MBD1 (methyl-CpG binding domain protein 1)

Gene

• Entrez ID: 4152
• Gene name: Methyl-CpG binding domain protein 1
• Gene symbol: MBD1
• Synonyms: CXXC3, PCM1, RFT
• Chromosome: 18
• Chromosome location: 18q21.1
• Summary: The protein encoded by this gene is a member of a family of nuclear proteins related by the presence of a methyl-CpG binding domain (MBD). These proteins are capable of binding specifically to methylated DNA, and some members can also repress transcriptio

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT007219	hsa-miR-195-5p	Luciferase reporter assay	23349673
MIRT050283	hsa-miR-25-3p	CLASH	23622248
MIRT047606	hsa-miR-10a-5p	CLASH	23622248
MIRT040325	hsa-miR-615-3p	CLASH	23622248
MIRT690077	hsa-miR-18a-5p	HITS-CLIP	23313552
MIRT690076	hsa-miR-18b-5p	HITS-CLIP	23313552
MIRT690075	hsa-miR-4735-3p	HITS-CLIP	23313552
MIRT690074	hsa-miR-6504-3p	HITS-CLIP	23313552
MIRT690073	hsa-miR-4761-5p	HITS-CLIP	23313552
MIRT690072	hsa-miR-6814-5p	HITS-CLIP	23313552
MIRT690071	hsa-miR-1234-3p	HITS-CLIP	23313552
MIRT690070	hsa-miR-7107-5p	HITS-CLIP	23313552
MIRT690069	hsa-miR-150-5p	HITS-CLIP	23313552
MIRT690068	hsa-miR-1913	HITS-CLIP	23313552
MIRT690067	hsa-miR-324-3p	HITS-CLIP	23313552
MIRT690066	hsa-miR-18a-3p	HITS-CLIP	23313552
MIRT690065	hsa-miR-619-5p	HITS-CLIP	23313552
MIRT690064	hsa-miR-6506-5p	HITS-CLIP	23313552
MIRT690063	hsa-miR-4707-3p	HITS-CLIP	23313552
MIRT690062	hsa-miR-6778-3p	HITS-CLIP	23313552
MIRT690061	hsa-miR-4731-5p	HITS-CLIP	23313552
MIRT690060	hsa-miR-5589-5p	HITS-CLIP	23313552
MIRT690059	hsa-miR-5095	HITS-CLIP	23313552
MIRT690058	hsa-miR-7151-3p	HITS-CLIP	23313552
MIRT690057	hsa-miR-5089-5p	HITS-CLIP	23313552
MIRT678996	hsa-miR-4797-5p	HITS-CLIP	23824327
MIRT678994	hsa-miR-5007-5p	HITS-CLIP	23824327
MIRT678995	hsa-miR-4524a-3p	HITS-CLIP	23824327
MIRT678992	hsa-miR-3672	HITS-CLIP	23824327
MIRT678993	hsa-miR-6864-3p	HITS-CLIP	23824327
MIRT678991	hsa-miR-8055	HITS-CLIP	23824327
MIRT290618	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT690077	hsa-miR-18a-5p	HITS-CLIP	23313552
MIRT690076	hsa-miR-18b-5p	HITS-CLIP	23313552
MIRT690075	hsa-miR-4735-3p	HITS-CLIP	23313552
MIRT690074	hsa-miR-6504-3p	HITS-CLIP	23313552
MIRT690073	hsa-miR-4761-5p	HITS-CLIP	23313552
MIRT690072	hsa-miR-6814-5p	HITS-CLIP	23313552
MIRT690071	hsa-miR-1234-3p	HITS-CLIP	23313552
MIRT690070	hsa-miR-7107-5p	HITS-CLIP	23313552
MIRT690069	hsa-miR-150-5p	HITS-CLIP	23313552
MIRT690068	hsa-miR-1913	HITS-CLIP	23313552
