methylation at lysine 4 on histone H3 (H3K4) is found at the 5′ end of active genes and contributes to transcriptional activation by recruiting chromatin-remodeling enzymes.
An adjacent arginine residue (H3R2) is also known to be asymmetrically dimethylated (H3R2me2a) in mammalian cells, but its location within genes and its function in transcription are unknown.
Here we show that H3R2 is also methylated in budding yeast (Saccharomyces cerevisiae), and by using an antibody specific for H3R2me2a in a chromatin immunoprecipitation-on-chip analysis we determine the distribution of this modification on the entire yeast genome.
We find that H3R2me2a is enriched throughout all heterochromatic loci and inactive euchromatic genes and is present at the 3′ end of moderately transcribed genes.
Histone H3R2 Methylation Antibody Panel Pack |
|||
| C10015-1 | EpiGentek | 3 x 25 ul | 470.8 EUR |
Histone H3R2 Methylation Antibody Panel Pack |
|||
| C10015 | EpiGentek |
|
|
Histone H3R2 Monomethyl (H3R2me1) Polyclonal Antibody |
|||
| A-3713-050 | EpiGentek | 50 ul | 299.2 EUR |
Histone H3R2 Monomethyl (H3R2me1) Polyclonal Antibody |
|||
| A-3713-100 | EpiGentek | 100 ul | 470.8 EUR |
Histone H3R2 Monomethyl (H3R2me1) Polyclonal Antibody |
|||
| A-3713 | EpiGentek |
|
|
Histone H3R2 Dimethyl Symmetric (H3R2me2s) Polyclonal Antibody |
|||
| A-3705-050 | EpiGentek | 50 ul | 299.2 EUR |
Histone H3R2 Dimethyl Symmetric (H3R2me2s) Polyclonal Antibody |
|||
| A-3705-100 | EpiGentek | 100 ul | 470.8 EUR |
Histone H3R2 Dimethyl Asymmetric (H3R2me2a) Polyclonal Antibody |
|||
| A-3714-050 | EpiGentek | 50 ul | 299.2 EUR |
Histone H3R2 Dimethyl Asymmetric (H3R2me2a) Polyclonal Antibody |
|||
| A-3714-100 | EpiGentek | 100 ul | 470.8 EUR |
Histone H3R2 Dimethyl Symmetric (H3R2me2s) Polyclonal Antibody |
|||
| A-3705 | EpiGentek |
|
|
Histone H3R2 Dimethyl Asymmetric (H3R2me2a) Polyclonal Antibody |
|||
| A-3714 | EpiGentek |
|
|
Histone H3K4 Methylation Antibody Panel Pack |
|||
| C10005-1 | EpiGentek | 3 x 25 ul | 470.8 EUR |
Histone H3K9 Methylation Antibody Panel Pack |
|||
| C10006-1 | EpiGentek | 3 x 25 ul | 470.8 EUR |
Histone H3K27 Methylation Antibody Panel Pack |
|||
| C10007-1 | EpiGentek | 3 x 25 ul | 470.8 EUR |
Histone H3K36 Methylation Antibody Panel Pack |
|||
| C10008-1 | EpiGentek | 3 x 25 ul | 470.8 EUR |
Histone H3K79 Methylation Antibody Panel Pack |
|||
| C10009-1 | EpiGentek | 3 x 25 ul | 470.8 EUR |
Histone H4K20 Methylation Antibody Panel Pack |
|||
| C10012-1 | EpiGentek | 3 x 25 ul | 470.8 EUR |
Histone H3R8 Methylation Antibody Panel Pack |
|||
| C10016-1 | EpiGentek | 3 x 25 ul | 470.8 EUR |
In all cases the pattern of H3R2 methylation is mutually exclusive with the trimethyl form of H3K4 (H3K4me3). We show that methylation at H3R2 abrogates the trimethylation of H3K4 by the Set1 methyltransferase.
The specific effect on H3K4me3 results from the occlusion of Spp1, a Set1 methyltransferase subunit necessary for trimethylation.
Thus, the inability of Spp1 to recognize H3 methylated at R2 prevents Set1 from trimethylating H3K4. These results provide the first mechanistic insight into the function of arginine methylation on chromatin.