ID REQU_HUMAN Reviewed; 391 AA.
AC Q92785; A8K7C9; B4DT58;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 27-MAR-2024, entry version 217.
DE RecName: Full=Zinc finger protein ubi-d4;
DE AltName: Full=Apoptosis response zinc finger protein;
DE AltName: Full=BRG1-associated factor 45D;
DE Short=BAF45D;
DE AltName: Full=D4, zinc and double PHD fingers family 2;
DE AltName: Full=Protein requiem;
GN Name=DPF2; Synonyms=BAF45D, REQ, UBID4;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RX PubMed=9253601; DOI=10.1101/gr.7.7.725;
RA Guru S.C., Agarwal S.K., Manickam P., Olufemi S.-E., Crabtree J.S.,
RA Weisemann J.M., Kester M.B., Kim Y.S., Wang Y., Emmert-Buck M.R.,
RA Liotta L.A., Spiegel A.M., Boguski M.S., Roe B.A., Collins F.S.,
RA Burns A.L., Marx S.J., Chandrasekharappa S.C.;
RT "A transcript map for the 2.8-Mb region containing the multiple endocrine
RT neoplasia type 1 locus.";
RL Genome Res. 7:725-735(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RX PubMed=9680388; DOI=10.1007/s003359900840;
RA Gabig T.G., Crean C.D., Klenk A., Long H., Copeland N.G., Gilbert D.J.,
RA Jenkins N.A., Quincey D., Parente F., Lespinasse F., Carle G.F.,
RA Gaudray P., Zhang C.X., Calender A., Hoeppener J., Kas K., Thakker R.V.,
RA Farnebo F., Teh B.T., Larsson C., Piehl F., Lagercrantz J., Khodaei S.,
RA Carson E., Weber G.;
RT "Expression and chromosomal localization of the Requiem gene.";
RL Mamm. Genome 9:660-665(1998).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RA Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S.,
RA Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y.,
RA Phelan M., Farmer A.;
RT "Cloning of human full-length CDSs in BD Creator(TM) system donor vector.";
RL Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RG NIEHS SNPs program;
RL Submitted (JAN-2003) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC TISSUE=Pericardium;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16554811; DOI=10.1038/nature04632;
RA Taylor T.D., Noguchi H., Totoki Y., Toyoda A., Kuroki Y., Dewar K.,
RA Lloyd C., Itoh T., Takeda T., Kim D.-W., She X., Barlow K.F., Bloom T.,
RA Bruford E., Chang J.L., Cuomo C.A., Eichler E., FitzGerald M.G.,
RA Jaffe D.B., LaButti K., Nicol R., Park H.-S., Seaman C., Sougnez C.,
RA Yang X., Zimmer A.R., Zody M.C., Birren B.W., Nusbaum C., Fujiyama A.,
RA Hattori M., Rogers J., Lander E.S., Sakaki Y.;
RT "Human chromosome 11 DNA sequence and analysis including novel gene
RT identification.";
RL Nature 440:497-500(2006).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [8]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Uterus;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [9]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 12-64.
RX PubMed=8812431; DOI=10.1006/geno.1996.0440;
RA Chestkov A.V., Baka I.D., Kost M.V., Georgiev G.P., Buchman V.L.;
RT "The d4 gene family in the human genome.";
RL Genomics 36:174-177(1996).
RN [10]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-142 AND THR-176, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [11]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in a
RT refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-142; TYR-172 AND THR-176, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Leukemic T-cell;
RX PubMed=19690332; DOI=10.1126/scisignal.2000007;
RA Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
RA Rodionov V., Han D.K.;
RT "Quantitative phosphoproteomic analysis of T cell receptor signaling
RT reveals system-wide modulation of protein-protein interactions.";
RL Sci. Signal. 2:RA46-RA46(2009).
RN [13]
RP FUNCTION, AND INTERACTION WITH SMARCA2; SMARCA4; SMARCB1 AND SMARCB1.
