Details for: PRDM11

Gene ID: 56981

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: PRDM11

Ensembl ID: ENSG00000019485

Description: PR/SET domain 11

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

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

  • caudal ganglionic eminence derived cortical interneuron CL4023064
    CSI 5.46
    rCSI 9.64%
    PRS 95.01
  • VIP GABAergic cortical interneuron CL4023016
    CSI 4.17
    rCSI 4.98%
    PRS 95.01
  • hepatic stellate cell CL0000632
    CSI 3.23
    rCSI 12.11%
    PRS 97.53
  • vascular leptomeningeal cell CL4023051
    CSI 2.72
    rCSI 4.77%
    PRS 97.11
  • cerebral cortex endothelial cell CL1001602
    CSI 2.69
    rCSI 4.65%
    PRS 96.84
  • pvalb GABAergic cortical interneuron CL4023018
    CSI 2.58
    rCSI 3.21%
    PRS 94.26
  • sst GABAergic cortical interneuron CL4023017
    CSI 2.35
    rCSI 3.03%
    PRS 95.61
  • ependymal cell CL0000065
    CSI 2.34
    rCSI 4.75%
    PRS 91.57
  • astrocyte of the cerebral cortex CL0002605
    CSI 2.16
    rCSI 4.83%
    PRS 95.05
  • cardiac muscle cell CL0000746
    CSI 1.89
    rCSI 2.71%
    PRS 95.21
  • parietal epithelial cell CL1000452
    CSI 1.83
    rCSI 4.89%
    PRS 97.36
  • lamp5 GABAergic cortical interneuron CL4023011
    CSI 1.82
    rCSI 3.06%
    PRS 95.28
  • inhibitory interneuron CL0000498
    CSI 1.72
    rCSI 3.98%
    PRS 95.29
  • lung pericyte CL0009089
    CSI 1.63
    rCSI 4.3%
    PRS 99.29
  • L2/3-6 intratelencephalic projecting glutamatergic neuron CL4023040
    CSI 1.56
    rCSI 3.8%
    PRS 93.78
  • kidney connecting tubule epithelial cell CL1000768
    CSI 1.45
    rCSI 3.69%
    PRS 97.1
  • ciliated columnar cell of tracheobronchial tree CL0002145
    CSI 1.12
    rCSI 2.56%
    PRS 95.13
  • L6b glutamatergic cortical neuron CL4023038
    CSI 0.84
    rCSI 2.64%
    PRS 95.26
  • direct pathway medium spiny neuron CL4023026
    CSI 0.34
    rCSI 8.2%
    PRS 93.05
  • indirect pathway medium spiny neuron CL4023029
    CSI 0.32
    rCSI 7.65%
    PRS 92.69

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.

Comma-separated if multiple.
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 [PRDM11](/details-gene/56981) is a protein-coding gene located on chromosome 11 that encodes PR/SET domain 11, a member of a family of transcriptional regulators characterized by the PR domain, which is related to the SET domain found in histone methyltransferases. Functional annotations suggest [PRDM11](/details-gene/56981) is involved in fundamental nuclear processes, including [chromatin binding](/details-cell/GO:0003682), [methylation](/details-cell/GO:0032259), and the negative regulation of gene expression ([GO:0045892](https://www.ebi.ac.uk/QuickGO/term/GO:0045892)) and cell growth ([GO:0030308](https://www.ebi.ac.uk/QuickGO/term/GO:0030308)). **Overall**, expression data indicate its highest significance is within the central nervous system, particularly in various subtypes of cortical interneurons. It has also been implicated as a tumor suppressor, with research showing its loss can promote MYC-driven lymphomagenesis ([Link](https://doi.org/10.1182/blood-2014-03-560805)). ## Cellular Roles and Expression Landscape The expression profile of [PRDM11](/details-gene/56981) strongly points to a specialized role within the central nervous system. **Overall**, the gene shows its highest significance in several distinct neuronal populations, most notably the [caudal ganglionic eminence derived cortical interneuron](/details-cell/CL4023064) (CSI: 5.46) and other GABAergic cortical interneurons, including [VIP](/details-cell/CL4023016), [pvalb](/details-cell/CL4023018), [sst](/details-cell/CL4023017), and [lamp5](/details-cell/CL4023011) subtypes. This pattern suggests a crucial function in the development, specification, or maintenance of inhibitory neuronal circuits in the cortex. Beyond interneurons, [PRDM11](/details-gene/56981) also demonstrates significant expression in other neural and neurovascular cell types, including [vascular leptomeningeal cells](/details-cell/CL4023051), [cerebral cortex endothelial cells](/details-cell/CL1001602), [ependymal cells](/details-cell/CL0000065), and [astrocytes of the cerebral cortex](/details-cell/CL0002605). Its notable expression in non-neural cell types such as [hepatic stellate cells](/details-cell/CL0000632) and [cardiac muscle cells](/details-cell/CL0000746) indicates that its function, while prominent in the nervous system, is not exclusively confined to it and may extend to tissue maintenance and regulation in other organs. ## Pathways and Molecular Function [PRDM11](/details-gene/56981) functions primarily as an epigenetic and transcriptional regulator, consistent with its localization to the [nucleus](/details-cell/GO:0005634). Its molecular functions include [chromatin binding](/details-cell/GO:0003682), potential [methyltransferase activity](/details-cell/GO:0008168), and [protein binding](/details-cell/GO:0005515). These activities underpin its role in key biological processes, such as the dual regulation of DNA-templated transcription, where it is annotated as both a negative ([GO:0045892](https://www.ebi.ac.uk/QuickGO/term/GO:0045892)) and positive ([GO:0045893](https://www.ebi.ac.uk/QuickGO/term/GO:0045893)) regulator, suggesting a context-dependent mechanism of action. Furthermore, its involvement in the [regulation of cell cycle](/details-cell/GO:0051726) and [negative regulation of cell growth](/details-cell/GO:0030308) aligns with findings from cancer biology that identify it as a potential tumor suppressor ([Link](https://doi.org/10.1182/blood-2014-03-560805)). The gene's connection to the [regulation of MAPK cascade](/details-cell/GO:0043408) suggests it may integrate epigenetic modifications with intracellular signaling pathways to control cellular fate. ## Research Directions Based on its function as a transcriptional regulator and its distinct expression pattern, several avenues for future research emerge. **Proposed Hypotheses:** 1. Given its high and specific expression in diverse subtypes of cortical interneurons, [PRDM11](/details-gene/56981) likely acts as a master epigenetic regulator required for the proper terminal differentiation and functional maintenance of these inhibitory neurons. Its dysregulation could contribute to neurodevelopmental disorders associated with excitatory/inhibitory imbalance. 2. Based on evidence that its loss promotes MYC-driven lymphoma ([Link](https://doi.org/10.1182/blood-2014-03-560805)), [PRDM11](/details-gene/56981) may function as a tumor suppressor by directly binding to and repressing the promoters of key oncogenes or cell cycle regulators, and its inactivation is a critical step in certain hematological malignancies. **Suggested Experimental Approach:** To test the first hypothesis regarding its role in interneuron development, a conditional knockout of [PRDM11](/details-gene/56981) could be generated in mice using a Cre-Lox system with a driver specific to cortical interneuron progenitors (e.g., *Nkx2.1-Cre*). The resulting adult mice could be analyzed using a combination of single-cell RNA sequencing to assess changes in interneuron subtype identity and proportions, and *in vivo* two-photon calcium imaging or *ex vivo* patch-clamp electrophysiology to measure alterations in their circuit integration and firing properties. **Therapeutic Potential:** The current literature suggests [PRDM11](/details-gene/56981) functions as a tumor suppressor, particularly in the context of lymphoma. This positions it as a target for therapeutic **activation** or functional restoration rather than inhibition. Strategies could include developing small molecules that stabilize the PRDM11 protein or enhance its enzymatic activity, or potentially gene-based therapies to restore its expression in malignant cells. However, its significant expression in the central nervous system would necessitate highly targeted delivery systems to avoid potential neurological side effects with systemic administration.

Genular Protein ID: 2781831326

Symbol: PRD11_HUMAN

Name: PR domain-containing protein 11

UniProtKB Accession Codes:

Q9NQV5 Q8N9F1

Database IDs:

ABCD 1 AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CDD 1 CTD 1 ChEMBL 1 ChiTaRS 1 DMDM 1 DNASU 1 DisGeNET 1 EC 1 EMBL 3 Ensembl 2 EvolutionaryTrace 1 ExpressionAtlas 1 GO 12 Gene3D 1 GeneCards 1 GeneTree 1 GenomeRNAi 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 3 KEGG 1 MIM 1 MINT 1 MassIVE 1 NCBI Taxonomy 1 OpenTargets 1 PANTHER 2 PDB 1 PDBsum 1 PRO 1 PROSITE 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 2 RNAct 1 RefSeq 3 SMR 1 STRING 1 SUPFAM 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 14702039

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

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 16554811

Title: Human chromosome 11 DNA sequence and analysis including novel gene identification.

PubMed ID: 16554811

DOI: 10.1038/nature04632

PubMed ID: 18669648

Title: A quantitative atlas of mitotic phosphorylation.

PubMed ID: 18669648

DOI: 10.1073/pnas.0805139105

PubMed ID: 24929828

Title: Genome-wide association analysis identifies six new loci associated with forced vital capacity.

PubMed ID: 24929828

DOI: 10.1038/ng.3011

PubMed ID: 25218447

Title: Uncovering global SUMOylation signaling networks in a site-specific manner.

PubMed ID: 25218447

DOI: 10.1038/nsmb.2890

PubMed ID: 25499759

Title: Loss of PRDM11 promotes MYC-driven lymphomagenesis.

PubMed ID: 25499759

DOI: 10.1182/blood-2014-03-560805

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

Sequence Information:

  • Length: 511
  • Mass: 57863
  • Checksum: 81DCAA502315EA5B
  • Sequence:
    • MLKMAEPIAS LMIVECRACL RCSPLFLYQR EKDRMTENMK ECLAQTNAAV GDMVTVVKTE 
VCSPLRDQEY GQPCSRRPDS SAMEVEPKKL KGKRDLIVPK SFQQVDFWFC ESCQEYFVDE 
CPNHGPPVFV SDTPVPVGIP DRAALTIPQG MEVVKDTSGE SDVRCVNEVI PKGHIFGPYE 
GQISTQDKSA GFFSWLIVDK NNRYKSIDGS DETKANWMRY VVISREEREQ NLLAFQHSER 
IYFRACRDIR PGEWLRVWYS EDYMKRLHSM SQETIHRNLA RGEKRLQREK SEQVLDNPED 
LRGPIHLSVL RQGKSPYKRG FDEGDVHPQA KKKKIDLIFK DVLEASLESA KVEAHQLALS 
TSLVIRKVPK YQDDAYSQCA TTMTHGVQNI GQTQGEGDWK VPQGVSKEPG QLEDEEEEPS 
SFKADSPAEA SLASDPHELP TTSFCPNCIR LKKKVRELQA ELDMLKSGKL PEPPVLPPQV 
LELPEFSDPA GKLVWMRLLS EGRVRSGLCG G

Genular Protein ID: 2291543449

Symbol: A0A087WWZ6_HUMAN

Name: N/A

UniProtKB Accession Codes:

A0A087WWZ6

Database IDs:

Antibodypedia 1 Bgee 1 BioGRID-ORCS 1 CDD 1 CTD 1 ChiTaRS 1 DNASU 1 DisGeNET 1 EMBL 1 Ensembl 3 Gene3D 1 GeneTree 1 HGNC 1 HOGENOM 1 InterPro 3 MANE-Select 1 NCBI Taxonomy 1 OMA 1 OrthoDB 1 PANTHER 2 PROSITE 2 PeptideAtlas 1 Pfam 1 Proteomes 2 ProteomicsDB 1 RefSeq 5 SAM 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: 15496913

Title: Finishing the euchromatic sequence of the human genome.

PubMed ID: 15496913

DOI: 10.1038/nature03001

PubMed ID: 16554811

Title: Human chromosome 11 DNA sequence and analysis including novel gene identification.

PubMed ID: 16554811

DOI: 10.1038/nature04632

PubMed ID: 18669648

Title: A quantitative atlas of mitotic phosphorylation.

PubMed ID: 18669648

DOI: 10.1073/pnas.0805139105

PubMed ID: 25218447

Title: Uncovering global SUMOylation signaling networks in a site-specific manner.

PubMed ID: 25218447

PubMed ID: 28112733

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

PubMed ID: 28112733

Sequence Information:

  • Length: 1177
  • Mass: 134261
  • Checksum: C059AB0B7C68D8C8
  • Sequence:
    • MTENMKECLA QTNAAVGDMV TVVKTEVCSP LRDQEYGQPC SRRPDSSAME VEPKKLKGKR 
DLIVPKSFQQ VDFWFCESCQ EYFVDECPNH GPPVFVSDTP VPVGIPDRAA LTIPQGMEVV 
KDTSGESDVR CVNEVIPKGH IFGPYEGQIS TQDKSAGFFS WLIVDKNNRY KSIDGSDETK 
ANWMRYVVIS REEREQNLLA FQHSERIYFR ACRDIRPGEW LRVWYSEDYM KRLHSMSQET 
IHRNLARGEK RLQREKSEQV LDNPEDLRGP IHLSVLRQGK SPYKRGFDEG DVHPQAKKKK 
IDLIFKDVLE ASLESAKVEA HQLALSTSLV IRKVPKYQDD AYSQCATTMT HGVQNIGQTQ 
GEGDWKVPQG VSKEPGQLED EEEEPSSFKA DSPAEASLAS DPHELPTTSF CPNCIRLKKK 
VRELQAELDM LKSGKLPEPP VLPPQVLELP EFSDPAASES MVSGPAIMED DDQEVDSADE 
SVSNDMMTAT DEPSKMSSAT GRRIRRFKQE WLKKFWFLRY SPTLNEMWCH VCRQYTVQSS 
RTSAFIIGSK QFKIHTIKLH SQSNLHKKCL QLYKLRMHPE KTEEMCRNMT LLFNTAYHLA 
LEGRPYLDFR PLAELLRKCE LKVVDQYMNE GDCQILIHHI ARALREDLVE RIRQSPCLSV 
ILDGQSDDLL ADTVAVYVQY TSSDGPPATE FLSLQELGFS STESYLQALD RAFSALGIRL 
QDEKPTVGLG VDGANITASL RASMFMTIRK TLPWLLCLPF MVHRPHLEIL DAISGKELPC 
LEELENNLKQ LLSFYRYSPR LMCELRSTAA TLCEETEFLG DIRAVRWIIG EQNVLNALIK 
DYLEVVAHLK EVSSQTQRAD ASAIALALLQ FLMDYQSIKL IYFLLDVIAV LSRLAYIFQG 
EYLLVSQVDD KIEEAIQEIS RLADSPGEYL QEFEENFRES FNGIAMKNLR VAEAKFQSIR 
EKICQKTQVI LAQRFDSRSR IFVKACQVFD LAAWPRSSEE LMSYGKEDMV QIFDHLEAIP 
TFSRDVCREG LDPRGSLLME WRELKADYYT KNGFKDLISH ICKYKQRFPL LNKIIQVLKV 
LPTSTACCEK GRNALQRVRK NHRSRLTLEQ LSDLLTIAVN GPPITNFDAK RALDSWFEEK 
SGNSYALSAE VLSRMSALEQ KPALQTMDHG TEFYPDI