PML

PML

PML nuclear body scaffold | MYL, RNF71, TRIM19

The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This phosphoprotein localizes to nuclear bodies where it functions as a transcription factor and tumor suppressor. Its expression is cell-cycle related and it regulates the p53 response to oncogenic signals. The gene is often involved in the translocation with the retinoic acid receptor alpha gene associated with acute promyelocytic leukemia (APL). Extensive alternative splicing of this gene results in several variations of the protein's central and C-terminal regions; all variants encode the same N-terminus. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

Biological processes 114 terms

DNA damage response, signal transduction by p53 class mediator (GO:0030330)DNA damage response, signal transduction by p53 class mediator (GO:0030330)PML body (GO:0016605)PML body (GO:0016605)PML body (GO:0016605)PML body (GO:0016605)PML body organization (GO:0030578)PML body organization (GO:0030578)PML body organization (GO:0030578)SMAD binding (GO:0046332)SUMO binding (GO:0032183)SUMO transferase activity (GO:0019789)SUMO transferase activity (GO:0019789)apoptotic process (GO:0006915)cellular senescence (GO:0090398)cellular senescence (GO:0090398)chromatin remodeling (GO:0006338)chromosome, telomeric region (GO:0000781)circadian regulation of gene expression (GO:0032922)circadian regulation of gene expression (GO:0032922)cobalt ion binding (GO:0050897)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytosol (GO:0005829)cytosol (GO:0005829)cytosol (GO:0005829)early endosome membrane (GO:0031901)endoplasmic reticulum calcium ion homeostasis (GO:0032469)endoplasmic reticulum calcium ion homeostasis (GO:0032469)endoplasmic reticulum membrane (GO:0005789)entrainment of circadian clock by photoperiod (GO:0043153)entrainment of circadian clock by photoperiod (GO:0043153)establishment of protein localization (GO:0045184)fibroblast migration (GO:0010761)identical protein binding (GO:0042802)innate immune response (GO:0045087)innate immune response (GO:0045087)innate immune response (GO:0045087)intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)maintenance of protein location in nucleus (GO:0051457)metal ion binding (GO:0046872)molecular adaptor activity (GO:0060090)negative regulation of DNA-templated transcription (GO:0045892)negative regulation of angiogenesis (GO:0016525)negative regulation of angiogenesis (GO:0016525)negative regulation of cell growth (GO:0030308)negative regulation of cell population proliferation (GO:0008285)negative regulation of cell population proliferation (GO:0008285)negative regulation of gene expression (GO:0010629)negative regulation of interleukin-1 beta production (GO:0032691)negative regulation of interleukin-1 production (GO:0032692)negative regulation of mitotic cell cycle (GO:0045930)negative regulation of telomere maintenance via telomerase (GO:0032211)negative regulation of translation in response to oxidative stress (GO:0032938)negative regulation of ubiquitin-dependent protein catabolic process (GO:2000059)nuclear body (GO:0016604)nuclear matrix (GO:0016363)nuclear matrix (GO:0016363)nuclear membrane (GO:0031965)nucleolus (GO:0005730)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)oncogene-induced cell senescence (GO:0090402)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)positive regulation of apoptotic signaling pathway (GO:2001235)positive regulation of defense response to virus by host (GO:0002230)positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)positive regulation of fibroblast proliferation (GO:0048146)positive regulation of protein localization to chromosome, telomeric region (GO:1904816)positive regulation of signal transduction by p53 class mediator (GO:1901798)positive regulation of telomere maintenance (GO:0032206)proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)protein binding (GO:0005515)protein heterodimerization activity (GO:0046982)protein homodimerization activity (GO:0042803)protein localization to nucleus (GO:0034504)protein stabilization (GO:0050821)protein sumoylation (GO:0016925)protein sumoylation (GO:0016925)protein targeting (GO:0006605)protein targeting (GO:0006605)protein-containing complex assembly (GO:0065003)regulation of DNA-templated transcription (GO:0006355)regulation of DNA-templated transcription (GO:0006355)regulation of calcium ion transport into cytosol (GO:0010522)regulation of calcium ion transport into cytosol (GO:0010522)regulation of cell adhesion (GO:0030155)regulation of cell cycle (GO:0051726)regulation of circadian rhythm (GO:0042752)regulation of circadian rhythm (GO:0042752)regulation of double-strand break repair (GO:2000779)regulation of protein metabolic process (GO:0051246)response to cytokine (GO:0034097)response to cytokine (GO:0034097)response to hypoxia (GO:0001666)response to hypoxia (GO:0001666)suppression of viral release by host (GO:0044790)suppression of viral release by host (GO:0044790)suppression of viral release by host (GO:0044790)transcription coactivator activity (GO:0003713)ubiquitin protein ligase binding (GO:0031625)ubiquitin-like protein ligase activity (GO:0061659)zinc ion binding (GO:0008270)zinc ion binding (GO:0008270)

Expression (TPM)

TFs regulating PML 0 TFs

Transcription factors with Perturb-seq knockdown data for PML. 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 = PML 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 PML

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of PML, 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
	chr15:73,733,109–73,733,828	261.2 kb	Distal (>10kb) Multiome	33
	chr15:73,752,465–73,753,181	241.9 kb	Distal (>10kb) Multiome	192
	chr15:73,926,301–73,928,142	66.9 kb	Distal (>10kb) Multiome	557
	chr15:73,964,793–73,965,395	29.7 kb	Distal (>10kb) Multiome	395
	chr15:73,972,958–73,973,626	21.6 kb	Distal (>10kb) Multiome	375
	chr15:73,991,853–73,992,729	2.4 kb	Proximal (<10kb) Multiome	723
	chr15:73,994,310–73,995,392	31 bp	At TSS Multiome	539
	chr15:74,124,047–74,124,500	129.6 kb	Distal (>10kb) Multiome	16
	chr15:74,127,396–74,128,614	133.0 kb	Distal (>10kb) Multiome	498
	chr15:74,129,520–74,130,600	135.3 kb	Distal (>10kb) Multiome	188
	chr15:74,134,110–74,134,917	139.8 kb	Distal (>10kb) Multiome	220
	chr15:74,135,992–74,136,743	141.7 kb	Distal (>10kb) Multiome	439
	chr15:74,202,453–74,203,387	208.2 kb	Distal (>10kb) Multiome	381
	chr15:74,208,748–74,209,470	214.4 kb	Distal (>10kb) Multiome	233
	chr15:74,245,168–74,245,975	250.8 kb	Distal (>10kb) Multiome	278
	chr15:74,291,174–74,291,950	296.8 kb	Distal (>10kb) Multiome	773

Genome Browser

Genomic view of the PML 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.