UHRF1 (ubiquitin like with PHD and ring finger domains 1)

Gene

• Entrez ID: 29128
• Gene name: Ubiquitin like with PHD and ring finger domains 1
• Gene symbol: UHRF1
• Synonyms: ICBP90, Np95, RNF106, TDRD22, hNP95, hUHRF1, huNp95
• Chromosome: 19
• Chromosome location: 19p13.3
• Summary: This gene encodes a member of a subfamily of RING-finger type E3 ubiquitin ligases. The protein binds to specific DNA sequences, and recruits a histone deacetylase to regulate gene expression. Its expression peaks at late G1 phase and continues during G2

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT001580	hsa-let-7b-5p	pSILAC	18668040
MIRT001324	hsa-miR-1-3p	pSILAC	18668040
MIRT002574	hsa-miR-124-3p	Microarray	15685193
MIRT002574	hsa-miR-124-3p	Microarray;Other	15685193
MIRT001324	hsa-miR-1-3p	Proteomics;Other	18668040
MIRT025268	hsa-miR-34a-5p	Proteomics	21566225
MIRT025268	hsa-miR-34a-5p	Proteomics	21566225
MIRT025268	hsa-miR-34a-5p	Proteomics	21566225
MIRT025644	hsa-miR-7-5p	Microarray	19073608
MIRT001580	hsa-let-7b-5p	Proteomics;Other	18668040
MIRT052615	hsa-let-7a-5p	CLASH	23622248
MIRT047656	hsa-miR-10a-5p	CLASH	23622248
MIRT047494	hsa-miR-10b-5p	CLASH	23622248
MIRT025268	hsa-miR-34a-5p	CLASH	23622248
MIRT046925	hsa-miR-221-3p	CLASH	23622248
MIRT045790	hsa-miR-191-5p	CLASH	23622248
MIRT039881	hsa-miR-615-3p	CLASH	23622248
MIRT039881	hsa-miR-615-3p	CLASH	23622248
MIRT021236	hsa-miR-146a-5p	Immunohistochemistry, Luciferase reporter assay, Microarray, Western blot	23982143
MIRT021236	hsa-miR-146a-5p	Immunohistochemistry, Luciferase reporter assay, Microarray, Western blot	23982143
MIRT053567	hsa-miR-146b-5p	Immunohistochemistry, Luciferase reporter assay, Microarray, Western blot	23982143
MIRT053567	hsa-miR-146b-5p	Immunohistochemistry, Luciferase reporter assay, Microarray, Western blot	23982143
MIRT052615	hsa-let-7a-5p	Luciferase reporter assay, qRT-PCR, Western blot	26049093
MIRT002574	hsa-miR-124-3p	Luciferase reporter assay, Western blot	26310391
MIRT002574	hsa-miR-124-3p	Luciferase reporter assay, Western blot	26310391
MIRT001580	hsa-let-7b-5p	Luciferase reporter assay, Western blotting, qRT-PCR	31873045
MIRT756026	hsa-miR-520d-3p	Luciferase reporter assay, Western blotting, qRT-PCR, ChIP-seq	35664070
MIRT1474167	hsa-miR-101	CLIP-seq
MIRT1474168	hsa-miR-1263	CLIP-seq
MIRT1474169	hsa-miR-1283	CLIP-seq
MIRT1474170	hsa-miR-1305	CLIP-seq
MIRT1474171	hsa-miR-144	CLIP-seq
MIRT1474172	hsa-miR-148a	CLIP-seq
MIRT1474173	hsa-miR-148b	CLIP-seq
MIRT1474174	hsa-miR-152	CLIP-seq
MIRT1474175	hsa-miR-3133	CLIP-seq
MIRT1474176	hsa-miR-4301	CLIP-seq
MIRT1474177	hsa-miR-4307	CLIP-seq
MIRT1474178	hsa-miR-4511	CLIP-seq
MIRT1474179	hsa-miR-548b-3p	CLIP-seq
MIRT1474180	hsa-miR-578	CLIP-seq
MIRT1474181	hsa-miR-606	CLIP-seq
MIRT1474182	hsa-miR-607	CLIP-seq
MIRT1474183	hsa-let-7a	CLIP-seq
MIRT1474184	hsa-let-7b	CLIP-seq
MIRT1474185	hsa-let-7c	CLIP-seq
MIRT1474186	hsa-let-7d	CLIP-seq
MIRT1474187	hsa-let-7e	CLIP-seq
MIRT1474188	hsa-let-7f	CLIP-seq
MIRT1474189	hsa-let-7g	CLIP-seq
MIRT1474190	hsa-let-7i	CLIP-seq
MIRT1474191	hsa-miR-1243	CLIP-seq
