DNA MODIFICATION PATHWAY (PW:0001340)

View Ontology Report

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 ar

Pathway Diagram:

Elsevier Inc. 5-methylcytosine cytosine 5-formylcytosine 5-carboxylcytosine 5-hydroxymethylcytosine S-adenosylmethionine histone modification pathway chromatin remodeling pathway Dnmt3b Dnmt3a cytosine ---> 5-methylcytosine S-adenosylmethionine ---> 5-methylcytosine gene expression cytosine ---- non-methylated CpG readers 5-methylcytosine ---> 5-hydroxymethylcytosine 5-hydroxymethylcytosine ---> 5-carboxylcytosine 5-hydroxymethylcytosine ---> 5-formylcytosine 5-methylcytosine ---- MBP proteins 5-hydroxymethylcytosine ---- MBP proteins TET interacting partners ---- TET proteins Dnmt1 TET interacting partners TET proteins MBP proteins cytosine ---> gene expression 5-hydroxymethylcytosine ---> gene expression 5-methylcytosine ---> gene expression non-methylated CpG readers base excision repair pathway 5-carboxylcytosine ---- MBP proteins
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Genes in Pathway:

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DNA modification pathway term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Cxxc1 CXXC finger protein 1 JBrowse link 18 70,192,520 70,197,871 RGD:9479164
G Dnmt1 DNA methyltransferase 1 JBrowse link 8 21,922,515 21,968,495 RGD:8695943
RGD:8695944
G Dnmt3a DNA methyltransferase 3 alpha JBrowse link 6 28,205,375 28,346,052 RGD:8695943
RGD:8695944
G Dnmt3b DNA methyltransferase 3 beta JBrowse link 3 149,131,541 149,170,061 RGD:8695943
RGD:8695944
G Kdm2a lysine demethylase 2A JBrowse link 1 219,566,130 219,642,294 RGD:9479164
G Kdm2b lysine demethylase 2B JBrowse link 12 39,021,924 39,161,954 RGD:9479164
G Kmt2a lysine methyltransferase 2A JBrowse link 8 49,110,407 49,185,872 RGD:9479164
G Kmt2c lysine methyltransferase 2C JBrowse link 4
4
82,506
6,083,650
109,986
6,294,413
RGD:9479164
G Mbd1 methyl-CpG binding domain protein 1 JBrowse link 18 70,248,568 70,263,190 RGD:8695954
G Mbd2 methyl-CpG binding domain protein 2 JBrowse link 18 65,814,026 65,885,115 RGD:8695954
G Mbd4 methyl-CpG binding domain 4 DNA glycosylase JBrowse link 4 147,744,673 147,756,462 RGD:8695954
G Mecp2 methyl CpG binding protein 2 JBrowse link X 156,650,389 156,713,813 RGD:8695954
G Nanog Nanog homeobox JBrowse link 4 155,531,906 155,539,268 RGD:8695944
G Ogt O-linked N-acetylglucosamine (GlcNAc) transferase JBrowse link X 71,540,870 71,585,906 RGD:8695944
G Pparg peroxisome proliferator-activated receptor gamma JBrowse link 4 147,274,055 147,399,383 RGD:8695944
G Sin3a SIN3 transcription regulator family member A JBrowse link 8 61,748,590 61,803,314 RGD:8695944
G Spi1 Spi-1 proto-oncogene JBrowse link 3 79,918,127 79,937,708 RGD:8695944
G Tet1 tet methylcytosine dioxygenase 1 JBrowse link 20 27,359,122 27,438,039 RGD:8695943
RGD:8695944
G Tet2 tet methylcytosine dioxygenase 2 JBrowse link 2 238,719,389 238,802,975 RGD:8695943
RGD:8695944
G Tet3 tet methylcytosine dioxygenase 3 JBrowse link 4 115,060,702 115,160,800 RGD:8695943
RGD:8695944
RGD:9479164
G Uhrf1 ubiquitin-like with PHD and ring finger domains 1 JBrowse link 9 10,738,211 10,758,403 RGD:8695954
G Uhrf2 ubiquitin like with PHD and ring finger domains 2 JBrowse link 1 248,228,496 248,291,984 RGD:8695954
G Zbtb33 zinc finger and BTB domain containing 33 JBrowse link X 124,319,299 124,326,506 RGD:8695954
G Zbtb38 zinc finger and BTB domain containing 38 JBrowse link 8 104,566,999 104,694,890 RGD:8695954
G Zbtb4 zinc finger and BTB domain containing 4 JBrowse link 10 56,367,586 56,388,296 RGD:8695954
G Zfp57 zinc finger protein 57 JBrowse link 20 2,014,177 2,020,488 RGD:8695954
altered DNA modification pathway term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Mbd4 methyl-CpG binding domain 4 DNA glycosylase JBrowse link 4 147,744,673 147,756,462 RGD:9588971

