BioPAX pathway converted from "PHF8 demethylates histone H4K20me1" in the Reactome database.PHF8 demethylates histone H4K20me1

PHF8 demethylates histone H4K20me1

PHF8, a PHD and Jumonji C domain-containing protein, is recruited to chromatin by binding to dimethylated or trimethylated histone H3 - H3K4me2 and/or H3K4me3. PHF8 demethylates monomethylated histone H4, H4K20me1, a docking site for the condesin II complex (Liu et al. 2010).

Authored: Orlic-Milacic, M, 2013-04-22Reviewed: Longworth, MS, 2013-10-14Edited: Matthews, L, 2013-04-23

Reactome DB_ID: 113671

nucleoplasmGO0005654

2-oxoglutarate(2-) [ChEBI:16810]

2-oxoglutarate(2-)

2-ketoglutaratealpha-ketoglutarate2-oxopentanedioic acid, ion(2-)2-oxoglutarate

Reactomehttp://www.reactome.orgChEBI16810

Reactome DB_ID: 113685

dioxygen [ChEBI:15379]

dioxygen

ChEBI15379

Reactome DB_ID: 2172686

PHF8:Nucleosome with H3K4me2/3:H4K20me1 [nucleoplasm]

PHF8:Nucleosome with H3K4me2/3:H4K20me1

Reactome DB_ID: 2245219

PHF8:Fe2+ [nucleoplasm]

PHF8:Fe2+

Converted from EntitySet in Reactome

Reactome DB_ID: 2245214

PHF8 [nucleoplasm]Converted from EntitySet in Reactome. Each synonym is a name of a PhysicalEntity, and each XREF points to one PhysicalEntityPHF8-2 [nucleoplasm]

Homo sapiens

NCBI Taxonomy9606UniProtQ9UPP1-2

Reactome DB_ID: 111793

iron(2+) [ChEBI:29033]

iron(2+)

FE (II) IONFe(2+)Fe(II)Ferrous ionFe2+iron ion(2+)

ChEBI29033Reactome Database ID Release 752245219Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2245219ReactomeR-HSA-2245219

Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=R-HSA-2245219.1

Reactome DB_ID: 2245190

Nucleosome with H3K4me2/3:H4K20me1 [nucleoplasm]

Nucleosome with H3K4me2/3:H4K20me1

Converted from EntitySet in Reactome

Reactome DB_ID: 181899

Histone H2A [nucleoplasm]Converted from EntitySet in Reactome. Each synonym is a name of a PhysicalEntity, and each XREF points to one PhysicalEntity

Converted from EntitySet in Reactome

Reactome DB_ID: 181911

Histone H2B [nucleoplasm]Converted from EntitySet in Reactome. Each synonym is a name of a PhysicalEntity, and each XREF points to one PhysicalEntity

