DNA MODIFICATION PATHWAY (PW:0001340)

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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 ---> gene expression 5-methylcytosine 5-hydroxymethylcytosine 5-carboxylcytosine 5-formylcytosine chromatin remodeling pathway histone modification pathway Dnmt3a Dnmt3b Dnmt1 gene expression S-adenosylmethionine cytosine cytosine ---> 5-methylcytosine S-adenosylmethionine ---> 5-methylcytosine 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 TET interacting partners TET proteins MBP proteins cytosine ---> gene expression 5-hydroxymethylcytosine ---> 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:9479164
RGD:8695944
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
abdominal obesity-metabolic syndromePparg
abetalipoproteinemiaDnmt1
ACANTHOCYTOSISDnmt1
acute kidney failurePparg
Acute Lung InjuryPparg
acute lymphocytic leukemiaKmt2a
acute monocytic leukemiaDnmt3a , Kmt2a
acute myeloid leukemiaDnmt1 , Dnmt3a , Dnmt3b , Kmt2a , Kmt2c , Spi1 , Tet2
acute myelomonocytic leukemiaKmt2a
acute promyelocytic leukemiaDnmt3a , Tet2
adenocarcinomaDnmt1 , Kmt2a , Kmt2c , Pparg
adenoid cystic carcinomaKmt2c , Uhrf1
Agenesis of Corpus CallosumSin3a
alcohol use disorderSpi1
alcoholic cardiomyopathyPparg
Alcoholic Fatty LiverDnmt1
alopecia areataDnmt1
Alzheimer's diseasePparg
amyotrophic lateral sclerosisDnmt3a
Anemia, Refractory, with Excess of BlastsTet2
Angelman syndromeMecp2
Animal Disease ModelsMecp2
antiphospholipid syndromePparg
anxiety disorderDnmt1 , Dnmt3b , Mecp2
aortic valve stenosisOgt
arteriosclerosisPparg
asthmaDnmt1
AtaxiaDnmt1
atherosclerosisPparg
attention deficit hyperactivity disorderMecp2
autism spectrum disorderDnmt3a , Dnmt3b , Sin3a , Tet1 , Tet3
Autism, Susceptibility to, X-Linked 3Mecp2
autistic disorderMbd1 , Mbd4 , Mecp2
Autoimmune DiseasesDnmt1
autoimmune thrombocytopenic purpuraDnmt3a , Dnmt3b
autosomal dominant cerebellar ataxia, deafness and narcolepsyDnmt1
autosomal dominant polycystic kidney diseasePparg
B- and T-cell mixed leukemiaKmt2a
Barrett's esophagusPparg
Beckwith-Wiedemann syndromeDnmt1
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 18Pparg
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 diseaseDnmt3a
Brain InjuriesDnmt1
Breast Cancer, FamilialTet2
Breast NeoplasmsDnmt1 , Dnmt3a , Dnmt3b , Ogt
bronchiolo-alveolar adenocarcinomaDnmt1
bruxismMecp2
CarcinogenesisDnmt1 , Dnmt3a
carcinomaDnmt1 , Dnmt3b
CardiomegalyOgt
cardiovascular system diseasePparg
carotid artery diseasePparg
Carotid Artery InjuriesPparg
Carotid Intimal Medial Thickness 1Pparg
cerebellar ataxiaDnmt1
cervical cancerKmt2a
cholangiocarcinomaKmt2c
choline deficiency diseaseDnmt1 , Mbd2
choreatic diseaseDnmt1
chromosome 15q24 deletion syndromeSin3a
Chromosome AberrationsKmt2a
Chronic Allograft NephropathyPparg
Chronic Lymphocytic Leukemia, B-CellDnmt3b
chronic myeloid leukemiaDnmt1 , Dnmt3a , Dnmt3b
chronic myelomonocytic leukemiaTet2
Chronobiology DisordersPparg
clear cell renal cell carcinomaDnmt1 , Dnmt3a
Cocaine-Related DisordersMecp2
cognitive disorderPparg
colon cancerPparg
colon carcinomaPparg
Colonic NeoplasmsDnmt1 , Nanog , Pparg , Uhrf1
colorectal adenocarcinomaDnmt3b
colorectal cancerPparg
colorectal carcinomaMbd4
