Details for: DPF3

Gene ID: 8110

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: DPF3

Ensembl ID: ENSG00000205683

Description: double PHD fingers 3

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • cardiac muscle cell CL0000746
    CSI 25.97
    rCSI 37.27%
    PRS 87.07
  • erythrocyte CL0000232
    CSI 14.55
    rCSI 33.01%
    PRS 91.63
  • retinal cone cell CL0000573
    CSI 13.83
    rCSI 22.26%
    PRS 87.32
  • erythroblast CL0000765
    CSI 11.81
    rCSI 31.33%
    PRS 93.79
  • cerebellar granule cell CL0001031
    CSI 9.73
    rCSI 14.3%
    PRS 89.8
  • VIP GABAergic cortical interneuron CL4023016
    CSI 9.14
    rCSI 10.92%
    PRS 83.94
  • innate lymphoid cell CL0001065
    CSI 8.86
    rCSI 18.3%
    PRS 88
  • GABAergic amacrine cell CL4030027
    CSI 8.36
    rCSI 28.63%
    PRS 83.23
  • glycinergic amacrine cell CL4030028
    CSI 7.46
    rCSI 19.43%
    PRS 88.68
  • glutamatergic neuron CL0000679
    CSI 6.42
    rCSI 13.19%
    PRS 83.96
  • ependymal cell CL0000065
    CSI 6.3
    rCSI 12.77%
    PRS 79.06
  • interneuron CL0000099
    CSI 6.17
    rCSI 12.39%
    PRS 89.15
  • S cone cell CL0003050
    CSI 6.13
    rCSI 26.94%
    PRS 90.28
  • GABAergic neuron CL0000617
    CSI 5.91
    rCSI 19.79%
    PRS 82.64
  • kidney loop of Henle thin ascending limb epithelial cell CL1001107
    CSI 5.45
    rCSI 14.09%
    PRS 91.92
  • retinal rod cell CL0000604
    CSI 5.23
    rCSI 9.22%
    PRS 90.29
  • regular atrial cardiac myocyte CL0002129
    CSI 4.84
    rCSI 15.58%
    PRS 90.47
  • Mueller cell CL0000636
    CSI 4.77
    rCSI 10.88%
    PRS 88.52
  • retinal ganglion cell CL0000740
    CSI 4.71
    rCSI 10.4%
    PRS 85.5
  • inhibitory interneuron CL0000498
    CSI 4.35
    rCSI 10.05%
    PRS 86.69
  • cerebral cortex endothelial cell CL1001602
    CSI 4.19
    rCSI 7.24%
    PRS 89.82
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 4.14
    rCSI 6.94%
    PRS 84.03
  • epithelial cell of proximal tubule CL0002306
    CSI 3.92
    rCSI 9.58%
    PRS 88.7
  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 3.87
    rCSI 6.84%
    PRS 83.38
  • naive B cell CL0000788
    CSI 3.7
    rCSI 3.18%
    PRS 96.12
  • neuroblast (sensu Vertebrata) CL0000031
    CSI 3.69
    rCSI 4.74%
    PRS 90.38
  • peripheral nervous system neuron CL2000032
    CSI 3.69
    rCSI 5.03%
    PRS 88.4
  • amacrine cell CL0000561
    CSI 3.66
    rCSI 10.6%
    PRS 87.02
  • cardiac endothelial cell CL0010008
    CSI 3.58
    rCSI 14.46%
    PRS 94.24
  • mature astrocyte CL0002627
    CSI 3.52
    rCSI 14.98%
    PRS 88.23
  • Bergmann glial cell CL0000644
    CSI 3.3
    rCSI 4.51%
    PRS 87.86
  • regular ventricular cardiac myocyte CL0002131
    CSI 2.95
    rCSI 18.42%
    PRS 88.5
  • sncg GABAergic cortical interneuron CL4023015
    CSI 2.86
    rCSI 4.6%
    PRS 84.93
  • differentiation-committed oligodendrocyte precursor CL4023059
    CSI 2.72
    rCSI 4.94%
    PRS 88.76
  • basket cell CL0000118
    CSI 2.48
    rCSI 15.55%
    PRS 76.68
  • kidney connecting tubule epithelial cell CL1000768
    CSI 2.41
    rCSI 6.1%
    PRS 89.58
  • astrocyte of the cerebral cortex CL0002605
    CSI 2.32
    rCSI 5.21%
    PRS 84.2
  • fast muscle cell CL0000190
    CSI 2.15
    rCSI 8.41%
    PRS 87.01
  • retinal pigment epithelial cell CL0002586
    CSI 2.08
    rCSI 4.13%
    PRS 90.94
  • cerebellar neuron CL1001611
    CSI 1.97
    rCSI 17.3%
    PRS 83.6
  • glial cell CL0000125
    CSI 1.91
    rCSI 7.28%
    PRS 88.29
  • macroglial cell CL0000126
    CSI 1.73
    rCSI 4.46%
    PRS 90.42
  • podocyte CL0000653
    CSI 1.69
    rCSI 7.51%
    PRS 93.84
  • eye photoreceptor cell CL0000287
    CSI 1.45
    rCSI 16.28%
    PRS 94.44
  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 1.42
    rCSI 3.46%
    PRS 81.8
  • L2/3 intratelencephalic projecting glutamatergic neuron CL4030059
    CSI 1.41
    rCSI 3.07%
    PRS 84.36
  • L4 intratelencephalic projecting glutamatergic neuron CL4030063
    CSI 1.25
    rCSI 2.99%
    PRS 85.48
  • primitive red blood cell CL0002355
    CSI 1.17
    rCSI 6.31%
    PRS 94.15
  • megakaryocyte CL0000556
    CSI 0.82
    rCSI 3.56%
    PRS 93.85
  • ON parasol ganglion cell CL4033052
    CSI 0.63
    rCSI 8.97%
    PRS 87.41
  • central nervous system neuron CL2000029
    CSI 0.35
    rCSI 2.59%
    PRS 87.62

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

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Comma-separated if multiple.
Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [DPF3](/details-gene/8110) (Double PHD Fingers 3) is a protein-coding gene located on chromosome 14q24.2. It functions as an epigenetic reader, specifically recognizing and binding to acetylated and methylated histones through its tandem plant homeodomain (PHD) zinc fingers. As a subunit of the BAF (SWI/SNF) chromatin remodeling complex, [DPF3](/details-gene/8110) plays a crucial role in regulating gene expression during development. **Overall** expression data highlight its profound significance in [cardiac muscle cell](/details-cell/CL0000746), with additional prominent roles in erythroid and neuronal cell lineages. Its function is primarily linked to the regulation of cell differentiation, particularly in muscle and nervous system development, as supported by multiple studies ([Link](https://doi.org/10.1101/gad.471408), [Link](https://doi.org/10.1093/nar/gkaa441)). The gene is associated with the OMIM entry [601672](https://omim.org/entry/601672). ## Cellular Roles and Expression Landscape The expression profile of [DPF3](/details-gene/8110) indicates highly specialized roles in distinct cell lineages. **Overall**, the gene's most significant expression is observed in [cardiac muscle cell](/details-cell/CL0000746) (CSI: 25.97), suggesting it is a key regulator of cardiac muscle identity and function. This is consistent with its established role in coordinating histone modification and chromatin remodeling to drive myogenic gene transcription ([Link](https://doi.org/10.1093/nar/gkaa441)). Beyond muscle tissue, [DPF3](/details-gene/8110) demonstrates significant expression in the hematopoietic system, particularly within the erythroid lineage, as shown by high CSI scores in [erythrocyte](/details-cell/CL0000232) and [erythroblast](/details-cell/CL0000765). This pattern suggests a potential role in regulating chromatin accessibility during red blood cell development and differentiation. A third major site of [DPF3](/details-gene/8110) activity is the nervous system. The gene shows notable significance in a variety of neuronal subtypes, including [retinal cone cell](/details-cell/CL0000573), [cerebellar granule cell](/details-cell/CL0001031), and multiple types of interneurons and amacrine cells. This broad yet specific expression pattern across different neuronal populations points towards a fundamental role in neurogenesis and the maintenance of terminally differentiated neuronal states. ## Pathways and Molecular Function The molecular function of [DPF3](/details-gene/8110) is intrinsically linked to its role as a core component of several SWI/SNF-family chromatin remodeling complexes, including the BAF ([GO:0016514](https://www.ebi.ac.uk/QuickGO/term/GO:0016514)), Brahma ([GO:0035060](https://www.ebi.ac.uk/QuickGO/term/GO:0035060)), and NBAF ([GO:0071565](https://www.ebi.ac.uk/QuickGO/term/GO:0071565)) complexes. Its ability to perform [protein binding](/details-ontology/GO:0005515) and [zinc ion binding](/details-ontology/GO:0008270) via its PHD fingers allows it to read histone post-translational modifications, thereby recruiting the remodeling machinery to specific genomic loci ([Link](https://doi.org/10.1038/nature09139)). This mechanism underpins its involvement in broad biological processes such as [gene expression (transcription)](/details-pathway/R-HSA-74160) and [epigenetic regulation of gene expression](/details-pathway/R-HSA-212165). Functionally, this translates to critical roles in key developmental pathways. - **Myogenesis:** [DPF3](/details-gene/8110) is a positive regulator of myoblast differentiation ([GO:0045663](https://www.ebi.ac.uk/QuickGO/term/GO:0045663)), which directly correlates with its high expression in [cardiac muscle cell](/details-cell/CL0000746). Its involvement in the broader process of [muscle organ development](/details-ontology/GO:0007517) is well-documented ([Link](https://doi.org/10.1101/gad.471408)). - **Neurodevelopment:** The gene's participation in [nervous system development](/details-ontology/GO:0007399) is consistent with its expression in diverse neuronal populations. - **Cell Cycle Control:** Annotations also link [DPF3](/details-gene/8110) to the regulation of cell cycle transitions, including [regulation of g0 to g1 transition](/details-ontology/GO:0070316) and [regulation of g1/s transition of mitotic cell cycle](/details-ontology/GO:2000045), suggesting it helps coordinate cell proliferation and differentiation decisions. ## Research Directions The specific expression patterns and known functions of [DPF3](/details-gene/8110) suggest several avenues for future investigation. **Proposed Hypotheses:** 1. Given its paramount importance in [cardiac muscle cell](/details-cell/CL0000746) and its role in myogenesis, aberrant [DPF3](/details-gene/8110) expression or function could be a contributing factor to congenital heart defects or cardiomyopathies that arise from dysregulated developmental gene programs. 2. The high significance of [DPF3](/details-gene/8110) in erythroid lineage cells ([erythroblast](/details-cell/CL0000765), [erythrocyte](/details-cell/CL0000232)) suggests a previously under-appreciated role in hematopoiesis. It may function by modulating chromatin accessibility at key globin loci or other master regulators of red blood cell differentiation, and its disruption could contribute to certain forms of anemia. 3. Its expression across multiple, distinct neuronal subtypes, including those in the retina and cerebellum, indicates that [DPF3](/details-gene/8110) may be a master regulator of terminal differentiation for specialized neurons. Its loss-of-function could lead to specific neurodevelopmental or neurodegenerative disorders characterized by the dysfunction of these cell populations. **Experimental Approach:** To test hypothesis #1, a cardiac-specific conditional knockout of [DPF3](/details-gene/8110) in a mouse model (e.g., using a *Myh6*-Cre driver) would be a definitive experiment. The resulting phenotype could be assessed through echocardiography to measure cardiac function, histology to examine cardiomyocyte structure and fibrosis, and single-cell RNA-sequencing of cardiomyocytes to identify downstream gene expression changes and dysregulated pathways. **Therapeutic Potential:** As an epigenetic reader, [DPF3](/details-gene/8110) is a potentially druggable target. Its high specificity for cardiac muscle suggests it could be a target for treating heart disease. For example, small molecules designed to enhance [DPF3](/details-gene/8110) function or expression could be explored as a strategy to promote cardiac regeneration after injury. Conversely, inhibiting its activity might be beneficial in conditions like cardiac hypertrophy where developmental gene programs are pathologically reactivated. However, its crucial roles in the nervous system and hematopoietic system pose a significant risk for off-target effects, necessitating the development of highly tissue-specific delivery mechanisms for any potential therapeutic.

Genular Protein ID: 826864343

Symbol: DPF3_HUMAN

Name: Zinc finger protein DPF3

UniProtKB Accession Codes:

Q92784 A8MSI3 B7Z276 F5H575 Q32UJ0 Q6P9E6 Q6ZT41 Q9H7Y5

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 BMRB 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 4 CDD 2 CTD 1 ChiTaRS 1 ComplexPortal 12 DIP 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 10 Ensembl 3 EvolutionaryTrace 1 ExpressionAtlas 1 GO 17 Gene3D 2 GeneCards 1 GeneTree 1 GenomeRNAi 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 IDEAL 1 InParanoid 1 IntAct 1 InterPro 8 KEGG 1 MANE-Select 1 MIM 1 MINT 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PDB 7 PDBsum 7 PRO 1 PROSITE 4 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 2 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 5 Pumba 1 RNAct 1 Reactome 2 RefSeq 6 SIGNOR 1 SMART 2 SMR 1 STRING 1 SUPFAM 2 SignaLink 1 SwissPalm 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 18765789

Title: Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex.

