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ONTOLOGY REPORT - ANNOTATIONS


Term:apoptotic DNA fragmentation
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Accession:GO:0006309 term browser browse the term
Definition:The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
Comment:DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases. In human, these include DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G) (reviewed in PMID:15723341). Caution is needed when apoptotic DNA laddering assays show presence of fragmented DNA. A positive assay may simply reflect the end point of a whole apoptotic process. Unless clear experimental evidence is available to show that a gene product is directly involved in fragmenting DNA, please do not annotate to GO:0006309 'apoptotic DNA fragmentation' and consider annotating instead to a more upstream process such as, e.g., GO:0042981 'regulation of apoptotic process', GO:0006915 'apoptotic process', GO:0097190 'apoptotic signaling pathway'. Also, note that gene products involved in compartmentalization of apoptotic nucleases and in activation or repression of their enzymatic activity should be annotated to the regulation term GO:1902510 'regulation of apoptotic DNA fragmentation' or to one of its children (see PMID:15723341).
Synonyms:exact_synonym: DNA catabolic process during apoptosis;   DNA catabolism during apoptosis;   DNA fragmentation involved in apoptotic nuclear change;   endonucleolytic DNA catabolic process involved in apoptosis
 broad_synonym: DNA fragmentation;   chromatinolysis
 alt_id: GO:0008178


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apoptotic DNA fragmentation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Dffa DNA fragmentation factor subunit alpha IEA GO_REF:0000002 InterPro GO_REF:0000002 NCBI chr 5:165,922,893...165,935,822
Ensembl chr 5:165,922,915...165,935,821
JBrowse link
G Dffb DNA fragmentation factor subunit beta IDA
IEA
IBA
ISO
GO_REF:0000002
PMID:21873635
(PMID:15572351), (PMID:22253444)
InterPro
RGD
PMID:15572351, PMID:22253444, PMID:11425895, PMID:21873635 GO_REF:0000002, RGD:628524, RGD:13792537 NCBI chr 5:171,250,559...171,261,875
Ensembl chr 5:171,249,633...171,262,119
JBrowse link
G Dicer1 dicer 1 ribonuclease III IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 6:128,388,084...128,453,234
Ensembl chr 6:128,388,053...128,434,183
JBrowse link
G Dnase1l3 deoxyribonuclease 1-like 3 TAS
ISO
IBA
(MGI:2385551|PMID:12050166)
PMID:21873635
(PMID:23229555)
RGD PMID:12050166, PMID:23229555, PMID:9665719, PMID:21873635 MGI:2385551, RGD:728743, RGD:13792537 NCBI chr15:18,710,492...18,736,476
Ensembl chr15:18,710,492...18,736,473
JBrowse link
G Dnase2 deoxyribonuclease 2, lysosomal IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr19:26,022,855...26,025,523
Ensembl chr19:26,022,849...26,025,532
JBrowse link
G Dnase2b deoxyribonuclease 2 beta IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 2:252,436,363...252,475,506
Ensembl chr 2:252,436,332...252,451,999
JBrowse link
G Endog endonuclease G IBA
ISO
PMID:21873635
MGI:3034030|MGI:3514265 (MGI:3029597|PMID:14663139)
RGD PMID:14663139, PMID:21873635 MGI:3029597, RGD:13792537 NCBI chr 3:8,741,833...8,744,414
Ensembl chr 3:8,741,766...8,744,592
JBrowse link
G Exog exo/endonuclease G IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 8:128,133,398...128,153,110
Ensembl chr 8:128,133,431...128,153,110
JBrowse link
G Foxl2 forkhead box L2 ISO (PMID:16153597) RGD PMID:16153597 NCBI chr 8:107,194,492...107,197,644
Ensembl chr 8:107,194,551...107,195,675
JBrowse link
negative regulation of apoptotic DNA fragmentation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Dffa DNA fragmentation factor subunit alpha ISO (PMID:15572351)
MGI:2179456 (MGI:2182584|PMID:10601318), (MGI:3029597|PMID:14663139)
RGD PMID:10601318, PMID:14663139, PMID:15572351 MGI:2182584, MGI:3029597 NCBI chr 5:165,922,893...165,935,822
Ensembl chr 5:165,922,915...165,935,821
JBrowse link
G Nmnat1 nicotinamide nucleotide adenylyltransferase 1 IMP RGD PMID:27184051 RGD:13781945 NCBI chr 5:166,409,460...166,430,291
Ensembl chr 5:166,409,461...166,430,254
JBrowse link
G Pam16 presequence translocase associated motor 16 IDA RGD PMID:24069394 RGD:13462066 NCBI chr10:11,146,359...11,153,936
Ensembl chr10:11,146,359...11,153,936
JBrowse link
positive regulation of apoptotic DNA fragmentation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bax BCL2 associated X, apoptosis regulator ISO
IEA
(PMID:11350920)
GO_REF:0000107
RGD
Ensembl
PMID:11350920 GO_REF:0000107 NCBI chr 1:101,451,801...101,457,207
Ensembl chr 1:101,451,802...101,457,207
JBrowse link
G Endog endonuclease G IMP RGD PMID:16407272 RGD:9685355 NCBI chr 3:8,741,833...8,744,414
Ensembl chr 3:8,741,766...8,744,592
JBrowse link
G Hsf1 heat shock transcription factor 1 IMP RGD PMID:21192280 RGD:10403035 NCBI chr 7:117,538,523...117,565,478
Ensembl chr 7:117,538,523...117,565,478
JBrowse link
G Igfbp3 insulin-like growth factor binding protein 3 IMP RGD PMID:15125883 RGD:10402776 NCBI chr14:87,457,647...87,465,374
Ensembl chr14:87,457,647...87,465,374
JBrowse link
G Il6 interleukin 6 ISO (PMID:28433754) RGD PMID:28433754 NCBI chr 4:3,043,231...3,047,807
Ensembl chr 4:3,043,231...3,047,807
JBrowse link
regulation of apoptotic DNA fragmentation term browser
Symbol Object Name Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Aifm1 apoptosis inducing factor, mitochondria associated 1 ISO MGI:1306796 (MGI:3577148|PMID:15703386) RGD PMID:15703386 MGI:3577148 NCBI chr  X:135,304,063...135,343,062
Ensembl chr  X:135,304,066...135,343,087
JBrowse link
G Apaf1 apoptotic peptidase activating factor 1 ISO MGI:1349414 (MGI:3577148|PMID:15703386) RGD PMID:15703386 MGI:3577148 NCBI chr 7:31,699,309...31,784,192
Ensembl chr 7:31,699,885...31,784,192
JBrowse link
G Cdkn2a cyclin-dependent kinase inhibitor 2A ISO (PMID:12082630) RGD PMID:12082630 NCBI chr 5:107,823,323...107,832,405
Ensembl chr 5:107,823,330...107,841,175
JBrowse link
G Cidea cell death-inducing DFFA-like effector a ISO (MGI:1203887|PMID:9564035) RGD PMID:9564035 MGI:1203887 NCBI chr18:63,082,861...63,108,450
Ensembl chr18:63,098,144...63,108,051
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 20020
    cellular process 18792
      execution phase of apoptosis 74
        cellular component disassembly involved in execution phase of apoptosis 30
          apoptotic nuclear changes 29
            apoptotic DNA fragmentation 19
              negative regulation of apoptotic DNA fragmentation 3
              positive regulation of apoptotic DNA fragmentation 5
              regulation of apoptotic DNA fragmentation + 12
Path 2
Term Annotations click to browse term
  biological_process 20020
    metabolic process 12263
      cellular metabolic process 11073
        heterocycle metabolic process 5619
          nucleobase-containing compound metabolic process 5488
            nucleic acid metabolic process 4984
              DNA metabolic process 923
                DNA catabolic process 36
                  DNA catabolic process, endonucleolytic 27
                    apoptotic DNA fragmentation 19
                      negative regulation of apoptotic DNA fragmentation 3
                      positive regulation of apoptotic DNA fragmentation 5
                      regulation of apoptotic DNA fragmentation + 12
paths to the root

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.