Colorectal NeoplasmsDnmt1 , Dnmt3b , Kdm2a , Mbd4 , Pparg
congenital generalized lipodystrophy type 2Pparg
congenital heart diseaseDnmt1 , Dnmt3a , Dnmt3b
congestive heart failureDnmt1 , Kdm2a , Ogt , Pparg
corneal neovascularizationPparg
Cornelia de Lange syndromeKmt2a
coronary artery diseasePparg
Craniofacial AbnormalitiesDnmt3a , Dnmt3b , Mecp2 , Sin3a
Crohn's diseaseDnmt3a , Pparg
cutaneous T cell lymphomaDnmt3a
Danon diseaseZbtb33
DeafnessMecp2
Deglutition DisordersDnmt1
dementiaDnmt1
Developmental DisabilitiesMecp2
diabetes mellitusPparg , Zfp57
diabetic encephalopathyPparg
Diabetic NephropathiesPparg
diabetic retinopathyPparg
disease of metabolismPparg
DwarfismSin3a
DysarthriaDnmt1
DyslipidemiasPparg
DysmenorrheaDnmt3b
Encephalopathy, Neonatal Severe, due to Mecp2 MutationsMecp2
end stage renal failurePparg
Endometrial NeoplasmsDnmt1 , Dnmt3b
Endometrioid CarcinomasDnmt1 , Dnmt3b
endometriosisDnmt1 , Dnmt3a , Dnmt3b
endometriosis of uterusDnmt1 , Dnmt3a , Dnmt3b
EndotoxemiaPparg
esophagus squamous cell carcinomaDnmt3b , Kmt2c , Mbd4
Experimental ArthritisDnmt1
Experimental Autoimmune MyocarditisPparg
Experimental Diabetes MellitusOgt , Pparg
Experimental Liver CirrhosisPparg , Zbtb4
Eye BurnsPparg
Eye InjuriesPparg
FaciesDnmt3a
familial combined hyperlipidemiaPparg
familial partial lipodystrophyPparg
fatty liver diseasePparg
Fetal Growth RetardationDnmt1 , Dnmt3b , Mecp2 , Pparg , Sin3a
FibrosisPparg
focal epilepsyMecp2
Follicular Thyroid CancerPparg
Gastrointestinal DiseasesMecp2
genetic diseaseDnmt3a , Kmt2a , Mecp2 , Ogt , Sin3a
Germ Cell and Embryonal NeoplasmsNanog
glioblastoma multiformePparg
glomerulonephritisPparg
glomerulosclerosisPparg
Graves OphthalmopathyPparg
Graves' diseaseDnmt1
Growth Deficiency and Mental Retardation with Facial DysmorphismKmt2a
Growth DisordersDnmt3a
head and neck squamous cell carcinomaDnmt3b
Hearing LossDnmt1 , Mecp2
hepatocellular carcinomaDnmt1 , Dnmt3a , Dnmt3b , Kmt2a , Kmt2c , Mecp2 , Pparg , Tet1
hereditary sensory and autonomic neuropathy, type IEDnmt1
hereditary sensory neuropathyDnmt1
hereditary sensory neuropathy type 1EDnmt1
Huntington's diseaseSin3a
hydrocephalusSin3a
HyperalgesiaDnmt1 , Sin3a
hyperandrogenismPparg
hypertensionPparg
hypertrophic cardiomyopathySpi1
Hypertrophy, Left VentricularPparg
Hypoxia-Ischemia, BrainDnmt3a , Mbd2 , Spi1
Immunoblastic LymphadenopathyDnmt3a , Tet2
immunodeficiency-centromeric instability-facial anomalies syndromeDnmt3b
immunodeficiency-centromeric instability-facial anomalies syndrome 1Dnmt3b
InflammationPparg
Insulin ResistancePparg
intellectual disabilityDnmt3a , Kmt2a , Mecp2 , Sin3a
Intestinal NeoplasmsMbd4
ischemiaPparg
juvenile myelomonocytic leukemiaDnmt3a
Kabuki syndromeDnmt3b , Kmt2a
kidney failurePparg
Kleefstra syndromeKmt2c
KLEEFSTRA SYNDROME 2Kmt2c
Language Development DisordersMecp2
learning disabilityMecp2
leukemiaKmt2a
leukostasisPparg
lipid storage diseasePparg
lipodystrophyPparg
liver cirrhosisDnmt1
liver neoplasmPparg
lung adenocarcinomaDnmt3a , Dnmt3b
lung cancerMbd1 , Mbd4
Lung NeoplasmsDnmt1 , Dnmt3a , Dnmt3b
lung small cell carcinomaDnmt3b , Kmt2a
Lymphatic MetastasisDnmt3b , Pparg
lymphoid leukemiaKmt2a
macular degenerationMbd2
malignant gliomaPparg
Mammary Neoplasms, ExperimentalDnmt3b
medulloblastomaDnmt1
melanomaPparg