Reactome DB_ID: 2172676

UniProt:P62805 H4C1

H4C1

H4FAH4FCH4FBH4FEH4FDH4FGH4FIH4FHH4FKH4FJH4FMH4FOH4FNH4C2H4C1H4C4H4C3H4C6H4C5H4-16H4C15H4C14HIST4H4H4C13H4C12HIST2H4H4C11H4F2H4/DH4/CH4/EH4/HH4/GH4/JH4/IH4/KH4/NH4/MH4/OHIST2H4AHIST2H4BH4C8H4C9HIST1H4KHIST1H4LHIST1H4AHIST1H4BHIST1H4HHIST1H4IHIST1H4JHIST1H4CHIST1H4DH4/BHIST1H4EH4/AHIST1H4FFUNCTION Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.SUBUNIT The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.PTM Acetylation at Lys-6 (H4K5ac), Lys-9 (H4K8ac), Lys-13 (H4K12ac) and Lys-17 (H4K16ac) occurs in coding regions of the genome but not in heterochromatin.PTM Citrullination at Arg-4 (H4R3ci) by PADI4 impairs methylation.PTM Monomethylation and asymmetric dimethylation at Arg-4 (H4R3me1 and H4R3me2a, respectively) by PRMT1 favors acetylation at Lys-9 (H4K8ac) and Lys-13 (H4K12ac). Demethylation is performed by JMJD6. Symmetric dimethylation on Arg-4 (H4R3me2s) by the PRDM1/PRMT5 complex may play a crucial role in the germ-cell lineage.PTM Monomethylated, dimethylated or trimethylated at Lys-21 (H4K20me1, H4K20me2, H4K20me3) (PubMed:12086618, PubMed:15964846, PubMed:17967882). Monomethylation is performed by KMT5A/SET8 (PubMed:15964846). Dimethylation and trimethylation is performed by KMT5B and KMT5C and induces gene silencing (By similarity). Monomethylated at Lys-13 (H4K12me1) by N6AMT1; H4K12me1 modification is present at the promoters of numerous genes encoding cell cycle regulators (PubMed:31061526).PTM Phosphorylated by PAK2 at Ser-48 (H4S47ph). This phosphorylation increases the association of H3.3-H4 with the histone chaperone HIRA, thus promoting nucleosome assembly of H3.3-H4 and inhibiting nucleosome assembly of H3.1-H4.PTM Ubiquitinated by the CUL4-DDB-RBX1 complex in response to ultraviolet irradiation. This may weaken the interaction between histones and DNA and facilitate DNA accessibility to repair proteins. Monoubiquitinated at Lys-92 of histone H4 (H4K91ub1) in response to DNA damage. The exact role of H4K91ub1 in DNA damage response is still unclear but it may function as a licensing signal for additional histone H4 post-translational modifications such as H4 Lys-21 methylation (H4K20me).PTM Ufmylated; monofmylated by UFL1 at Lys-32 (H4K31Ufm1) in response to DNA damage.PTM Sumoylated, which is associated with transcriptional repression.PTM Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes.PTM Butyrylation of histones marks active promoters and competes with histone acetylation.PTM Glutarylation at Lys-92 (H4K91glu) destabilizes nucleosomes by promoting dissociation of the H2A-H2B dimers from nucleosomes.DISEASE Chromosomal aberrations involving HISTONE H4 is a cause of B-cell non-Hodgkin lymphomas (B-cell NHL). Translocation t(3;6)(q27;p21), with BCL6.SIMILARITY Belongs to the histone H4 family.

UniProtP62805

N6-methyl-L-lysine at 21

EQUAL

N6-methyl-L-lysine [MOD:00085]

Chain Coordinates

EQUAL

103

EQUAL

Converted from EntitySet in Reactome

Reactome DB_ID: 2245189

H3K4me2/3 [nucleoplasm]Converted from EntitySet in Reactome. Each synonym is a name of a PhysicalEntity, and each XREF points to one PhysicalEntity

Reactome Database ID Release 752245190Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2245190ReactomeR-HSA-2245190

Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=R-HSA-2245190.1Reactome Database ID Release 752172686Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2172686ReactomeR-HSA-2172686

Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=R-HSA-2172686.1

Reactome DB_ID: 29478

formaldehyde [ChEBI:16842]

formaldehyde

ChEBI16842

Reactome DB_ID: 2172681

PHF8:Nucleosome with H3K4me2/3 [nucleoplasm]

PHF8:Nucleosome with H3K4me2/3

Reactome DB_ID: 2245219

Reactome DB_ID: 2245194

Nucleosome with H3K4me2/3 [nucleoplasm]

Nucleosome with H3K4me2/3

Converted from EntitySet in Reactome

Reactome DB_ID: 181899

Converted from EntitySet in Reactome

Reactome DB_ID: 181911

Reactome DB_ID: 181902

EQUAL

103

EQUAL

Converted from EntitySet in Reactome

Reactome DB_ID: 2245189

Reactome Database ID Release 752245194Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2245194ReactomeR-HSA-2245194

Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=R-HSA-2245194.1Reactome Database ID Release 752172681Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2172681ReactomeR-HSA-2172681

Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=R-HSA-2172681.1

Reactome DB_ID: 159939

succinate(2-) [ChEBI:30031]

succinate(2-)

succinate(-)OOC-CH2-CH2-COO(-)butanedioic acid, ion(2-)butanedioate

ChEBI30031

Reactome DB_ID: 159942

carbon dioxide [ChEBI:16526]

carbon dioxide

ChEBI16526PHYSIOL-LEFT-TO-RIGHT

ACTIVATION

Reactome DB_ID: 2172686

GO0035575

GO molecular function

Reactome Database ID Release 752172687Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2172687Reactome Database ID Release 752172678Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2172678ReactomeR-HSA-2172678

Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=R-HSA-2172678.120622854Pubmed2010PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progressionLiu, WTanasa, BTyurina, OVZhou, TYGassmann, RLiu, WTOhgi, KABenner, CGarcia-Bassets, IAggarwal, AKDesai, ADorrestein, PCGlass, CKRosenfeld, MGNature 466:508-12