Pathway Gene Annotations

Disease Annotations Associated with Genes in the DNA modification pathway
Disease TermsGene Symbols
15q24 MicrodeletionSin3a
AbetalipoproteinemiaDnmt1
Abnormalities, MultipleDnmt3a , Kmt2a , Ogt
Acute Kidney InjuryPparg
Acute Lung InjuryPparg
AdenocarcinomaDnmt1 , Kmt2a , Kmt2c , Pparg
Adenocarcinoma of LungDnmt3a , Dnmt3b
Adenocarcinoma, Bronchiolo-AlveolarDnmt1
Adenocarcinoma, ColorectalDnmt3b
Adenocarcinoma, ProstaticDnmt1 , Dnmt3a , Dnmt3b
AdenomyosisDnmt1 , Dnmt3a , Dnmt3b
Agenesis of Corpus CallosumSin3a
AlcoholismSpi1
Alopecia AreataDnmt1
Alzheimer DiseasePparg
Amyotrophic Lateral SclerosisDnmt3a
Anemia, Refractory, with Excess of BlastsTet2
Angelman SyndromeMecp2
Antiphospholipid SyndromePparg
Anxiety DisordersDnmt1 , Dnmt3b , Mecp2
Aortic Valve StenosisOgt
ArteriosclerosisPparg
Arthritis, ExperimentalDnmt1
Arthritis, RheumatoidDnmt1 , Dnmt3b , Mbd2 , Mbd4
AsthmaDnmt1
AtaxiaDnmt1
AtherosclerosisPparg
Attention Deficit Disorder with HyperactivityMecp2
Autism Spectrum DisorderDnmt3a , Dnmt3b , Sin3a , Tet1 , Tet3
Autism, Susceptibility To, X-Linked 3Mecp2
Autistic DisorderMbd1 , Mbd4 , Mecp2
Autoimmune DiseasesDnmt1
Barrett EsophagusPparg
Binge DrinkingDnmt1
Body Mass Index Quantitative Trait Locus 10Pparg
Body Mass Index Quantitative Trait Locus 11Pparg
Body Mass Index Quantitative Trait Locus 12Pparg
Body Mass Index Quantitative Trait Locus 14Pparg
Body Mass Index Quantitative Trait Locus 4Pparg
Body Mass Index Quantitative Trait Locus 7Pparg
Body Mass Index Quantitative Trait Locus 8Pparg
Body Mass Index Quantitative Trait Locus 9Pparg
Bone Marrow DiseasesDnmt3a
Brain InjuriesDnmt1
Breast Cancer, FamilialTet2
Breast NeoplasmsDnmt1 , Dnmt3a , Dnmt3b , Ogt
CarcinogenesisDnmt1 , Dnmt3a
CarcinomaDnmt1 , Dnmt3b
Carcinoma, Adenoid CysticKmt2c , Uhrf1
Carcinoma, EndometrioidDnmt1 , Dnmt3b
Carcinoma, HepatocellularDnmt1 , Dnmt3a , Dnmt3b , Kmt2a , Kmt2c , Mecp2 , Pparg , Tet1
Carcinoma, MucoepidermoidDnmt1
Carcinoma, Non-Small-Cell LungKdm2a
Carcinoma, Pancreatic DuctalDnmt1 , Dnmt3b , Kdm2b , Pparg
Carcinoma, Renal CellTet2
Carcinoma, Squamous CellKmt2c
Carcinoma, Squamous Cell of Head and NeckDnmt3b
Carcinoma, Transitional CellKmt2a , Kmt2c
CardiomegalyOgt
Cardiomyopathy, AlcoholicPparg
Cardiovascular DiseasesPparg
Carotid Artery DiseasesPparg
Carotid Artery InjuriesPparg
Carotid Intimal Medial Thickness 1Pparg
Cerebellar AtaxiaDnmt1
Cerebellar Ataxia, Deafness, and NarcolepsyDnmt1
Child Development Disorders, PervasiveMecp2
CholangiocarcinomaKmt2c
Choline DeficiencyDnmt1 , Mbd2
ChoreaDnmt1
Chromosome AberrationsKmt2a
Chronic Myeloproliferative DisorderTet2
Chronobiology DisordersPparg
Cocaine-Related DisordersMecp2
Colonic NeoplasmsDnmt1 , Mbd4 , Nanog , Pparg , Uhrf1
Colorectal NeoplasmsDnmt1 , Dnmt3b , Kdm2a , Mbd4 , Pparg
Corneal NeovascularizationPparg
Coronary Artery DiseasePparg
Cranioectodermal DysplasiaMbd4
Craniofacial AbnormalitiesDnmt3a , Dnmt3b , Mecp2 , Sin3a
