BNIP3

BNIP3

BCL2 interacting protein 3 | HABON, Nip3

This gene is encodes a mitochondrial protein that contains a BH3 domain and acts as a pro-apoptotic factor. The encoded protein interacts with anti-apoptotic proteins, including the E1B 19 kDa protein and Bcl2. This gene is silenced in tumors by DNA methylation. [provided by RefSeq, Dec 2014]

Member of: DE-4 DE-4.1 Developmental clusters: GC2

Biological processes 87 terms

GTPase binding (GO:0051020)autophagic cell death (GO:0048102)autophagy of mitochondrion (GO:0000422)cardiac muscle cell apoptotic process (GO:0010659)cellular response to cobalt ion (GO:0071279)cellular response to hydrogen peroxide (GO:0070301)cellular response to hypoxia (GO:0071456)cellular response to hypoxia (GO:0071456)cellular response to hypoxia (GO:0071456)cellular response to mechanical stimulus (GO:0071260)cerebral cortex development (GO:0021987)cytoplasm (GO:0005737)cytoplasm (GO:0005737)defense response to virus (GO:0051607)dendrite (GO:0030425)dendrite (GO:0030425)endoplasmic reticulum (GO:0005783)endoplasmic reticulum (GO:0005783)endoplasmic reticulum membrane (GO:0005789)endoplasmic reticulum membrane (GO:0005789)endoplasmic reticulum-autophagosome adaptor activity (GO:0140506)granzyme-mediated programmed cell death signaling pathway (GO:0140507)identical protein binding (GO:0042802)identical protein binding (GO:0042802)intrinsic apoptotic signaling pathway in response to hypoxia (GO:1990144)membrane (GO:0016020)mitochondrial envelope (GO:0005740)mitochondrial fragmentation involved in apoptotic process (GO:0043653)mitochondrial fragmentation involved in apoptotic process (GO:0043653)mitochondrial membrane (GO:0031966)mitochondrial membrane (GO:0031966)mitochondrial membrane (GO:0031966)mitochondrial outer membrane (GO:0005741)mitochondrial outer membrane (GO:0005741)mitochondrial outer membrane (GO:0005741)mitochondrial outer membrane (GO:0005741)mitochondrial outer membrane permeabilization (GO:0097345)mitochondrial protein catabolic process (GO:0035694)mitochondrion (GO:0005739)mitochondrion (GO:0005739)mitochondrion (GO:0005739)mitochondrion (GO:0005739)mitochondrion autophagosome adaptor activity (GO:0140580)mitochondrion autophagosome adaptor activity (GO:0140580)mitophagy (GO:0000423)mitophagy (GO:0000423)negative regulation of apoptotic process (GO:0043066)negative regulation of membrane potential (GO:0045837)negative regulation of mitochondrial fusion (GO:0010637)negative regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902109)negative regulation of mitochondrial membrane potential (GO:0010917)negative regulation of programmed cell death (GO:0043069)neuron apoptotic process (GO:0051402)neuron apoptotic process (GO:0051402)nuclear envelope (GO:0005635)nuclear envelope (GO:0005635)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)nucleus (GO:0005634)oligodendrocyte differentiation (GO:0048709)positive regulation of apoptotic process (GO:0043065)positive regulation of apoptotic process (GO:0043065)positive regulation of apoptotic process (GO:0043065)positive regulation of autophagy (GO:0010508)positive regulation of autophagy of mitochondrion (GO:1903599)positive regulation of cardiac muscle cell apoptotic process (GO:0010666)positive regulation of macroautophagy (GO:0016239)positive regulation of mitochondrial calcium ion concentration (GO:0051561)positive regulation of mitochondrial fission (GO:0090141)positive regulation of programmed cell death (GO:0043068)positive regulation of protein-containing complex disassembly (GO:0043243)positive regulation of release of cytochrome c from mitochondria (GO:0090200)postsynaptic density (GO:0014069)protein binding (GO:0005515)protein homodimerization activity (GO:0042803)reactive oxygen species metabolic process (GO:0072593)regulation of mitochondrial membrane permeability (GO:0046902)response to axon injury (GO:0048678)response to hyperoxia (GO:0055093)response to hypoxia (GO:0001666)response to hypoxia (GO:0001666)response to oxygen-glucose deprivation (GO:0090649)reticulophagy (GO:0061709)reticulophagy (GO:0061709)substrate localization to autophagosome (GO:0061753)

Expression (TPM)

TFs regulating BNIP3 0 TFs

Transcription factors with Perturb-seq knockdown data for BNIP3. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = BNIP3 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to BNIP3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of BNIP3, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Accessibility	Element	Dist. to TSS	Link type	TFs
	chr10:131,874,962–131,875,578	106.8 kb	Distal (>10kb) Multiome	227
	chr10:131,899,878–131,901,850	81.2 kb	Distal (>10kb) Multiome	732
	chr10:131,929,125–131,929,784	52.5 kb	Distal (>10kb) Multiome	62
	chr10:131,979,865–131,980,027	1.9 kb	Proximal (<10kb)	200
	chr10:131,980,800–131,981,157	765 bp	At TSS	277
	chr10:131,981,341–131,982,864	136 bp	At TSS Multiome	815
	chr10:131,998,677–131,999,655	17.3 kb	Distal (>10kb) Multiome	271
	chr10:132,001,275–132,002,395	19.8 kb	Distal (>10kb) Multiome	161
	chr10:132,002,510–132,004,411	21.6 kb	Distal (>10kb) Multiome	240
	chr10:132,035,668–132,037,081	54.7 kb	Distal (>10kb) Multiome	214
	chr10:132,112,772–132,114,093	131.4 kb	Distal (>10kb) Multiome	141
	chr10:132,163,327–132,163,783	181.6 kb	Distal (>10kb) Multiome	240
	chr10:132,185,497–132,188,136	203.8 kb	Distal (>10kb) Multiome	418

Genome Browser

Genomic view of the BNIP3 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.