MIRT690067	hsa-miR-324-3p	HITS-CLIP	23313552
MIRT690066	hsa-miR-18a-3p	HITS-CLIP	23313552
MIRT690065	hsa-miR-619-5p	HITS-CLIP	23313552
MIRT690064	hsa-miR-6506-5p	HITS-CLIP	23313552
MIRT690063	hsa-miR-4707-3p	HITS-CLIP	23313552
MIRT690062	hsa-miR-6778-3p	HITS-CLIP	23313552
MIRT690061	hsa-miR-4731-5p	HITS-CLIP	23313552
MIRT690060	hsa-miR-5589-5p	HITS-CLIP	23313552
MIRT690059	hsa-miR-5095	HITS-CLIP	23313552
MIRT690058	hsa-miR-7151-3p	HITS-CLIP	23313552
MIRT690057	hsa-miR-5089-5p	HITS-CLIP	23313552
MIRT678996	hsa-miR-4797-5p	HITS-CLIP	23824327
MIRT678994	hsa-miR-5007-5p	HITS-CLIP	23824327
MIRT678995	hsa-miR-4524a-3p	HITS-CLIP	23824327
MIRT678992	hsa-miR-3672	HITS-CLIP	23824327
MIRT678993	hsa-miR-6864-3p	HITS-CLIP	23824327
MIRT678991	hsa-miR-8055	HITS-CLIP	23824327
MIRT290618	hsa-miR-129-5p	HITS-CLIP	23824327
MIRT1134787	hsa-miR-1343	CLIP-seq
MIRT1134788	hsa-miR-4268	CLIP-seq
MIRT1134789	hsa-miR-4286	CLIP-seq
MIRT1134790	hsa-miR-4448	CLIP-seq
MIRT1134791	hsa-miR-498	CLIP-seq
MIRT1134792	hsa-miR-4676-5p	CLIP-seq
MIRT1134793	hsa-miR-575	CLIP-seq
MIRT1134794	hsa-miR-634	CLIP-seq
MIRT1134795	hsa-miR-125a-3p	CLIP-seq
MIRT1134796	hsa-miR-3157-5p	CLIP-seq
MIRT1134797	hsa-miR-33a	CLIP-seq
MIRT1134798	hsa-miR-33b	CLIP-seq
MIRT1134799	hsa-miR-3934	CLIP-seq
MIRT1134800	hsa-miR-4291	CLIP-seq
MIRT1134801	hsa-miR-4310	CLIP-seq
MIRT1134802	hsa-miR-4424	CLIP-seq
MIRT1134803	hsa-miR-4461	CLIP-seq
MIRT1134804	hsa-miR-4468	CLIP-seq
MIRT1134805	hsa-miR-4519	CLIP-seq
MIRT1134806	hsa-miR-4691-3p	CLIP-seq
MIRT1134807	hsa-miR-4792	CLIP-seq
MIRT1134808	hsa-miR-764	CLIP-seq
MIRT2442351	hsa-miR-3124-3p	CLIP-seq
MIRT2442352	hsa-miR-4274	CLIP-seq
MIRT1134805	hsa-miR-4519	CLIP-seq
MIRT2465608	hsa-miR-1915	CLIP-seq
MIRT2465609	hsa-miR-624	CLIP-seq
MIRT2465610	hsa-miR-720	CLIP-seq
MIRT2567884	hsa-miR-1287	CLIP-seq
MIRT2567885	hsa-miR-1293	CLIP-seq
MIRT2567886	hsa-miR-216b	CLIP-seq
MIRT2567887	hsa-miR-3135b	CLIP-seq
MIRT1134796	hsa-miR-3157-5p	CLIP-seq
MIRT1134797	hsa-miR-33a	CLIP-seq
MIRT1134798	hsa-miR-33b	CLIP-seq
MIRT2567888	hsa-miR-376a	CLIP-seq
MIRT2567889	hsa-miR-376b	CLIP-seq
MIRT2567890	hsa-miR-4314	CLIP-seq
MIRT2567891	hsa-miR-4417	CLIP-seq
MIRT2567892	hsa-miR-4483	CLIP-seq
MIRT1134792	hsa-miR-4676-5p	CLIP-seq
MIRT2567893	hsa-miR-541	CLIP-seq
MIRT1134793	hsa-miR-575	CLIP-seq
MIRT1134794	hsa-miR-634	CLIP-seq
MIRT2567894	hsa-miR-642b	CLIP-seq
MIRT2567895	hsa-miR-654-5p	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
HDAC3	Unknown	16432238