Crohn DiseaseDnmt3a , Pparg
De Lange SyndromeKmt2a
DeafnessMecp2
Deglutition DisordersDnmt1
DementiaDnmt1
Depressive DisorderDnmt3a
Developmental DisabilitiesMecp2
Diabetes MellitusPparg , Zfp57
Diabetes Mellitus, ExperimentalOgt , Pparg
Diabetes Mellitus, Transient Neonatal, 1Zfp57
Diabetes Mellitus, Type 1Dnmt3b
Diabetes Mellitus, Type 2Dnmt1 , Pparg
Diabetic EncephalopathiesPparg
Diabetic NephropathiesPparg
Diabetic RetinopathyPparg
DwarfismSin3a
DysarthriaDnmt1
DyslipidemiasPparg
DysmenorrheaDnmt3b
Encephalopathy, Neonatal Severe, due to Mecp2 MutationsMecp2
Endometrial NeoplasmsDnmt1 , Dnmt3b
EndometriosisDnmt1 , Dnmt3a , Dnmt3b
EndotoxemiaPparg
Epilepsies, PartialMecp2
Esophageal Squamous Cell CarcinomaDnmt3b , Kmt2c , Mbd4
Eye BurnsPparg
Eye InjuriesPparg
FaciesDnmt3a
Fatty LiverPparg
Fatty Liver, AlcoholicDnmt1
Fetal Growth RetardationDnmt1 , Dnmt3b , Mecp2 , Pparg , Sin3a
FibrosisPparg
Gastrointestinal DiseasesMecp2
Genetic Diseases, InbornDnmt3a , Kmt2a , Ogt
GlioblastomaPparg
GliomaPparg
GlomerulonephritisPparg
GlomerulosclerosisPparg
Glycogen Storage Disease Type IIbZbtb33
Graves DiseaseDnmt1
Graves OphthalmopathyPparg
Growth Deficiency and Mental Retardation with Facial DysmorphismKmt2a
Growth DisordersDnmt3a
Hearing LossDnmt1 , Mecp2
Heart Defects, CongenitalDnmt1 , Dnmt3a , Dnmt3b
Heart FailureDnmt1 , Kdm2a , Ogt , Pparg
Hereditary Sensory and Autonomic NeuropathiesDnmt1
Huntington DiseaseSin3a
HydrocephalusSin3a
HyperalgesiaDnmt1 , Sin3a
HyperandrogenismPparg
Hyperlipidemia, Familial CombinedPparg
HypertensionPparg
Hypertrophy, Left VentricularPparg
Hypoxia-Ischemia, BrainDnmt3a , Mbd2 , Spi1
Immunoblastic LymphadenopathyDnmt3a , Tet2
Immunodeficiency Syndrome, VariableDnmt3b
Immunodeficiency-Centromeric Instability-Facial Anomalies Syndrome 1Dnmt3b
Immunologic Deficiency SyndromesDnmt3b
Infarction, Middle Cerebral ArteryDnmt1 , Dnmt3a
InflammationPparg
Insulin ResistancePparg
Intellectual DisabilityDnmt3a , Kmt2a , Mecp2 , Sin3a
Intestinal NeoplasmsMbd4
IschemiaPparg
Ischemic Attack, TransientMbd1 , Mbd2 , Mecp2 , Pparg , Sin3a
Kidney Failure, ChronicPparg
Kleefstra SyndromeKmt2c
Language Development DisordersMecp2
Learning DisordersMecp2
LeukemiaKmt2a
Leukemia, Biphenotypic, AcuteKmt2a
Leukemia, Lymphocytic, Chronic, B-CellDnmt3b
Leukemia, LymphoidKmt2a
Leukemia, Monocytic, AcuteDnmt3a , Kmt2a
Leukemia, Myelogenous, Chronic, BCR-ABL PositiveDnmt1 , Dnmt3a , Dnmt3b
Leukemia, MyeloidKmt2a , Spi1
Leukemia, Myeloid, AcuteDnmt1 , Dnmt3a , Dnmt3b , Kmt2a , Kmt2c , Spi1 , Tet2
Leukemia, Myelomonocytic, AcuteKmt2a
Leukemia, Myelomonocytic, ChronicTet2
Leukemia, Myelomonocytic, JuvenileDnmt3a
Leukemia, Promyelocytic, AcuteDnmt3a , Tet2
LeukostasisPparg
Lichen Planus, OralDnmt1 , Dnmt3b
LipidosesPparg
LipodystrophyPparg
Lipodystrophy, Familial PartialPparg
Liver CirrhosisDnmt1
Liver Cirrhosis, ExperimentalPparg , Zbtb4
Liver Diseases, ParasiticKmt2c
