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KDM1B lysine demethylase 1B [ Homo sapiens (human) ]

Gene ID: 221656, updated on 22-Aug-2021

Summary

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Official Symbol
KDM1Bprovided by HGNC
Official Full Name
lysine demethylase 1Bprovided by HGNC
Primary source
HGNC:HGNC:21577
See related
Ensembl:ENSG00000165097 MIM:613081
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AOF1; LSD2; C6orf193
Summary
Flavin-dependent histone demethylases, such as KDM1B, regulate histone lysine methylation, an epigenetic mark that regulates gene expression and chromatin function (Karytinos et al., 2009 [PubMed 19407342]).[supplied by OMIM, Oct 2009]
Expression
Broad expression in thyroid (RPKM 17.9), testis (RPKM 11.6) and 23 other tissues See more
Orthologs
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Genomic context

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See KDM1B in Genome Data Viewer
Location:
6p22.3
Exon count:
23
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (18155388..18223854)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (18155653..18224085)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene NHL repeat containing E3 ubiquitin protein ligase 1 Neighboring gene thiopurine S-methyltransferase Neighboring gene Sharpr-MPRA regulatory region 13525 Neighboring gene DEK proto-oncogene Neighboring gene RNA, U6 small nuclear 263, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Expression profile of H3K4 demethylases with their clinical and pathological correlation in patients with clear cell renal cell carcinoma. Kumar A, et al. Gene, 2020 May 20. PMID 32097694
  2. Knockdown of KDM1B inhibits cell proliferation and induces apoptosis of pancreatic cancer cells. Wang Y, et al. Pathol Res Pract, 2019 May. PMID 30846414
  3. Lysine-specific demethylase 2 suppresses lipid influx and metabolism in hepatic cells. Nagaoka K, et al. Mol Cell Biol, 2015 Apr. PMID 25624347, Free PMC Article
  4. Inhibition of histone demethylase, LSD2 (KDM1B), attenuates DNA methylation and increases sensitivity to DNMT inhibitor-induced apoptosis in breast cancer cells. Katz TA, et al. Breast Cancer Res Treat, 2014 Jul. PMID 24924415
  5. [Expression and Clinical Significance of MiR-215 and KDM1B in Patients with Diffuse Large B Cell Lymphoma]. Wu RJ, et al. Zhongguo Shi Yan Xue Ye Xue Za Zhi, 2020 Oct. PMID 33067956

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. In vitro evidence of NLRP3 inflammasome regulation by histone demethylase LSD2 in renal cancer: a pilot study.
    Title: In vitro evidence of NLRP3 inflammasome regulation by histone demethylase LSD2 in renal cancer: a pilot study.
  2. [Expression and Clinical Significance of MiR-215 and KDM1B in Patients with Diffuse Large B Cell Lymphoma].
    Title: [Expression and Clinical Significance of MiR-215 and KDM1B in Patients with Diffuse Large B Cell Lymphoma].
  3. Reduction in H3K4me patterns due to aberrant expression of methyltransferases and demethylases in renal cell carcinoma: prognostic and therapeutic implications.
    Title: Reduction in H3K4me patterns due to aberrant expression of methyltransferases and demethylases in renal cell carcinoma: prognostic and therapeutic implications.
  4. While LSD1/CoREST forms a nucleosome docking platform at silenced gene promoters, LSD2/NPAC is a multifunctional enzyme complex with flexible linkers, tailored for rapid chromatin modification, in conjunction with the advance of the RNA polymerase on actively transcribed genes.
    Title: A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.
  5. The expression of LSD2 was associated with higher TNM stage and metastasis of the tumor and thus, might serve as a useful marker for Clear cell renal cell carcinoma (ccRCC) progression.
    Title: Expression profile of H3K4 demethylases with their clinical and pathological correlation in patients with clear cell renal cell carcinoma.
  6. our findings provided new insights into the critical and multifaceted roles of KDM1B in the regulation of cell proliferation and apoptosis, and offered a potentially novel target in preventing the progression of pancreatic cancer.
    Title: Knockdown of KDM1B inhibits cell proliferation and induces apoptosis of pancreatic cancer cells.
  7. These results suggest that LSD2 achieves a promoting effect on small cell lung cancer by indirectly regulating TFPI2 expression through the mediation of DNMT3B expression or through the regulation of the demethylation of H3K4me1 in the promoter region of the TFPI2 gene.
    Title: Lysine‑specific demethylase 2 contributes to the proliferation of small cell lung cancer by regulating the expression of TFPI‑2.
  8. This review focuses on published small-molecule inhibitors targeted at the two flavin adenine dinucleotide-dependent lysine demethylases, lysine-specific demethylases 1 and 2, and how the inhibitors interact with the tertiary structures of the enzymes.
    Title: Structural insight into inhibitors of flavin adenine dinucleotide-dependent lysine demethylases.
  9. These results demonstrate an important role for LSD2 in regulation of DNA methylation and gene silencing in breast cancer.
    Title: Inhibition of histone demethylase, LSD2 (KDM1B), attenuates DNA methylation and increases sensitivity to DNMT inhibitor-induced apoptosis in breast cancer cells.
  10. Histone demethylase LSD2 acts as an E3 ubiquitin ligase and inhibits cancer cell growth through promoting proteasomal degradation of OGT.
    Title: Histone demethylase LSD2 acts as an E3 ubiquitin ligase and inhibits cancer cell growth through promoting proteasomal degradation of OGT.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ33898, FLJ34109, FLJ43328, DKFZp686I0412

