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Structural basis of paralog-specific KDM2A/B nucleosome recognition

ABSTRACT: The nucleosome acidic patch is a major interaction hub for chromatin, providing a platform for enzymes to dock and orient for nucleosome-targeted activities. In order to define the molecular basis of acidic patch recognition proteome-wide, we performed an amino acid resolution acidic patch interactome screen. We discovered that the histone H3 lysine 36 (H3K36) demethylase KDM2A, but not its closely related paralog, KDM2B, requires the acidic patch for nucleosome binding. These KDM2 family JumonjiC (JmjC) domain lysine demethylases are critical to heterochromatin formation and are commonly misregulated in cancer. Despite fundamental roles in transcriptional regulation in health and disease, the molecular mechanisms governing nucleosome substrate specificity of KDM2A/B, or any other JmjC lysine demethylases, remain unclear. We used a covalent JmjC inhibitor to solve cryo-EM structures of KDM2A and KDM2B trapped in action on the nucleosome. Our structures show that KDM2-nucleosome binding is paralog-specific and facilitated by dynamic nucleosomal DNA unwrapping and histone charge shielding that mobilize the H3K36 sequence for demethylation.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

SUBMITTER: Dennis Goldfarb

LAB HEAD: Robert McGiinty

PROVIDER: PXD032791 | Pride | 2023-02-14

REPOSITORIES: Pride

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			Action	DRS
	Human_sp_iso_2019-08-27_withContaminants_withMutantHistones.fasta	Fasta
	MC025_HEK293T_Nucleosomes_TMTpro_run1.mzML	Mzml
	MC025_HEK293T_Nucleosomes_TMTpro_run1.pin.percolator.decoy.mzid.gz	Mzid
	MC025_HEK293T_Nucleosomes_TMTpro_run1.pin.percolator.target.mzid.gz	Mzid
	MC025_HEK293T_Nucleosomes_TMTpro_run1.raw	Raw

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Project description:We have characterized two post-translational histone modifications in C. elegans on a genomic scale. Micrococcal nuclease digestion and immunoprecipitation were used to obtain distinct populations of single nucleosome cores, which were analyzed using massively parallel DNA sequencing to obtain positional and coverage maps. Two methylated histone H3 populations were chosen for comparison: H3K4 histone methylation (associated with active chromosomal regions) and H3K9 histone methylation (associated with inactivity). From analysis of the sequence data, we found nucleosome cores with these modifications to be enriched in two distinct partitions of the genome; H3K4 methylation was particularly prevalent in promoter regions of widely-expressed genes while H3K9 methylation was enriched on specific chromosomal arms. For each of the six chromosomes, the highest level of H3K9 methylation corresponds to the pairing center responsible for chromosome alignment during meiosis. H3K9 enrichment at pairing centers appears to be an early mark in meiotic chromosome sorting, occurring in the absence of components required for proper pairing of homologous chromosomes. H3K9 methylation shows an intricate pattern within the chromosome arms, with a particular anti-correlation to regions that display a strong ~10 bp periodicity of AA/TT dinucleotides that is known to associate with germline trancription. By contrast to the global features observed with H3K9 methylation, H3K4 methylation profiles were most striking in their local characteristics around promoters, providing a unique promoter-central landmark for 3903 C. elegans genes and allowing a precise analysis of nucleosome positioning in the context of transcriptional initiation. Keywords: epigenetics Examination of total nucleosome and nucleosomes with 2 different histone modifications in C. elegans. 5 samples are analyzed: 1. total mononucleosome core DNA from C. elegans wild type strain N2, 2. anti-H3K4me2/3 precipitated mononucleosome core DNA from C. elegans wild type strain N2, 3. anti-H3K9me3 precipitated mononucleosome core DNA from C. elegans wild type strain N2, 4. total mononucleosome core DNA from C. elegans mutant strain zim-2(tm-574), 5. anti-H3K9me3 precipitated mononucleosome core DNA from C. elegans mutant strain zim-2(tm-574)

Project description:Methylation of DNA at CpG dinucleotides represents one of the most important epigenetic mechanisms involved in the control of gene expression in vertebrate cells. In this report, we conducted high-throughput nucleosome reconstitution experiments on 572 KB of human DNA and 668 KB of mouse DNA that was unmethylated or methylated in order to investigate the effects of this epigenetic modification on the positioning and stability of nucleosomes. The DNA loci from both species contained the genes that encode the serum albumin family, the MYC protein, and the tumor suppressor p53. The results demonstrated that a small subset of nucleosomes positioned by nucleotide sequence was sensitive to methylation where the modification increased the affinity of these sequences for the histone octamer. The features that distinguished these nucleosomes from the bulk of the methylation-insensitive nucleosomes were an increase in the frequency of CpG dinucleotides and a unique rotational orientation of CpGs such that their minor grooves tended to face toward the histones in the nucleosome rather than away. We propose that these features serve to enhance the affinity of methylated DNA for the histone octamer and that this effect could be involved in gene regulatory mechanisms such as silencing. These methylation-sensitive nucleosomes were preferentially associated with exons as compared to introns while unmethylated CpG islands near transcription start sites became enriched in nucleosomes upon methylation. The results of this study suggest that the effects of DNA methylation on nucleosome stability in vitro can recapitulate what has been observed in the cell and provide a direct link between DNA methylation and the structure and function of chromatin. For the human data, there were 3 unmethylated nucleosome replicates, 2 methylated nucleosome replicates, an unmethylated MNase control, and an unmethylated sonicated control. For the mouse data, there were 2 unmethylated nucleosome replicates, 2 methylated nucleosome replicates, an unmethylated MNase control, a methylated MNase control, and an unmethylated sonicated control.

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Structural basis of paralog-specific KDM2A/B nucleosome recognition

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