Liver NeoplasmsPparg
Lubs X-Linked Mental Retardation SyndromeMecp2
Lung NeoplasmsDnmt1 , Dnmt3a , Dnmt3b , Mbd1 , Mbd4
Lupus Erythematosus, SystemicDnmt1
Lymphatic MetastasisDnmt3b , Pparg
Lymphoma, Non-HodgkinKmt2a
Lymphoma, T-CellKdm2b , Pparg
Lymphoma, T-Cell, CutaneousDnmt3a
Lymphoma, T-Cell, PeripheralDnmt3a , Tet2
Macular DegenerationMbd2
Mammary Neoplasms, ExperimentalDnmt3b
MedulloblastomaDnmt1
MelanomaPparg
Melanoma, Cutaneous MalignantDnmt3b
Mental DisordersKmt2a
Mental Retardation, X-LinkedMecp2
MENTAL RETARDATION, X-LINKED 106Ogt
Mental Retardation, X-Linked, Syndromic 13Mecp2
Metabolic DiseasesPparg
Metabolic Syndrome XPparg
MicrocephalyKdm2b , Mecp2 , Sin3a
MicrognathismMecp2
MonocytosisTet2
Muscle HypotoniaMecp2
Myelodysplastic SyndromesDnmt3a , Tet2
Myocardial Reperfusion InjuryPparg
Myocarditis, Autoimmune, ExperimentalPparg
MyoclonusMecp2
Neoplasm MetastasisDnmt3b
Neoplasm Recurrence, LocalDnmt3a , Tet2
Neoplasms, Germ Cell and EmbryonalNanog
Neoplasms, Multiple PrimaryDnmt3b
Nerve DegenerationPparg
Neural Tube DefectsKdm2b
Neurocognitive DisordersPparg
Neurodevelopmental DisordersKmt2a , Kmt2c , Mecp2
Neuropathy, Hereditary Sensory and Autonomic, Type IEDnmt1
ObesityPparg
Obesity, MorbidPparg
Oral Squamous Cell CarcinomaDnmt3b
OsteoarthritisPparg
Ovarian NeoplasmsDnmt1
Oxygen-Induced RetinopathyPparg
PainPparg
Pancreatic Intraepithelial NeoplasiaDnmt1
Pancreatic NeoplasmsPparg
PancreatitisPparg
Parkinson DiseaseNanog
Peritoneal FibrosisDnmt1
Pituitary ACTH HypersecretionPparg
Polycystic Kidney, Autosomal DominantPparg
Pre-EclampsiaPparg
Precursor Cell Lymphoblastic Leukemia-LymphomaDnmt3a , Kdm2b , Kmt2a
Precursor T-Cell Lymphoblastic Leukemia-LymphomaDnmt3a
Proliferative Diabetic RetinopathyPparg
Prostatic Intraepithelial NeoplasiaDnmt1
Prostatic NeoplasmsDnmt1 , Dnmt3b , Kmt2a , Kmt2c , Mbd2 , Tet2
ProstatitisDnmt3a , Dnmt3b
PsoriasisPparg
Psychomotor DisordersMecp2
Pulmonary FibrosisMecp2
Purpura, Thrombocytopenic, IdiopathicDnmt3a , Dnmt3b
Renal InsufficiencyPparg
Reperfusion InjuryPparg
Respiratory InsufficiencyMecp2
RetrognathiaMecp2
Rett SyndromeMecp2
Rett Syndrome, AtypicalMecp2
Rett Syndrome, Zappella VariantMecp2
Rhinitis, Allergic, PerennialPparg
SchizophreniaDnmt1 , Dnmt3b , Kdm2b , Mbd2 , Mecp2
Sciatic NeuropathyDnmt3a
SeizuresMbd1 , Mbd2 , Mecp2
Sezary SyndromeDnmt3a , Kmt2c , Tet2
Small Cell Lung CarcinomaDnmt3b , Kmt2a
Smith-Magenis SyndromeMecp2
Stomach NeoplasmsDnmt1 , Dnmt3a , Dnmt3b , Kmt2a , Kmt2c , Pparg
TATTON-BROWN-RAHMAN SYNDROMEDnmt3a
TeratomaNanog
ThymomaDnmt3b
Thyroid Cancer, FollicularPparg
Thyroid NeoplasmsPparg
Transplant RejectionSpi1
Urinary Bladder NeoplasmsDnmt1 , Kmt2a , Kmt2c , Pparg
Uterine Cervical NeoplasmsDnmt1 , Dnmt3b , Kmt2a
Pathway Annotations Associated with Genes in the DNA modification pathway

References Associated with the DNA modification pathway:

Ontology Path Diagram:

paths to the root

Import into Pathway Studio: