id: PW:0001340 rgd_url: https://rgd.mcw.edu/rgdweb/pathway/pathwayRecord.html?processType=view&species=Rat&acc_id=PW:0001340 title: dna modification pathway description: 'Epigenetic changes, the modification and remodeling of chromatin, play a key role in the differential expression of genes. Chromatin modification and remodeling directly affect the relative relaxation or compaction of chromatin and thus, the extent to which DNA replication, transcription, damage response and repair, associated RNA processing and splicing are promoted or are silenced, respectively. The basic unit of chromatin is the nucleosome - it consists of 145-147 base pairs of DNA wrapped around an octameric structure formed by core histones. Repeating nucleosomes assemble into higher-order structures stabilized by a linker histone. Chromatin modification involves the methylation of cytosine residues in DNA and the many ways in which the histone residues are modified. Histone modifications mostly targets the histone tails which extend from the core fold of the nucleosome and thus, are accessible for modifications and interactions. The modification pathways bring together the enzymes that catalyze the modification and those that catalyze its removal or change, known as ''writer'' and ''erasers'', respectively, the proteins whose particular domains recognize the modification, known as the ''readers'' and the various other interactors or regulators. The remodeling of chromatin involves the ATP-dependent eviction, sliding, deposition or exchange of entire nucleosomes. It is carried out by four protein complexes representing four remodeling pathways with distinct functions. The replication-dependent and independent assembly of nucleosomes is mediated by histone chaperone proteins. Epigenetic changes are heritable and independent of DNA sequence. However, DNA sequence variation can affect the function of players involved and thus, of epigenetic outcomes. An intimate dialog exists between the pathways of chromatin modification and remodeling to finely tune the epigenetic responses. The interaction of chromatin modifying enzymes and readers with non-coding RNA, particularly long non-coding RNA (lncRNA), further modulates the epigenetic landscape and the outcomes of regulated gene expression. Chromatin modifying enzymes and readers are target of drug development, primarily for cancer treatment. Several members are also found mutated in a number of human cancers. The DNA modification pathway is presented here. DNA methylation occurs within CpG genomic dinucletodies and is found on up to 80% of the genome. However, non-methylated regions, known as CpG islands (CGI) are found in ~70-80% of vertebrate promoters. DNA methylation controls the X-chromosome inactivation and the expression of imprinted genes which are important regulators of development, among others. It generally represses gene expression and serves as an important marker that influences not only chromatin changes, remodeling and transcription but also splicing. Three DNA methyltransferase (DNMTs) carry out the reaction; DNMT1 is considered a maintenance methyltransferase and the other two mostly function as de novo methyltransferases. DNMT1 is responsible for reinstating the methylation pattern to daughter strand during replication. S-adenosylmethionine (SAM) intermediate generated in the methionine cycle metabolic pathway is the methyl donor and the product of the reaction is 5-methylcytosine (5mC). The methylated cytosines are recognized by methyl binding proteins (MBPs) or factors which can then recruit other chromatin modifiers, modelers and regulators. The methyl binding proteins can be classified into three structural families: methyl-CpG binding domain (MBD), the zinc finger family and the SET and RING finger-associated (SRA) family. Of these, MBD1, 2 and 4 and MeCP2 are members of MBD family, Zbtb33 known as Kaiso, Zbtb4, Zbtb38 and Zfp57 are members of the zinc family and Uhrf1 and 2 are members of SRA family. The are no known demethylase enzymes that directly act upon 5mC. 5mC can be converted to 5-hydroxymethylcytosine (5hmC) which can be further oxidized to 5-formylcytosine (5fC) and 5-carboxycytosine (5caC) by the members of ten-eleven translocation (TET) family. The proteins are 2-oxoglutarate and Fe(II)-dependent dioxygenases. Of the three TET proteins, Tet2 and 3 are ubiquitously expressed; the expression of Tet 1 is confined to embryonic cells. Some of the 5mC intermediates interact with members of the MBPs protein families and they can be more than just posts along the demethylation route. 