RX PubMed=20460684; DOI=10.1074/jbc.m109.087783;
RA Tando T., Ishizaka A., Watanabe H., Ito T., Iida S., Haraguchi T.,
RA Mizutani T., Izumi T., Isobe T., Akiyama T., Inoue J., Iba H.;
RT "Requiem protein links RelB/p52 and the Brm-type SWI/SNF complex in a
RT noncanonical NF-kappaB pathway.";
RL J. Biol. Chem. 285:21951-21960(2010).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-142; THR-176 AND SER-200, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full phosphorylation
RT site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [15]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [16]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-142; THR-176 AND SER-244, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21406692; DOI=10.1126/scisignal.2001570;
RA Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T.,
RA Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.;
RT "System-wide temporal characterization of the proteome and phosphoproteome
RT of human embryonic stem cell differentiation.";
RL Sci. Signal. 4:RS3-RS3(2011).
RN [17]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-142; THR-176; SER-200 AND
RP SER-280, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma, and Erythroleukemia;
RX PubMed=23186163; DOI=10.1021/pr300630k;
RA Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
RA Mohammed S.;
RT "Toward a comprehensive characterization of a human cancer cell
RT phosphoproteome.";
RL J. Proteome Res. 12:260-271(2013).
RN [18]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
RA Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L.,
RA Ye M., Zou H.;
RT "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver
RT phosphoproteome.";
RL J. Proteomics 96:253-262(2014).
RN [19]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-99 AND LYS-107, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25218447; DOI=10.1038/nsmb.2890;
RA Hendriks I.A., D'Souza R.C., Yang B., Verlaan-de Vries M., Mann M.,
RA Vertegaal A.C.;
RT "Uncovering global SUMOylation signaling networks in a site-specific
RT manner.";
RL Nat. Struct. Mol. Biol. 21:927-936(2014).
RN [20]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-10, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25772364; DOI=10.1016/j.celrep.2015.02.033;
RA Hendriks I.A., Treffers L.W., Verlaan-de Vries M., Olsen J.V.,
RA Vertegaal A.C.;
RT "SUMO-2 orchestrates chromatin modifiers in response to DNA damage.";
RL Cell Rep. 10:1778-1791(2015).
RN [21]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-99 AND LYS-107, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=25755297; DOI=10.1074/mcp.o114.044792;
RA Xiao Z., Chang J.G., Hendriks I.A., Sigurdsson J.O., Olsen J.V.,
RA Vertegaal A.C.;
RT "System-wide analysis of SUMOylation dynamics in response to replication
RT stress reveals novel small ubiquitin-like modified target proteins and
RT acceptor lysines relevant for genome stability.";
RL Mol. Cell. Proteomics 14:1419-1434(2015).
RN [22]
RP SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-10; LYS-99; LYS-107; LYS-108;
RP LYS-178; LYS-196 AND LYS-281, AND IDENTIFICATION BY MASS SPECTROMETRY
RP [LARGE SCALE ANALYSIS].
RX PubMed=28112733; DOI=10.1038/nsmb.3366;
RA Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
RA Nielsen M.L.;
RT "Site-specific mapping of the human SUMO proteome reveals co-modification
RT with phosphorylation.";
RL Nat. Struct. Mol. Biol. 24:325-336(2017).
RN [23]
RP SUBUNIT, SUBCELLULAR LOCATION, INVOLVEMENT IN CSS7, VARIANTS CSS7 PHE-276;
RP TRP-330; GLY-346; HIS-350 AND ARG-369, AND CHARACTERIZATION OF VARIANTS
RP CSS7 PHE-276; TRP-330 AND HIS-350.
RX PubMed=29429572; DOI=10.1016/j.ajhg.2018.01.014;
RG Deciphering Developmental Disorders Study;
RA Vasileiou G., Vergarajauregui S., Endele S., Popp B., Buettner C.,
RA Ekici A.B., Gerard M., Bramswig N.C., Albrecht B., Clayton-Smith J.,
RA Morton J., Tomkins S., Low K., Weber A., Wenzel M., Altmueller J., Li Y.,
RA Wollnik B., Hoganson G., Plona M.R., Cho M.T., Thiel C.T., Luedecke H.J.,
RA Strom T.M., Calpena E., Wilkie A.O.M., Wieczorek D., Engel F.B., Reis A.;
RT "Mutations in the BAF-complex subunit DPF2 are associated with Coffin-Siris
RT syndrome.";
RL Am. J. Hum. Genet. 102:468-479(2018).
RN [24]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 203-249.
RX PubMed=21888896; DOI=10.1016/j.bbrc.2011.08.043;
RA Zhang W., Xu C., Bian C., Tempel W., Crombet L., MacKenzie F., Min J.,
RA Liu Z., Qi C.;
RT "Crystal structure of the Cys2His2-type zinc finger domain of human DPF2.";
RL Biochem. Biophys. Res. Commun. 413:58-61(2011).
RN [25]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 270-391, FUNCTION, SUBUNIT, AND
RP INTERACTION WITH NUCLEOSOMES.
RX PubMed=27775714; DOI=10.1038/nchembio.2218;
RA Xiong X., Panchenko T., Yang S., Zhao S., Yan P., Zhang W., Xie W., Li Y.,
RA Zhao Y., Allis C.D., Li H.;
RT "Selective recognition of histone crotonylation by double PHD fingers of
RT MOZ and DPF2.";
RL Nat. Chem. Biol. 12:1111-1118(2016).
RN [26]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 270-391, FUNCTION, SUBCELLULAR
RP LOCATION, SUBUNIT, INTERACTION WITH SMARCC1; SMARCC2; ACTL6A AND RUNX1, AND
RP MUTAGENESIS OF PHE-275; ARG-300 AND ASP-346.
RX PubMed=28533407; DOI=10.1073/pnas.1700328114;
RA Huber F.M., Greenblatt S.M., Davenport A.M., Martinez C., Xu Y., Vu L.P.,
RA Nimer S.D., Hoelz A.;
RT "Histone-binding of DPF2 mediates its repressive role in myeloid
RT differentiation.";
RL Proc. Natl. Acad. Sci. U.S.A. 114:6016-6021(2017).
CC -!- FUNCTION: Plays an active role in transcriptional regulation by binding
CC modified histones H3 and H4 (PubMed:28533407, PubMed:27775714). Is a
CC negative regulator of myeloid differentiation of hematopoietic
CC progenitor cells (PubMed:28533407). Might also have a role in the
CC development and maturation of lymphoid cells (By similarity). Involved
CC in the regulation of non-canonical NF-kappa-B pathway
CC (PubMed:20460684). {ECO:0000250|UniProtKB:Q61103,
CC ECO:0000269|PubMed:20460684, ECO:0000269|PubMed:27775714,
CC ECO:0000269|PubMed:28533407}.
CC -!- SUBUNIT: Interacts with the nucleosomes, in particular nucleosomes
CC bearing histone H3 crotonylated at 'Lys-14' (H3K14cr) for which DPF2
CC has high affinity (PubMed:27775714). Also interacts (via PHD-type zinc
CC finger domains) with histone H3 butyrylated at 'Lys-14' (H3K14bu),
CC histone H3 propionylated at 'Lys-14' (H3K14pr), and histone H3
CC acetylated at 'Lys-14' (H3K14ac) (PubMed:29429572, PubMed:28533407,
CC PubMed:27775714). Interacts with histone H3 acetylated at 'Lys-9'
CC (H3K9ac), histone H3 di-methylated at 'Lys-9' (H3K9me2), and histone H3
CC tri-methylated at 'Lys-9' (H3K9me3) (PubMed:29429572). Interacts with
CC histone H4 acetylated at 'Lys-12' (H4K12ac) (PubMed:29429572).
CC Interacts with histone H4 acetylated at 'Lys-16' (H4K16ac)
CC (PubMed:28533407). Interacts with SWI/SNF complex components
CC (PubMed:20460684, PubMed:28533407). Interacts with SMARCA2, SMARCA4,
CC SMARCB1 and SMARCD1 (PubMed:20460684). Interacts with SMARCC1, SMARCC2
CC and ACTL6A (PubMed:28533407). Interacts with RUNX1 (PubMed:28533407).
CC {ECO:0000269|PubMed:20460684, ECO:0000269|PubMed:28533407,
CC ECO:0000269|PubMed:29429572}.
CC -!- INTERACTION:
CC Q92785; A6NEM1: GOLGA6L9; NbExp=3; IntAct=EBI-359932, EBI-5916454;
CC Q92785; O75031: HSF2BP; NbExp=6; IntAct=EBI-359932, EBI-7116203;
CC Q92785; O95751: LDOC1; NbExp=6; IntAct=EBI-359932, EBI-740738;
CC Q92785; Q8TBB1: LNX1; NbExp=3; IntAct=EBI-359932, EBI-739832;
CC Q92785; Q6FHY5: MEOX2; NbExp=3; IntAct=EBI-359932, EBI-16439278;
CC Q92785; Q9NRD5: PICK1; NbExp=3; IntAct=EBI-359932, EBI-79165;
CC Q92785; Q6NUQ1: RINT1; NbExp=3; IntAct=EBI-359932, EBI-726876;
CC Q92785; Q92622: RUBCN; NbExp=3; IntAct=EBI-359932, EBI-2952709;
CC Q92785; Q6PF05: TTC23L; NbExp=3; IntAct=EBI-359932, EBI-8656864;
CC Q92785; O95881: TXNDC12; NbExp=3; IntAct=EBI-359932, EBI-2564581;
CC Q92785; Q8N720: ZNF655; NbExp=3; IntAct=EBI-359932, EBI-625509;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:28533407,
CC ECO:0000269|PubMed:29429572}. Cytoplasm {ECO:0000269|PubMed:28533407}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q92785-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q92785-2; Sequence=VSP_055860;
CC -!- TISSUE SPECIFICITY: Ubiquitous.
CC -!- DISEASE: Coffin-Siris syndrome 7 (CSS7) [MIM:618027]: A form of Coffin-
CC Siris syndrome, a congenital multiple malformation syndrome with broad
CC phenotypic and genetic variability. Cardinal features are intellectual
CC disability, coarse facial features, hypertrichosis, and hypoplastic or
CC absent fifth digit nails or phalanges. Additional features include
CC malformations of the cardiac, gastrointestinal, genitourinary, and/or
CC central nervous systems. Sucking/feeding difficulties, poor growth,
CC ophthalmologic abnormalities, hearing impairment, and spinal anomalies
CC are common findings. Both autosomal dominant and autosomal recessive
CC inheritance patterns have been reported. CSS7 inheritance is autosomal
CC dominant. {ECO:0000269|PubMed:29429572}. Note=The disease is caused by
CC variants affecting the gene represented in this entry.
CC -!- SIMILARITY: Belongs to the requiem/DPF family. {ECO:0000305}.
CC -!- WEB RESOURCE: Name=NIEHS-SNPs;
CC URL="http://egp.gs.washington.edu/data/req/";
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DR EMBL; AF001433; AAB81203.1; -; mRNA.
DR EMBL; U94585; AAB58307.1; -; mRNA.
DR EMBL; BT006718; AAP35364.1; -; mRNA.
DR EMBL; AY220877; AAO26041.1; -; Genomic_DNA.
DR EMBL; AK291944; BAF84633.1; -; mRNA.
DR EMBL; AK300061; BAG61870.1; -; mRNA.
DR EMBL; AP000944; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471076; EAW74375.1; -; Genomic_DNA.
DR EMBL; BC014889; AAH14889.1; -; mRNA.
DR EMBL; U43920; AAC50687.1; -; Genomic_DNA.
DR CCDS; CCDS8100.1; -. [Q92785-1]
DR RefSeq; NP_006259.1; NM_006268.4. [Q92785-1]
DR PDB; 3IUF; X-ray; 1.80 A; A=203-249.
DR PDB; 5B79; X-ray; 2.60 A; A=270-391.
DR PDB; 5VDC; X-ray; 1.60 A; A=270-391.
DR PDB; 6LTH; EM; 3.00 A; R=1-391.
DR PDB; 6LTJ; EM; 3.70 A; R=1-100, R=209-391.
DR PDBsum; 3IUF; -.
DR PDBsum; 5B79; -.
DR PDBsum; 5VDC; -.
DR PDBsum; 6LTH; -.
DR PDBsum; 6LTJ; -.
DR AlphaFoldDB; Q92785; -.
DR EMDB; EMD-0974; -.
DR SMR; Q92785; -.
DR BioGRID; 111909; 340.
DR ComplexPortal; CPX-1195; Embryonic stem cell-specific SWI/SNF ATP-dependent chromatin remodeling complex.
DR CORUM; Q92785; -.
DR DIP; DIP-27575N; -.
DR IntAct; Q92785; 106.
DR MINT; Q92785; -.
DR STRING; 9606.ENSP00000252268; -.
DR GlyGen; Q92785; 1 site, 1 O-linked glycan (1 site).
DR iPTMnet; Q92785; -.
DR PhosphoSitePlus; Q92785; -.
DR SwissPalm; Q92785; -.
DR BioMuta; DPF2; -.
DR DMDM; 2842711; -.
DR EPD; Q92785; -.
DR jPOST; Q92785; -.
DR MassIVE; Q92785; -.
DR MaxQB; Q92785; -.
DR PaxDb; 9606-ENSP00000436901; -.
DR PeptideAtlas; Q92785; -.
DR ProteomicsDB; 5076; -.
DR ProteomicsDB; 75469; -. [Q92785-1]
DR Pumba; Q92785; -.
DR Antibodypedia; 15846; 381 antibodies from 38 providers.
DR DNASU; 5977; -.
DR Ensembl; ENST00000415073.6; ENSP00000399714.2; ENSG00000133884.11. [Q92785-2]
DR Ensembl; ENST00000528416.6; ENSP00000436901.1; ENSG00000133884.11. [Q92785-1]
DR GeneID; 5977; -.
DR KEGG; hsa:5977; -.
DR MANE-Select; ENST00000528416.6; ENSP00000436901.1; NM_006268.5; NP_006259.1.
DR UCSC; uc001odm.4; human. [Q92785-1]
DR AGR; HGNC:9964; -.
DR CTD; 5977; -.
DR DisGeNET; 5977; -.
DR GeneCards; DPF2; -.
DR GeneReviews; DPF2; -.
DR HGNC; HGNC:9964; DPF2.
DR HPA; ENSG00000133884; Low tissue specificity.
DR MalaCards; DPF2; -.
DR MIM; 601671; gene.
DR MIM; 618027; phenotype.
DR neXtProt; NX_Q92785; -.
DR OpenTargets; ENSG00000133884; -.
DR Orphanet; 1465; Coffin-Siris syndrome.
DR PharmGKB; PA34331; -.
DR VEuPathDB; HostDB:ENSG00000133884; -.
DR eggNOG; KOG1244; Eukaryota.
DR GeneTree; ENSGT00940000155070; -.
DR HOGENOM; CLU_038980_0_1_1; -.
DR InParanoid; Q92785; -.
DR OrthoDB; 5490909at2759; -.
DR PhylomeDB; Q92785; -.
DR TreeFam; TF318971; -.
DR PathwayCommons; Q92785; -.
DR SignaLink; Q92785; -.
DR SIGNOR; Q92785; -.
DR BioGRID-ORCS; 5977; 169 hits in 1184 CRISPR screens.
DR ChiTaRS; DPF2; human.
DR EvolutionaryTrace; Q92785; -.
DR GeneWiki; DPF2; -.
DR GenomeRNAi; 5977; -.
DR Pharos; Q92785; Tbio.
DR PRO; PR:Q92785; -.
DR Proteomes; UP000005640; Chromosome 11.
DR RNAct; Q92785; Protein.
DR Bgee; ENSG00000133884; Expressed in oocyte and 201 other cell types or tissues.
DR ExpressionAtlas; Q92785; baseline and differential.
DR Genevisible; Q92785; HS.
DR GO; GO:0005813; C:centrosome; IDA:HPA.
DR GO; GO:0000785; C:chromatin; IDA:ARUK-UCL.
DR GO; GO:0005829; C:cytosol; IDA:HPA.
DR GO; GO:0043231; C:intracellular membrane-bounded organelle; IDA:HPA.
DR GO; GO:0071565; C:nBAF complex; IBA:GO_Central.
DR GO; GO:0005654; C:nucleoplasm; IDA:HPA.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0016514; C:SWI/SNF complex; NAS:ComplexPortal.
DR GO; GO:0062072; F:H3K9me3 modified histone binding; IDA:UniProtKB.
DR GO; GO:0070577; F:lysine-acetylated histone binding; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003714; F:transcription corepressor activity; TAS:ARUK-UCL.
DR GO; GO:0006915; P:apoptotic process; TAS:ProtInc.
DR GO; GO:0097190; P:apoptotic signaling pathway; TAS:ProtInc.
DR GO; GO:0006338; P:chromatin remodeling; NAS:ComplexPortal.
DR GO; GO:1905454; P:negative regulation of myeloid progenitor cell differentiation; IMP:UniProtKB.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; TAS:ARUK-UCL.
DR GO; GO:0007399; P:nervous system development; IBA:GO_Central.
DR GO; GO:2000781; P:positive regulation of double-strand break repair; NAS:ComplexPortal.
DR GO; GO:1902459; P:positive regulation of stem cell population maintenance; NAS:ComplexPortal.
DR GO; GO:0070316; P:regulation of G0 to G1 transition; NAS:ComplexPortal.
DR GO; GO:2000045; P:regulation of G1/S transition of mitotic cell cycle; NAS:ComplexPortal.
DR GO; GO:0030071; P:regulation of mitotic metaphase/anaphase transition; NAS:ComplexPortal.
DR GO; GO:2000819; P:regulation of nucleotide-excision repair; NAS:ComplexPortal.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; NAS:ComplexPortal.
DR CDD; cd15691; PHD1_DPF2_like; 1.
DR CDD; cd15530; PHD2_d4; 1.
DR Gene3D; 3.30.160.60; Classic Zinc Finger; 1.
DR Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 1.
DR InterPro; IPR025750; DPF1-3_N.
DR InterPro; IPR036236; Znf_C2H2_sf.
DR InterPro; IPR013087; Znf_C2H2_type.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR PANTHER; PTHR23057; JUXTAPOSED WITH ANOTHER ZINC FINGER PROTEIN 1; 1.
DR PANTHER; PTHR23057:SF3; ZINC FINGER PROTEIN DPF3; 1.
DR Pfam; PF14051; DPF1-3_N; 1.
DR Pfam; PF00628; PHD; 2.
DR SMART; SM00249; PHD; 2.
DR SMART; SM00355; ZnF_C2H2; 1.
DR SUPFAM; SSF57667; beta-beta-alpha zinc fingers; 1.
DR SUPFAM; SSF57903; FYVE/PHD zinc finger; 2.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 2.
DR PROSITE; PS00028; ZINC_FINGER_C2H2_1; 1.
DR PROSITE; PS50157; ZINC_FINGER_C2H2_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative splicing; Apoptosis;
KW Chromatin regulator; Cytoplasm; Disease variant; Intellectual disability;
KW Isopeptide bond; Metal-binding; Nucleus; Phosphoprotein;
KW Reference proteome; Repeat; Transcription; Transcription regulation;
KW Ubl conjugation; Zinc; Zinc-finger.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:19413330"
FT CHAIN 2..391
FT /note="Zinc finger protein ubi-d4"
FT /id="PRO_0000168149"
FT ZN_FING 209..232
FT /note="C2H2-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00042"
FT ZN_FING 270..330
FT /note="PHD-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 327..377
FT /note="PHD-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 79..146
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 165..196
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 233..266
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 124..142
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:19413330"
FT MOD_RES 142
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18669648,
FT ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231,
FT ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163"
FT MOD_RES 172
FT /note="Phosphotyrosine"
FT /evidence="ECO:0007744|PubMed:19690332"
FT MOD_RES 176
FT /note="Phosphothreonine"
FT /evidence="ECO:0007744|PubMed:18669648,
FT ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231,
FT ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163"
FT MOD_RES 200
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:20068231,
FT ECO:0007744|PubMed:23186163"
FT MOD_RES 244
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21406692"
FT MOD_RES 280
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:23186163"
FT CROSSLNK 10
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:25772364,
FT ECO:0007744|PubMed:28112733"
FT CROSSLNK 99
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:25218447,
FT ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:28112733"
FT CROSSLNK 107
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:25218447,
FT ECO:0007744|PubMed:25755297, ECO:0007744|PubMed:28112733"
FT CROSSLNK 108
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CROSSLNK 178
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CROSSLNK 196
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT CROSSLNK 281
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0007744|PubMed:28112733"
FT VAR_SEQ 156..339
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_055860"
FT VARIANT 276
FT /note="C -> F (in CSS7; abolishes interaction with
FT acetylated or methylated histone H3; dbSNP:rs1555031372)"
FT /evidence="ECO:0000269|PubMed:29429572"
FT /id="VAR_081047"
FT VARIANT 330
FT /note="C -> W (in CSS7; abolishes interaction with
FT acetylated or methylated histone H3; dbSNP:rs1555031500)"
FT /evidence="ECO:0000269|PubMed:29429572"
FT /id="VAR_081048"
FT VARIANT 346
FT /note="D -> G (in CSS7; dbSNP:rs1555032044)"
FT /evidence="ECO:0000269|PubMed:29429572"
FT /id="VAR_081049"
FT VARIANT 350
FT /note="R -> H (in CSS7; abolishes interaction with
FT acetylated histone H3; strongly decreased interaction with
FT methylated histone H3; dbSNP:rs1555032051)"
FT /evidence="ECO:0000269|PubMed:29429572"
FT /id="VAR_081050"
FT VARIANT 369
FT /note="W -> R (in CSS7)"
FT /evidence="ECO:0000269|PubMed:29429572"
FT /id="VAR_081051"
FT MUTAGEN 275
FT /note="F->A: Strongly decreased interaction with histones
FT H3 and H4 and loss of function; when associated with A-300
FT and A-346."
FT /evidence="ECO:0000269|PubMed:28533407"
FT MUTAGEN 300
FT /note="R->A: Strongly decreased interaction with histones
FT H3 and H4 and loss of function; when associated with A-275
FT and A-346."
FT /evidence="ECO:0000269|PubMed:28533407"
FT MUTAGEN 346
FT /note="D->A: Strongly decreased interaction with histones
FT H3 and H4 and loss of function; when associated with A-275
FT and A-300."
FT /evidence="ECO:0000269|PubMed:28533407"
FT HELIX 14..37
FT /evidence="ECO:0007829|PDB:6LTH"
FT STRAND 40..42
FT /evidence="ECO:0007829|PDB:6LTH"
FT STRAND 44..46
FT /evidence="ECO:0007829|PDB:6LTH"
FT STRAND 49..52
FT /evidence="ECO:0007829|PDB:6LTH"
FT HELIX 59..61
FT /evidence="ECO:0007829|PDB:6LTH"
FT STRAND 70..73
FT /evidence="ECO:0007829|PDB:6LTH"
FT TURN 204..206
FT /evidence="ECO:0007829|PDB:3IUF"
FT TURN 212..214
FT /evidence="ECO:0007829|PDB:3IUF"
FT STRAND 217..220
FT /evidence="ECO:0007829|PDB:3IUF"
FT HELIX 221..230
FT /evidence="ECO:0007829|PDB:3IUF"
FT TURN 274..276
FT /evidence="ECO:0007829|PDB:5VDC"
FT TURN 284..286
FT /evidence="ECO:0007829|PDB:5VDC"
FT TURN 296..298
FT /evidence="ECO:0007829|PDB:5VDC"
FT TURN 304..308
FT /evidence="ECO:0007829|PDB:5VDC"
FT HELIX 311..316
FT /evidence="ECO:0007829|PDB:5VDC"
FT TURN 317..321
FT /evidence="ECO:0007829|PDB:5VDC"
FT TURN 325..327
FT /evidence="ECO:0007829|PDB:5VDC"
FT TURN 331..333
FT /evidence="ECO:0007829|PDB:5VDC"
FT HELIX 339..341
FT /evidence="ECO:0007829|PDB:5VDC"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:5VDC"
FT TURN 346..348
FT /evidence="ECO:0007829|PDB:5VDC"
FT STRAND 351..353
FT /evidence="ECO:0007829|PDB:5VDC"
FT TURN 354..356
FT /evidence="ECO:0007829|PDB:5VDC"
FT STRAND 357..359
FT /evidence="ECO:0007829|PDB:5VDC"
FT HELIX 372..378
FT /evidence="ECO:0007829|PDB:5VDC"
FT HELIX 379..381
FT /evidence="ECO:0007829|PDB:5VDC"
SQ SEQUENCE 391 AA; 44155 MW; 1044B4D3036075FC CRC64;
MAAVVENVVK LLGEQYYKDA MEQCHNYNAR LCAERSVRLP FLDSQTGVAQ SNCYIWMEKR
HRGPGLASGQ LYSYPARRWR KKRRAHPPED PRLSFPSIKP DTDQTLKKEG LISQDGSSLE
ALLRTDPLEK RGAPDPRVDD DSLGEFPVTN SRARKRILEP DDFLDDLDDE DYEEDTPKRR
GKGKSKGKGV GSARKKLDAS ILEDRDKPYA CDICGKRYKN RPGLSYHYAH SHLAEEEGED
KEDSQPPTPV SQRSEEQKSK KGPDGLALPN NYCDFCLGDS KINKKTGQPE ELVSCSDCGR
SGHPSCLQFT PVMMAAVKTY RWQCIECKCC NICGTSENDD QLLFCDDCDR GYHMYCLTPS
MSEPPEGSWS CHLCLDLLKE KASIYQNQNS S
//