PubMed ID: 18765789

DOI: 10.1101/gad.471408

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 12508121

Title: The DNA sequence and analysis of human chromosome 14.

PubMed ID: 12508121

DOI: 10.1038/nature01348

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 8812431

Title: The d4 gene family in the human genome.

PubMed ID: 8812431

DOI: 10.1006/geno.1996.0440

PubMed ID: 28112733

Title: Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation.

PubMed ID: 28112733

DOI: 10.1038/nsmb.3366

PubMed ID: 32459350

Title: HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription.

PubMed ID: 32459350

DOI: 10.1093/nar/gkaa441

PubMed ID: 20613843

Title: Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b.

PubMed ID: 20613843

DOI: 10.1038/nature09139

Sequence Information:

  • Length: 378
  • Mass: 43084
  • Checksum: 7E6A6FD07A0E4668
  • Sequence:
    • MATVIHNPLK ALGDQFYKEA IEHCRSYNSR LCAERSVRLP FLDSQTGVAQ NNCYIWMEKR 
HRGPGLAPGQ LYTYPARCWR KKRRLHPPED PKLRLLEIKP EVELPLKKDG FTSESTTLEA 
LLRGEGVEKK VDAREEESIQ EIQRVLENDE NVEEGNEEED LEEDIPKRKN RTRGRARGSA 
GGRRRHDAAS QEDHDKPYVC DICGKRYKNR PGLSYHYAHT HLASEEGDEA QDQETRSPPN 
HRNENHRPQK GPDGTVIPNN YCDFCLGGSN MNKKSGRPEE LVSCADCGRS GHPTCLQFTL 
NMTEAVKTYK WQCIECKSCI LCGTSENDDQ LLFCDDCDRG YHMYCLNPPV AEPPEGSWSC 
HLCWELLKEK ASAFGCQA

Genular Protein ID: 778234778

Symbol: F8W7T1_HUMAN

Name: N/A

UniProtKB Accession Codes:

F8W7T1

Database IDs:

ARBA 4 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID-ORCS 1 CTD 1 ChiTaRS 1 DNASU 1 DisGeNET 1 EMBL 6 Ensembl 2 ExpressionAtlas 1 GO 1 Gene3D 1 GeneTree 1 HGNC 1 InterPro 4 MassIVE 1 NCBI Taxonomy 1 OrthoDB 1 PANTHER 2 PROSITE 2 PeptideAtlas 1 Pfam 1 PhylomeDB 1 Proteomes 2 ProteomicsDB 1 RefSeq 1 SMART 1 SMR 1 SUPFAM 1 SwissPalm 1 UCSC 1 VEuPathDB 1

Citations:

PubMed ID: 11237011

Title: Initial sequencing and analysis of the human genome.

PubMed ID: 11237011

DOI: 10.1038/35057062

PubMed ID: 12508121

Title: The DNA sequence and analysis of human chromosome 14.

PubMed ID: 12508121

DOI: 10.1038/nature01348

PubMed ID: 15496913

Title: Finishing the euchromatic sequence of the human genome.

PubMed ID: 15496913

DOI: 10.1038/nature03001

PubMed ID: 28112733

Title: Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation.

PubMed ID: 28112733

Sequence Information:

  • Length: 412
  • Mass: 46445
  • Checksum: BBE03D204CA249F8
  • Sequence:
    • MFYGRINGRN FAASSLPVAF AATPLMLFLP NPQLIFSFPI SSRNHITGLM PPGKLKLENL 
FHMCTRLGDQ FYKEAIEHCR SYNSRLCAER SVRLPFLDSQ TGVAQNNCYI WMEKRHRGPG 
LAPGQLYTYP ARCWRKKRRL HPPEDPKLRL LEIKPEVELP LKKDGFTSES TTLEALLRGE 
GVEKKVDARE EESIQEIQRV LENDENVEEG NEEEDLEEDI PKRKNRTRGR ARGSAGGRRR 
HDAASQEDHD KPYVCDICGK RYKNRPGLSY HYAHTHLASE EGDEAQDQET RSPPNHRNEN 
HRPQKGPDGT VIPNNYCDFC LGGSNMNKKS GRPEELVSCA DCGRSAHLGG EGRKEKEAAA 
AARTTEDLFG STSESDTSTF HGFDEDDLEE PRSCRGRRSG RGSPTADKKG SC