HCSGD entry for KDM2B
1. General information
| Official gene symbol | KDM2B |
|---|---|
| Entrez ID | 84678 |
| Gene full name | lysine (K)-specific demethylase 2B |
| Other gene symbols | CXXC2 FBXL10 Fbl10 JHDM1B PCCX2 |
| Links to Entrez Gene | Links to Entrez Gene |
2. Neighbors in the network
3. Gene ontology annotation
GO ID | GO term | Evidence | Category |
|---|---|---|---|
| GO:0000122 | Negative regulation of transcription from RNA polymerase II promoter | IEA ISS | biological_process |
| GO:0003677 | DNA binding | NAS | molecular_function |
| GO:0005515 | Protein binding | IPI | molecular_function |
| GO:0005634 | Nucleus | NAS | cellular_component |
| GO:0005730 | Nucleolus | IEA | cellular_component |
| GO:0006351 | Transcription, DNA-templated | IEA | biological_process |
| GO:0007283 | Spermatogenesis | IEA ISS | biological_process |
| GO:0008270 | Zinc ion binding | IEA | molecular_function |
| GO:0016577 | Histone demethylation | TAS | biological_process |
| GO:0019843 | RRNA binding | IEA | molecular_function |
| GO:0021555 | Midbrain-hindbrain boundary morphogenesis | IEA ISS | biological_process |
| GO:0021592 | Fourth ventricle development | IEA ISS | biological_process |
| GO:0021670 | Lateral ventricle development | IEA ISS | biological_process |
| GO:0021678 | Third ventricle development | IEA ISS | biological_process |
| GO:0021993 | Initiation of neural tube closure | IEA ISS | biological_process |
| GO:0030900 | Forebrain development | ISS | biological_process |
| GO:0030901 | Midbrain development | IEA ISS | biological_process |
| GO:0030902 | Hindbrain development | ISS | biological_process |
| GO:0031519 | PcG protein complex | IDA | cellular_component |
| GO:0032452 | Histone demethylase activity | TAS | molecular_function |
| GO:0035518 | Histone H2A monoubiquitination | IDA | biological_process |
| GO:0043524 | Negative regulation of neuron apoptotic process | IEA ISS | biological_process |
| GO:0048596 | Embryonic camera-type eye morphogenesis | IEA ISS | biological_process |
| GO:0051864 | Histone demethylase activity (H3-K36 specific) | IEA | molecular_function |
| GO:0070988 | Demethylation | TAS | biological_process |
| GO:2000178 | Negative regulation of neural precursor cell proliferation | IEA ISS | biological_process |
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4. Expression levels in datasets
- Meta-analysis result
| p-value up | p-value down | FDR up | FDR down |
|---|---|---|---|
| 0.9805999240 | 0.0120274610 | 0.9999902473 | 0.2164006152 |
- Individual experiment result
( "-" represent NA in the specific microarray platform )
( "-" represent NA in the specific microarray platform )
| Data source | Up or down | Log fold change |
|---|---|---|
| GSE11954 | Down | -0.9233322338 |
| GSE13712_SHEAR | Down | -0.1290495599 |
| GSE13712_STATIC | Down | -0.1539335809 |
| GSE19018 | Down | -0.5835126647 |
| GSE19899_A1 | Down | -0.6343149926 |
| GSE19899_A2 | Down | -0.8194294798 |
| PubMed_21979375_A1 | Up | 0.1106274110 |
| PubMed_21979375_A2 | Down | -0.6539417092 |
| GSE35957 | Down | -0.7934788664 |
| GSE36640 | Down | -1.6686903091 |
| GSE54402 | Up | 0.2364133191 |
| GSE9593 | Down | -0.5220288757 |
| GSE43922 | Down | -0.2262167343 |
| GSE24585 | Up | 0.0831314246 |
| GSE37065 | Up | 0.0768095761 |
| GSE28863_A1 | Up | 0.1842468725 |
| GSE28863_A2 | Up | 0.0754247641 |
| GSE28863_A3 | Up | 0.0411142118 |
| GSE28863_A4 | Down | -0.0057116876 |
| GSE48662 | Down | -0.1605379071 |
5. Regulation relationships with compounds/drugs/microRNAs
- Compounds
Not regulated by compounds
- Drugs
Not regulated by drugs
- MicroRNAs
- mirTarBase
MiRNA_name | mirBase ID | miRTarBase ID | Experiment | Support type | References (Pubmed ID) |
|---|---|---|---|---|---|
| hsa-miR-1 | MIMAT0000416 | MIRT024040 | Microarray | Functional MTI (Weak) | 18668037 |
| hsa-miR-324-3p | MIMAT0000762 | MIRT042973 | CLASH | Functional MTI (Weak) | 23622248 |
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- mirRecord
No target information from mirRecord
6. Text-mining results about the gene
Gene occurances in abstracts of cellular senescence-associated articles: 9 abstracts the gene occurs.