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables FAD binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables flavin adenine dinucleotide binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables histone binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone demethylase activity TAS
Traceable Author Statement
more info
  
enables oxidoreductase activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables zinc ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA methylation involved in gamete generation IEA
Inferred from Electronic Annotation
more info
  
involved_in histone H3-K4 demethylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in histone H3-K4 demethylation ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in regulation of DNA methylation ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in regulation of gene expression by genetic imprinting ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of nucleosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 

General protein information

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Preferred Names
lysine-specific histone demethylase 1B
Names
flavin-containing amine oxidase domain-containing protein 1
lysine (K)-specific demethylase 1B
lysine-specific histone demethylase 2
NP_001351543.1
NP_694587.3
XP_005248982.1
XP_005248985.1
XP_011512687.1
XP_011512688.1
XP_016865929.1
XP_016865930.1
XP_016865931.1
XP_016865932.1
XP_016865934.1
XP_016865935.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001364614.2 → NP_001351543.1  lysine-specific histone demethylase 1B 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL031774, AL589723
    Related
    ENSP00000499208.1, ENST00000650836.2
    Conserved Domains (2) summary
    pfam07496
    Location:138 → 191
    zf-CW; CW-type Zinc Finger
    cl27535
    Location:302 → 819
    Amino_oxidase; Flavin containing amine oxidoreductase

  2. NM_153042.4 → NP_694587.3  lysine-specific histone demethylase 1B isoform 2

    See identical proteins and their annotated locations for NP_694587.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant contains multiple differences, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    AA332652, AJ420481, AK125318, AL031774, DA099422
    Consensus CDS
    CCDS34343.1
    UniProtKB/Swiss-Prot
    Q8NB78
    Related
    ENSP00000297792.5, ENST00000297792.9
    Conserved Domains (2) summary
    pfam01593
    Location:267 → 587
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam07496
    Location:138 → 191
    zf-CW; CW-type Zinc Finger

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    18155388..18223854
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010440.2 → XP_016865929.1  lysine-specific histone demethylase 1B isoform X1

  2. XM_017010441.2 → XP_016865930.1  lysine-specific histone demethylase 1B isoform X2

  3. XM_017010445.2 → XP_016865934.1  lysine-specific histone demethylase 1B isoform X6

  4. XM_005248925.2 → XP_005248982.1  lysine-specific histone demethylase 1B isoform X3

    Related
    ENSP00000405669.2, ENST00000449850.2
    Conserved Domains (3) summary
    pfam01593
    Location:399 → 820
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam04433
    Location:281 → 363
    SWIRM; SWIRM domain
    pfam07496
    Location:138 → 191
    zf-CW; CW-type Zinc Finger

  5. XM_011514385.2 → XP_011512687.1  lysine-specific histone demethylase 1B isoform X7

    Conserved Domains (2) summary
    pfam01593
    Location:267 → 688
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam07496
    Location:138 → 191
    zf-CW; CW-type Zinc Finger

  6. XM_011514386.2 → XP_011512688.1  lysine-specific histone demethylase 1B isoform X10

    Conserved Domains (2) summary
    pfam01593
    Location:267 → 687
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam07496
    Location:138 → 191
    zf-CW; CW-type Zinc Finger

  7. XM_005248928.2 → XP_005248985.1  lysine-specific histone demethylase 1B isoform X8

    Conserved Domains (2) summary
    pfam01593
    Location:254 → 675
    Amino_oxidase; Flavin containing amine oxidoreductase
    pfam07496
    Location:138 → 174
    zf-CW; CW-type Zinc Finger

  8. XM_017010446.1 → XP_016865935.1  lysine-specific histone demethylase 1B isoform X9

  9. XM_017010443.2 → XP_016865932.1  lysine-specific histone demethylase 1B isoform X1

  10. XM_017010442.2 → XP_016865931.1  lysine-specific histone demethylase 1B isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NB78.3 GenPept UniProtKB/Swiss-Prot:Q8NB78

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