USP16

ubiquitin specific peptidase 16 | Ubp-M

This gene encodes a deubiquitinating enzyme that is phosphorylated at the onset of mitosis and then dephosphorylated at the metaphase/anaphase transition. It can deubiquitinate H2A, one of two major ubiquitinated proteins of chromatin, in vitro and a mutant form of the protein was shown to block cell division. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

Developmental clusters: GC5

Biological processes 45 terms

DNA damage response (GO:0006974)chromatin remodeling (GO:0006338)cysteine-type deubiquitinase activity (GO:0004843)cysteine-type deubiquitinase activity (GO:0004843)cysteine-type deubiquitinase activity (GO:0004843)cysteine-type endopeptidase activity (GO:0004197)cysteine-type endopeptidase activity (GO:0004197)cysteine-type endopeptidase activity (GO:0004197)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasm (GO:0005737)histone H2A deubiquitinase activity (GO:0140950)histone H2A deubiquitinase activity (GO:0140950)histone H2A deubiquitinase activity (GO:0140950)histone binding (GO:0042393)histone binding (GO:0042393)mitotic cell cycle (GO:0000278)mitotic nuclear division (GO:0140014)monoubiquitinated protein deubiquitination (GO:0035520)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of DNA-templated transcription (GO:0045893)positive regulation of ribosome biogenesis (GO:0090070)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of translational elongation (GO:0045901)protein binding (GO:0005515)protein deubiquitination (GO:0016579)protein deubiquitination (GO:0016579)protein homotetramerization (GO:0051289)protein homotetramerization (GO:0051289)regulation of cell cycle (GO:0051726)regulation of gene expression (GO:0010468)regulation of transcription by RNA polymerase II (GO:0006357)regulation of transcription by RNA polymerase II (GO:0006357)ribosomal small subunit binding (GO:0043024)transcription coactivator activity (GO:0003713)transcription coactivator activity (GO:0003713)ubiquitin binding (GO:0043130)ubiquitin binding (GO:0043130)zinc ion binding (GO:0008270)zinc ion binding (GO:0008270)

Expression (TPM)

TFs regulating USP16 0 TFs

Transcription factors with Perturb-seq knockdown data for USP16. 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 = USP16 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 USP16

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of USP16, 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.

Element	Dist. to TSS	Link type	TFs
chr21:28,884,897–28,885,668	139.4 kb	Distal (>10kb) Multiome	1089
chr21:28,922,250–28,923,423	102.1 kb	Distal (>10kb) Multiome	112
chr21:28,992,126–28,993,365	31.7 kb	Distal (>10kb) Multiome	927
chr21:29,002,426–29,003,155	21.9 kb	Distal (>10kb) Multiome	924
chr21:29,018,921–29,019,505	5.4 kb	Proximal (<10kb) Multiome	771
chr21:29,024,275–29,025,379	125 bp	At TSS Multiome	850
chr21:29,072,977–29,074,186	49.1 kb	Distal (>10kb) Multiome	1002
chr21:29,298,181–29,300,594	274.2 kb	Distal (>10kb) Multiome	929

Genome Browser

Genomic view of the USP16 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.