PubMed ID of the article | Sentenece the gene occurs |
|---|---|
| 27114850 | In addition, HIF-1alpha induces the expression of KDM2B and KDM5B, which repress transcription by demethylating H3K4me2,3 sites (activating marks) |
| 26984996 | The Histone Demethylase FBXL10 Regulates the Proliferation of Spermatogonia and Ensures Long-Term Sustainable Spermatogenesis in Mice |
| 26984996 | The F-box and leucine-rich repeat protein 10 (Fbxl10) gene encodes a protein that catalyzes demethylation of H3K4 and H3K36 |
| 26984996 | In this study, we show the important roles of FBXL10 as a histone demethylase in sustainable sperm production using mice in which the JmjC domain of Fbxl10 was deleted (Fbxl10(DeltaJ/DeltaJ)) |
| 26984996 | These data suggest that Fbxl10 plays important roles in long-term sustainable spermatogenesis via regulating cell cycle |
| 25273595 | JHDM1B expression regulates ribosome biogenesis and cancer cell growth in a p53 dependent manner |
| 25273595 | JHDM1B (Jumonji C histone demethylase 1B) is a histone demethylase able to regulate the accessibility of rRNA genes |
| 25273595 | In this study, we aimed to define the contribution of JHDM1B expression to the features of breast cancer, a tumor type whose behavior is related to the rate of ribosome biogenesis |
| 25273595 | We show that, in breast cancer-derived cell lines, the increase in rRNA transcription that follows JHDM1B knock-down is mirrored by an augmented cell proliferation only in p53 compromised cells, while p53 competent cells undergo cellular senescence and death |
| 25273595 | In breast cancers, lower JHDM1B expression correlates with an increased size of specifically stained nucleolar organized regions, a morphological parameter directly related to the rate of ribosome biogenesis and with a poorer prognosis |
| 25273595 | In addition, in tumors lacking the controller function of p53, a lower expression of JHDM1B is associated with an increased tumor size at diagnosis |
| 25273595 | Altogether, our data indicate that epigenetic activation of rDNA genes induced by JHDM1B depletion is associated with a p53-dependent growth arrest, but may promote cancer cell growth when p53 is lacking |
| 23321669 | KDM2B promotes pancreatic cancer via Polycomb-dependent and -independent transcriptional programs |
| 23321669 | We found that KDM2B (also known as Ndy1, FBXL10, and JHDM1B), an H3K36 histone demethylase implicated in bypass of cellular senescence and somatic cell reprogramming, is markedly overexpressed in human PDAC, with levels increasing with disease grade and stage, and highest expression in metastases |
| 23321669 | KDM2B silencing abrogated tumorigenicity of PDAC cell lines exhibiting loss of epithelial differentiation, whereas KDM2B overexpression cooperated with KrasG12D to promote PDAC formation in mouse models |
| 23321669 | Gain- and loss-of-function experiments coupled to genome-wide gene expression and ChIP studies revealed that KDM2B drives tumorigenicity through 2 different transcriptional mechanisms |
| 23321669 | KDM2B repressed developmental genes through cobinding with Polycomb group (PcG) proteins at transcriptional start sites, whereas it activated a module of metabolic genes, including mediators of protein synthesis and mitochondrial function, cobound by the MYC oncogene and the histone demethylase KDM5A |
| 22100412 | Jhdm1b also cooperates with Oct4 to activate the microRNA cluster 302/367, an integral component of the pluripotency machinery |
| 21757686 | Lysine-specific demethylase 2B (KDM2B)-let-7-enhancer of zester homolog 2 (EZH2) pathway regulates cell cycle progression and senescence in primary cells |
| 21757686 | Sustained expression of the histone demethylase, KDM2B (Ndy1/FBXL10/JHDM1B), bypasses cellular senescence in primary mouse embryonic fibroblasts (MEFs) |
| 21757686 | Here, we show that KDM2B is a conserved regulator of lifespan in multiple primary cell types and defines a program in which this chromatin-modifying enzyme counteracts the senescence-associated down-regulation of the EZH2 histone methyltransferase |
| 21757686 | Forced expression of KDM2B promotes immortalization by silencing these miRNAs through locus-specific histone H3 K36me2 demethylation, leading to EZH2 up-regulation |
| 21757686 | Overexpression of let-7b down-regulates EZH2, induces premature senescence, and counteracts immortalization of MEFs driven by KDM2B |
| 21310926 | Here, we demonstrate that ectopic expression of Kdm2b/Jhdm1b is sufficient to transform hematopoietic progenitors |
| 21310926 | Conversely, depletion of Kdm2b/Jhdm1b in hematopoietic progenitors significantly impairs Hoxa9/Meis1-induced leukemic transformation |
| 21310926 | In leukemic stem cells, knockdown of Kdm2b/Jhdm1b impairs their self-renewing capability in vitro and in vivo |
| 21310926 | Thus, our study suggests that Kdm2b/Jhdm1b functions as an oncogene and plays a critical role in leukemia development and maintenance |
| 19852816 | BACKGROUND: CG11033 (dKDM2) is the Drosophila homolog of the gene KDM2B |
| 18836456 | JmjC domain-containing histone demethylase 1b (Jhdm1b, also known as Kdm2b and Fbxl10), the mammalian paralog of the histone demethylase Jhdm1a (also known as Kdm2a and Fbxl11), has been implicated in cell-cycle regulation and tumorigenesis |
| 18836456 | In this report, we show that Jhdm1b is a histone H3 lysine 36 (H3K36) demethylase |
| 18836456 | Knockdown of Jhdm1b in primary mouse embryonic fibroblasts inhibits cell proliferation and induces cellular senescence in a pRb- and p53 pathway-dependent manner |
| 18836456 | Chromatin immunoprecipitation on ectopically expressed Jhdm1b demonstrates that Jhdm1b targets the p15(Ink4b) locus and regulates its expression in an enzymatic activity-dependent manner |
| 18836456 | Alteration of Jhdm1b level affects Ras-induced neoplastic transformation |
| 18836456 | Collectively, our results indicate that Jhdm1b is an H3K36 demethylase that regulates cell proliferation and senescence through p15(Ink4b) |
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