MIRT1474192	hsa-miR-1275	CLIP-seq
MIRT1474193	hsa-miR-1278	CLIP-seq
MIRT1474194	hsa-miR-1292	CLIP-seq
MIRT1474195	hsa-miR-1304	CLIP-seq
MIRT1474170	hsa-miR-1305	CLIP-seq
MIRT1474196	hsa-miR-135a	CLIP-seq
MIRT1474197	hsa-miR-135b	CLIP-seq
MIRT1474198	hsa-miR-1827	CLIP-seq
MIRT1474199	hsa-miR-188-5p	CLIP-seq
MIRT1474200	hsa-miR-200b	CLIP-seq
MIRT1474201	hsa-miR-200c	CLIP-seq
MIRT1474202	hsa-miR-202	CLIP-seq
MIRT1474203	hsa-miR-2909	CLIP-seq
MIRT1474204	hsa-miR-3119	CLIP-seq
MIRT1474175	hsa-miR-3133	CLIP-seq
MIRT1474205	hsa-miR-3162-5p	CLIP-seq
MIRT1474206	hsa-miR-323-3p	CLIP-seq
MIRT1474207	hsa-miR-339-5p	CLIP-seq
MIRT1474208	hsa-miR-3545-3p	CLIP-seq
MIRT1474209	hsa-miR-3646	CLIP-seq
MIRT1474210	hsa-miR-3654	CLIP-seq
MIRT1474211	hsa-miR-371-5p	CLIP-seq
MIRT1474212	hsa-miR-374c	CLIP-seq
MIRT1474213	hsa-miR-378	CLIP-seq
MIRT1474214	hsa-miR-378b	CLIP-seq
MIRT1474215	hsa-miR-378c	CLIP-seq
MIRT1474216	hsa-miR-378d	CLIP-seq
MIRT1474217	hsa-miR-378e	CLIP-seq
MIRT1474218	hsa-miR-378f	CLIP-seq
MIRT1474219	hsa-miR-378h	CLIP-seq
MIRT1474220	hsa-miR-378i	CLIP-seq
MIRT1474221	hsa-miR-3929	CLIP-seq
MIRT1474222	hsa-miR-3973	CLIP-seq
MIRT1474223	hsa-miR-422a	CLIP-seq
MIRT1474224	hsa-miR-4251	CLIP-seq
MIRT1474225	hsa-miR-4261	CLIP-seq
MIRT1474226	hsa-miR-4274	CLIP-seq
MIRT1474227	hsa-miR-4282	CLIP-seq
MIRT1474228	hsa-miR-429	CLIP-seq
MIRT1474229	hsa-miR-4299	CLIP-seq
MIRT1474177	hsa-miR-4307	CLIP-seq
MIRT1474230	hsa-miR-4419b	CLIP-seq
MIRT1474231	hsa-miR-4447	CLIP-seq
MIRT1474232	hsa-miR-4456	CLIP-seq
MIRT1474233	hsa-miR-4458	CLIP-seq
MIRT1474234	hsa-miR-4461	CLIP-seq
MIRT1474235	hsa-miR-4464	CLIP-seq
MIRT1474236	hsa-miR-4472	CLIP-seq
MIRT1474237	hsa-miR-4478	CLIP-seq
MIRT1474238	hsa-miR-4496	CLIP-seq
MIRT1474239	hsa-miR-4500	CLIP-seq
MIRT1474240	hsa-miR-4501	CLIP-seq
MIRT1474178	hsa-miR-4511	CLIP-seq
MIRT1474241	hsa-miR-4525	CLIP-seq
MIRT1474242	hsa-miR-4638-3p	CLIP-seq
MIRT1474243	hsa-miR-4665-5p	CLIP-seq
MIRT1474244	hsa-miR-4668-3p	CLIP-seq
MIRT1474245	hsa-miR-4723-5p	CLIP-seq
MIRT1474246	hsa-miR-4731-3p	CLIP-seq
MIRT1474247	hsa-miR-4748	CLIP-seq
MIRT1474248	hsa-miR-4801	CLIP-seq
MIRT1474249	hsa-miR-541	CLIP-seq
MIRT1474250	hsa-miR-548k	CLIP-seq
MIRT1474251	hsa-miR-548q	CLIP-seq
MIRT1474252	hsa-miR-553	CLIP-seq
MIRT1474253	hsa-miR-580	CLIP-seq
MIRT1474182	hsa-miR-607	CLIP-seq
MIRT1474254	hsa-miR-622	CLIP-seq
MIRT1474255	hsa-miR-625	CLIP-seq
MIRT1474256	hsa-miR-654-5p	CLIP-seq
MIRT1474257	hsa-miR-655	CLIP-seq
MIRT1474258	hsa-miR-7	CLIP-seq
MIRT1474259	hsa-miR-873	CLIP-seq
MIRT1474260	hsa-miR-9	CLIP-seq
MIRT1474261	hsa-miR-98	CLIP-seq
MIRT1474172	hsa-miR-148a	CLIP-seq
MIRT1474173	hsa-miR-148b	CLIP-seq
MIRT1474174	hsa-miR-152	CLIP-seq
MIRT1474204	hsa-miR-3119	CLIP-seq
MIRT1474206	hsa-miR-323-3p	CLIP-seq
MIRT1474212	hsa-miR-374c	CLIP-seq
MIRT2142725	hsa-miR-4662a-5p	CLIP-seq
MIRT2142726	hsa-miR-4676-5p	CLIP-seq
MIRT2142727	hsa-miR-548c-3p	CLIP-seq
MIRT2142728	hsa-miR-575	CLIP-seq
MIRT1474257	hsa-miR-655	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
E2F1	Activation	12838312;15361834
E2F1	Unknown	23023523
TP53	Repression	18220474;19501055