5hmC for instance, has been shown to have both transcriptional activation and silencing roles. There are no known enzymes catalyzing the removal of formyl or carbonyl groups from 5fC or5caC, but they may be substrates for glycosylases and subsequent targeting by the base excision repair (BER) pathway. Tet enzymes are partners for proteins with roles in shaping the state of chromatin and the regulation of gene expression, modulating but also extending the function of Tet proteins beyond 5mC modification. There is a complex interplay between DNA methylation and histone modification, particularly histone lysine methylation. Proteins that bind methylated CpG interact with histones and histone modifying enzymes. In addition, proteins with the ZF-CxxC (cysteine-rich zinc finger-CxxC) domain, bind non-methylated CpG to modulate histone methylation. ZF-CxxC members group together histone and DNA modifying enzymes, components of modifying complexes such as COMPASS. The DNA methylation pathway is frequently altered in several conditions, including cancer. Hypermethylation of tumor suppressor and hypomethylation of oncogene gene promoters have been reported. To link to the Ontology Report for annotations, GViewer and download, click here' diagram_image: https://rgd.mcw.edu/pathway/PW0001340/DNA%20modification%20pathway/pwmap.png pathway_studio_file: https://rgd.mcw.edu/pathway/PW0001340/DNA%20modification%20pathway/DNA%20modification%20pathway.gpp diagram_pathway_links: - id: PW:0000129 label: base excision repair pathway - id: PW:0001338 label: histone modification pathway - id: PW:0001339 label: chromatin remodeling pathway diagram_gene_links: - id: RGD:620979 label: Dnmt1 - id: RGD:1303336 label: Dnmt3a - id: RGD:1303274 label: Dnmt3b diagram_chemicals: - id: CHEBI:16040 label: cytosine - id: CHEBI:15414 label: S-adenosylmethionine diagram_edges: - source: 5-carboxylcytosine relation: associated_with target: MBP proteins - source: 5-hydroxymethylcytosine relation: associated_with target: MBP proteins - source: 5-hydroxymethylcytosine relation: positively_affects target: 5-carboxylcytosine - source: 5-hydroxymethylcytosine relation: positively_affects target: 5-formylcytosine - source: 5-hydroxymethylcytosine relation: positively_affects target: gene expression - source: 5-methylcytosine relation: associated_with target: MBP proteins - source: 5-methylcytosine relation: positively_affects target: 5-hydroxymethylcytosine - source: 5-methylcytosine relation: positively_affects target: gene expression - source: S-adenosylmethionine relation: positively_affects target: 5-methylcytosine - source: TET interacting partners relation: associated_with target: TET proteins - source: cytosine relation: associated_with target: non-methylated CpG readers - source: cytosine relation: positively_affects target: 5-methylcytosine - source: cytosine relation: positively_affects target: gene expression diagram_labels: - gene expression diagram_other_links: - href: /wg/home/pathway2/molecular-pathways2/mbps label: MBP proteins - href: /wg/home/pathway2/molecular-pathways2/non-methylated-cpg-readers label: non-methylated CpG readers - href: /wg/home/pathway2/molecular-pathways2/tet-interacting-partners label: TET interacting partners - href: /wg/home/pathway2/molecular-pathways2/tet-proteins label: TET proteins - href: http://www.rcsb.org/pdb/explore/explore.do?structureId=4GJU label: 5-methylcytosine - href: http://www.rcsb.org/pdb/explore/explore.do?structureId=5D9Y label: 5-formylcytosine - href: http://www.rcsb.org/pdb/explore/explore.do?structureId=5DEU label: 5-hydroxymethylcytosine - href: http://www.rcsb.org/pdb/explore/explore.do?structureId=5EXH label: 5-carboxylcytosine references: - id: RGD:8695943 citation: 'Dawson MA and Kouzarides T, Cell. 2012 Jul 6;150(1):12-27. doi: 10.1016/j.cell.2012.06.013.' - id: RGD:8695944 citation: 'Delatte B, etal., EMBO J. 2014 Jun 2;33(11):1198-211. doi: 10.15252/embj.201488290. 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