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003677	Function	DNA binding	TAS	9774669
GO:0005515	Function	Protein binding	IPI	12665582, 12711603, 16432238, 19498464, 19666599, 23275563
GO:0005634	Component	Nucleus	NAS	10454587
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0006366	Process	Transcription by RNA polymerase II	TAS	9774669
GO:0008270	Function	Zinc ion binding	IDA	29276034
GO:0008327	Function	Methyl-CpG binding	IDA	25284789
GO:0008327	Function	Methyl-CpG binding	NAS	10454587
GO:0010385	Function	Double-stranded methylated DNA binding	IDA	11371345
GO:0016363	Component	Nuclear matrix	ISS
GO:0016607	Component	Nuclear speck	ISS
GO:0045322	Function	Unmethylated CpG binding	IDA	29276034
GO:0045892	Process	Negative regulation of transcription, DNA-templated	NAS	10454587

Other IDs

• MIM: 156535
• HGNC: 6916
• e!Ensembl: ENSG00000141644

Protein

• UniProt ID: Q9UIS9
• Protein name: Methyl-CpG-binding domain protein 1 (CXXC-type zinc finger protein 3) (Methyl-CpG-binding protein MBD1) (Protein containing methyl-CpG-binding domain 1)
• Protein function: Transcriptional repressor that binds CpG islands in promoters where the DNA is methylated at position 5 of cytosine within CpG dinucleotides. Binding is abolished by the presence of 7-mG that is produced by DNA damage by methylmethanesulfonate (
• PDB: 1D9N, 1IG4, 4D4W, 5W9Q, 6D1T
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01429	MBD	1 → 88	Methyl-CpG binding domain	Domain
  PF02008	zf-CXXC	168 → 215	CXXC zinc finger domain	Domain
  PF02008	zf-CXXC	217 → 262	CXXC zinc finger domain	Domain
  PF02008	zf-CXXC	330 → 377	CXXC zinc finger domain	Domain

• Sequence:

  MAEDWLDCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPACDLT
  LFDFKQGILCYPAPKAHPVAVASKKRKKPSRPAKTRKRQVGPQSGEVRKEAPRDETKADT
  DTAPASFPAPGCCENCGISFSGDGTQRQRLKTLCKDCRAQRIAFNREQRMFKRVGCGECA
  ACQVTEDCGACSTCLLQLPHDVASGLFCKCERRRCLRIVERSRGCGVCRGCQTQEDCGHC
  PICLRPPRPGLRRQWKCVQRRCLRGKHARRKGGCDSKMAARRRPGAQPLPPPPPSQSPEP
  TEPHPRALAPSPPAEFIYYCVDEDELQPYTNRRQNRKCGACAACLRRMDCGRCDFCCDKP
  KFGGSNQKRQKCRWRQCLQFAMKRLLPSVWSESEDGAGSPPPYRRRKRPSSARRHHLGPT
  LKPTLATRTAQPDHTQAPTKQEAGGGFVLPPPGTDLVFLREGASSPVQVPGPVAASTEAL
  LQEAQCSGLSWVVALPQVKQEKADTQDEWTPGTAVLTSPVLVPGCPSKAVDPGLPSVKQE
  PPDPEEDKEENKDDSASKLAPEEEAGGAGTPVITEIFSLGGTRFRDTAVWLPRSKDLKKP
  GARKQ

• Sequence length: 605

Pathways

Reactome:

SUMOylation of transcription cofactors

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Prostate cancer	Malignant neoplasm of prostate	rs121909139, rs121909140, rs121909141, rs121909142, rs121909143, rs606231169, rs606231170, rs137852584, rs137852578, rs137852580, rs137852581, rs137852582	29610475

Unknown
Disease name	Disease term	dbSNP ID	References
Prostatic neoplasms	Prostatic Neoplasms		29610475