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IDA	21777816
GO:0000785	Component	Chromatin	IDA	17673620
GO:0000785	Component	Chromatin	ISS
GO:0000791	Component	Euchromatin	IDA	21777816
GO:0000792	Component	Heterochromatin	IDA	17967883, 21489993, 21777816
GO:0000987	Function	Cis-regulatory region sequence-specific DNA binding	IDA	10646863
GO:0004842	Function	Ubiquitin-protein transferase activity	IDA	17967883, 21745816, 22945642
GO:0005515	Function	Protein binding	IPI	15361834, 17673620, 17934516, 19798101, 21745816, 22945642
GO:0005634	Component	Nucleus	IDA	10646863
GO:0005654	Component	Nucleoplasm	IDA
GO:0005657	Component	Replication fork	IDA	17673620
GO:0006281	Process	DNA repair	IEA
GO:0006511	Process	Ubiquitin-dependent protein catabolic process	IDA	22945642
GO:0007049	Process	Cell cycle	IEA
GO:0008270	Function	Zinc ion binding	IDA	21777816
GO:0008327	Function	Methyl-CpG binding	IDA	15361834, 21029866
GO:0010216	Process	Maintenance of DNA methylation	IBA	21873635
GO:0010216	Process	Maintenance of DNA methylation	IMP	17673620
GO:0010390	Process	Histone monoubiquitination	IBA	21873635
GO:0010390	Process	Histone monoubiquitination	ISS
GO:0016363	Component	Nuclear matrix	ISS
GO:0016567	Process	Protein ubiquitination	IBA	21873635
GO:0016574	Process	Histone ubiquitination	IDA	17967883
GO:0031493	Function	Nucleosomal histone binding	ISS
GO:0032270	Process	Positive regulation of cellular protein metabolic process	IDA	10646863
GO:0035064	Function	Methylated histone binding	IDA	17967883, 21029866, 21489993
GO:0042393	Function	Histone binding	IDA	21777816
GO:0042802	Function	Identical protein binding	ISS
GO:0044729	Function	Hemi-methylated DNA-binding	IDA	17673620
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IC	10646863
GO:0050678	Process	Regulation of epithelial cell proliferation	IMP	15361834
GO:0051865	Process	Protein autoubiquitination	IDA	17967883, 21745816
GO:0061630	Function	Ubiquitin protein ligase activity	IBA	21873635
GO:0061630	Function	Ubiquitin protein ligase activity	ISS
GO:2000373	Process	Positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity	IC	10646863