mental depressionDnmt3a
Mental Retardation, X-LinkedMecp2
Metabolic SyndromePparg
microcephalyKdm2b , Mecp2 , Sin3a
MicrognathismMecp2
middle cerebral artery infarctionDnmt1 , Dnmt3a
MonocytosisTet2
morbid obesityPparg
mucoepidermoid carcinomaDnmt1
Multiple AbnormalitiesDnmt3a , Kmt2a , Ogt
Muscle HypotoniaMecp2
myelodysplastic syndromeDnmt3a , Tet2
myeloid leukemiaKmt2a , Spi1
myeloproliferative neoplasmTet2
Myocardial Reperfusion InjuryPparg
MyoclonusMecp2
Neoplasm InvasivenessDnmt1
Neoplasm MetastasisDnmt3b
Neoplasm Recurrence, LocalDnmt3a , Tet2
Neoplasms, Multiple PrimaryDnmt3b
nephroblastomaTet2
Nerve DegenerationPparg
neural tube defectKdm2b
Neurodevelopmental DisordersKmt2a , Kmt2c , Mecp2
non-Hodgkin lymphomaKmt2a
non-small cell lung carcinomaKdm2a
obesityPparg
Oral Lichen PlanusDnmt1 , Dnmt3b
oral squamous cell carcinomaDnmt3b
osteoarthritisPparg
Ovarian NeoplasmsDnmt1
Oxygen-Induced RetinopathyPparg
PainPparg
pancreatic cancerPparg
pancreatic ductal carcinomaDnmt1 , Dnmt3b , Kdm2b , Pparg
Pancreatic Intraepithelial NeoplasiaDnmt1
pancreatitisPparg
Parasitic Liver DiseasesKmt2c
Parkinson's diseaseNanog
Perennial Allergic RhinitisPparg
peripheral T-cell lymphomaDnmt3a , Tet2
Peritoneal FibrosisDnmt1
Pervasive Child Development DisordersMecp2
pituitary-dependent Cushing's diseasePparg
pre-eclampsiaPparg
precursor lymphoblastic lymphoma/leukemiaDnmt3a , Kdm2b , Kmt2a
precursor T-lymphoblastic lymphoma/leukemiaDnmt3a , Spi1
primary immunodeficiency diseaseDnmt3b
primary pulmonary hypertensionPparg
proliferative diabetic retinopathyPparg
prostate adenocarcinomaDnmt1 , Dnmt3a , Dnmt3b
prostate carcinoma in situDnmt1
Prostatic NeoplasmsDnmt1 , Dnmt3b , Kmt2a , Kmt2c , Mbd1 , Mbd2 , Tet2
prostatitisDnmt3a , Dnmt3b
psoriasisPparg
Psychomotor DisordersMecp2
pulmonary fibrosisMecp2
renal cell carcinomaTet2
Reperfusion InjuryPparg
respiratory failureMecp2
RetrognathiaMecp2
Rett syndromeMecp2
Rett Syndrome, AtypicalMecp2
Rett Syndrome, Zappella VariantMecp2
rheumatoid arthritisDnmt1 , Dnmt3b , Mbd2 , Mbd4
schizophreniaDnmt1 , Dnmt3b , Kdm2b , Mbd2 , Mecp2
sciatic neuropathyDnmt3a
Sensenbrenner syndromeMbd4
Sezary's diseaseDnmt3a , Kmt2c , Tet2
skin melanomaDnmt3b
Smith-Magenis syndromeMecp2
squamous cell carcinomaKmt2c
Stomach NeoplasmsDnmt1 , Dnmt3a , Dnmt3b , Kmt2a , Kmt2c , Pparg
syndromic X-linked intellectual disability Lubs typeMecp2
systemic lupus erythematosusDnmt1 , Pparg
T-Cell LymphomaKdm2b , Pparg
TATTON-BROWN-RAHMAN SYNDROMEDnmt3a
teratomaNanog
thymomaDnmt3b
Thyroid NeoplasmsPparg
transient cerebral ischemiaMbd1 , Mbd2 , Mecp2 , Pparg , Sin3a
transient neonatal diabetes mellitusZfp57
Transient Neonatal Diabetes Mellitus, 1Zfp57
transitional cell carcinomaKmt2a , Kmt2c
Transplant RejectionSpi1
type 1 diabetes mellitusDnmt3b
type 2 diabetes mellitusDnmt1 , Pparg
urinary bladder cancerDnmt1 , Kmt2a , Kmt2c , Pparg
Uterine Cervical NeoplasmsDnmt1 , Dnmt3b
visual epilepsyMbd1 , Mbd2 , Mecp2
X-linked intellectual disability-psychosis-macroorchidism syndromeMecp2
X-linked mental retardation 106Ogt
Pathway Annotations Associated with Genes in the DNA modification pathway

References Associated with the DNA modification pathway:

Ontology Path Diagram:

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