Other IDs

• MIM: 607990
• HGNC: 12556
• e!Ensembl: ENSG00000276043

Protein

• UniProt ID: Q96T88
• Protein name: E3 ubiquitin-protein ligase UHRF1 (EC 2.3.2.27) (Inverted CCAAT box-binding protein of 90 kDa) (Nuclear protein 95) (Nuclear zinc finger protein Np95) (HuNp95) (hNp95) (RING finger protein 106) (RING-type E3 ubiquitin transferase UHRF1) (Transcription fac
• Protein function: Multidomain protein that acts as a key epigenetic regulator by bridging DNA methylation and chromatin modification. Specifically recognizes and binds hemimethylated DNA at replication forks via its YDG domain and recruits DNMT1 methyltransferase
• PDB: 2FAZ, 2L3R, 2LGG, 2LGK, 2LGL, 2PB7, 3ASK, 3ASL, 3BI7, 3CLZ, 3DB3, 3DB4, 3DWH, 3FL2, 3SHB, 3SOU, 3SOW, 3SOX, 3T6R, 3ZVY, 3ZVZ, 4GY5, 4QQD, 5C6D, 5IAY, 5XPI, 5YY9, 5YYA, 6B9M, 6IIW, 6VCS, 6VED, 6VYJ, 6W92, 7FB7, 8JIG, 8WMS, 8XV4, 8XV6, 8XV7, 8XV8
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00240	ubiquitin	3 → 76	Ubiquitin family	Domain
  PF12148	TTD	132 → 284	Tandem tudor domain within UHRF1	Domain
  PF00628	PHD	317 → 366	PHD-finger	Domain
  PF02182	SAD_SRA	417 → 586	SAD/SRA domain	Domain

• Sequence:

  MWIQVRTMDGRQTHTVDSLSRLTKVEELRRKIQELFHVEPGLQRLFYRGKQMEDGHTLFD
  YEVRLNDTIQLLVRQSLVLPHSTKERDSELSDTDSGCCLGQSESDKSSTHGEAAAETDSR
  PADEDMWDETELGLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEE
  DVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNPKERGFWYD
  AEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGP
  SCKHCKDDVNRLCRVCACHLCGGRQDPDKQLMCDECDMAFHIYCLDPPLSSVPSEDEWYC
  PECRNDASEVVLAGERLRESKKKAKMASATSSSQRDWGKGMACVGRTKECTIVPSNHYGP
  IPGIPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVDHGNFFTYTG
  SGGRDLSGNKRTAEQSCDQKLTNTNRALALNCFAPINDQEGAEAKDWRSGKPVRVVRNVK
  GGKNSKYAPAEGNRYDGIYKVVKYWPEKGKSGFLVWRYLLRRDDDEPGPWTKEGKDRIKK
  LGLTMQYPEGYLEALANREREKENSKREEEEQQEGGFASPRTGKGKWKRKSAGGGPSRAG
  SPRRTSKKTKVEPYSLTAQQSSLIREDKSNAKLWNEVLASLKDRPASGSPFQLFLSKVEE
  TFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYDLGRSYAMQVNQPLQT
  VLNQLFPGYGNGR

• Sequence length: 793

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Adenocarcinoma	Adenoid Cystic Carcinoma	rs121913530, rs886039394, rs121913474	23685749
Myocardial infarction	Myocardial Infarction	rs12316150, rs41303970, rs909253, rs7291467, rs2234693	21211798

Unknown
Disease name	Disease term	dbSNP ID	References
Cardiovascular diseases	Cardiovascular Diseases		30595370
Liver carcinoma	Liver carcinoma		28284560