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Information on EC 1.14.99.66 - [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase and Organism(s) Mus musculus and UniProt Accession Q6ZQ88
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1.14.99.66 [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylaseIUBMB Comments
The enzyme specifically removes methyl groups from mono- and dimethylated lysine4 of histone 3. During the reaction the substrate is oxidized by the FAD cofactor of the enzyme to generate the corresponding imine, which is subsequently hydrolysed in the form of formaldehyde.The enzyme is similar to flavin amine oxidases, and differs from all other known histone lysine demethylases, which are iron(II)- and 2-oxoglutarate-dependent dioxygenases. The physiological electron acceptor is not known with certainty. In vitro the enzyme can use oxygen, which is reduced to hydrogen peroxide, but generation of hydrogen peroxide in the chromatin environment is unlikely as it will result in oxidative damage of DNA.
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Word Map
- 1.14.99.66
- chromatin
-
demethylation
- corest
-
corepressors
- deacetylases
-
chromatin-modifying
- tranylcypromine
-
lsd1-mediated
- lys4
-
demethylase-1
-
di-methylated
-
swirm
-
h3k4me1
- pargyline
- diagnostics
- drug development
The taxonomic range for the selected organisms is: Mus musculus
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
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Synonyms
demethylase lsd1, spr-5, lsd1/kdm1a, lysine-specific histone demethylase, lysine-specific histone demethylase 1a, histone lysine-specific demethylase 1, lysine-specific demethylase 2, bhc110/lsd1, lysine demethylase 1b, h3k4me2/1 histone demethylase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
AOF1
histone H3K4 demethylase
KDM1
-
-
-
-
KDM1B
LSD1
lysine-specific demethylase 1
lysine-specific histone demethylase 1
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additional information
LSD1
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SYSTEMATIC NAME
IUBMB Comments
[histone H3]-N6,N6-dimethyl-L-lysine4:acceptor oxidoreductase (demethylating)
The enzyme specifically removes methyl groups from mono- and dimethylated lysine4 of histone 3. During the reaction the substrate is oxidized by the FAD cofactor of the enzyme to generate the corresponding imine, which is subsequently hydrolysed in the form of formaldehyde.The enzyme is similar to flavin amine oxidases, and differs from all other known histone lysine demethylases, which are iron(II)- and 2-oxoglutarate-dependent dioxygenases. The physiological electron acceptor is not known with certainty. In vitro the enzyme can use oxygen, which is reduced to hydrogen peroxide, but generation of hydrogen peroxide in the chromatin environment is unlikely as it will result in oxidative damage of DNA.
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
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-
-
?
[histone H3 peptide 21mer P16A]-N6-methyl-L-lysine4 + 2-oxoglutarate + O2
?
-
-
-
-
?
[histone H3 peptide 21mer]-N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
[histone H3 peptide 21mer]-L-lysine4 + succinate + formaldehyde + CO2
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-
-
-
?
[histone H3 peptide 21mer]-N6,N6-dimethyl-L-lysine4-dimethyl-L-lysine9 + 2-oxoglutarate + O2
?
-
-
-
-
?
[histone H3 peptide 21mer]-N6-methyl-L-lysine4 + 2-oxoglutarate + O2
[histone H3 peptide 21mer]-L-lysine4 + succinate + formaldehyde + CO2
-
no activity with a monomethylated H3-Lys4 peptide with Arg2 mutated to Ala, Arg2 is central to substrate recognition also in LSD2
-
-
?
[histone H3 peptide 21mer]-N6-methyl-L-lysine4-acetyl-L-lysine9 + 2-oxoglutarate + O2
[histone H3 peptide 21mer]-L-lysine4-acetyl-L-lysine9 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3 peptide 21mer]-N6-methyl-L-lysine4-methyl-L-arginine17 + 2-oxoglutarate + O2
?
-
-
-
-
?
[histone H3 peptide 21mer]-N6-methyl-L-lysine4-methyl-L-lysine9 + 2-oxoglutarate + O2
?
-
-
-
-
?
[histone H3 peptide 30mer]-N6-methyl-L-lysine4 + 2-oxoglutarate + O2
[histone H3 peptide 30mer]-L-lysine4 + succinate + formaldehyde + CO2
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-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2
[histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2
[histone H3]-N6,N6-dimethyl-L-lysine4 + 2 2-oxoglutarate + 2 O2
[histone H3]-L-lysine4 + 2 succinate + 2 formaldehyde + 2 CO2
[histone H3]-N6,N6-methyl-L-lysine4 + 2-oxoglutarate + O2
[histone H3]-L-lysine4 + succinate + formaldehyde + CO2
[histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2
[histone H3]-L-lysine 4 + succinate + formaldehyde + CO2
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
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-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
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-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2
[histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2
[histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine4 + 2 2-oxoglutarate + 2 O2
[histone H3]-L-lysine4 + 2 succinate + 2 formaldehyde + 2 CO2
-
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine4 + 2 2-oxoglutarate + 2 O2
[histone H3]-L-lysine4 + 2 succinate + 2 formaldehyde + 2 CO2
-
demethylation of H3K4 is critical for establishing the DNA methylation imprints during oogenesis
-
-
?
[histone H3]-N6,N6-methyl-L-lysine4 + 2-oxoglutarate + O2
[histone H3]-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
[histone H3]-N6,N6-methyl-L-lysine4 + 2-oxoglutarate + O2
[histone H3]-L-lysine4 + succinate + formaldehyde + CO2
-
demethylation of H3K4 is critical for establishing the DNA methylation imprints during oogenesis
-
-
?
[histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2
[histone H3]-L-lysine 4 + succinate + formaldehyde + CO2
-
-
-
?
[histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2
[histone H3]-L-lysine 4 + succinate + formaldehyde + CO2
-
-
-
?
additional information
?
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amine oxidase flavin-containing domain 1, AOF1, also called lysine demethylase 1B , KDM1B, is a protein related to the lysine demethylase KDM1or LSD1, it functions as a H3K4 demethylase and is required for de novo DNA methylation of some imprinted genes in oocytes
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?
additional information
?
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p53 directly interacts with LSD1 to alter chromatin structure and confer developmental repression of the tumor marker alpha-fetoprotein, AFP, p53 and LSD1 cooccupy a p53 response element, concomitant with dimethylated histone H3 lysine 4 demethylation and postnatal repression of AFP transcription, overview
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?
additional information
?
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the enzyme is organized in histone demethylase complexes containing LSD1, RE1 silencing transcription factor corepressor, CoREST, histone deacetylase 1, HDAC1, and histone deacetylase 2 in erythroleukemia and T cell leukemia cells. the Complex interacts with TAL, a critical transcription factor required for hematopoiesis, overview. The enzymatic domain of LSD1 plays an important role in repressing the TAL1-directed transcription, overview. TAL1-associated LSD1 and HDM activity are dynamically regulated during hematopoiesis
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-
?
additional information
?
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recombinant KDM1B shows no activity with H3K4me3, H3K9me2, H3K27me2 and H3K36me2
-
-
?
additional information
?
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substrate specificity and effect of epigenetic marks, overview. No activity with peptide substrate of chain length below 21. Activity determinations of recombinant wild-type and mutant enzymes by horseradish peroxidase-coupled and formaldehyde dehydrogenase-coupled assays with histone H3 peptides as substrates, method optimization, e.g. with respect to pH and ionic strength, overview
-
-
?
additional information
?
-
LSD1 demethylates mono- and dimethylated H3K4 and H3K9, but does not alter trimethylated H3K4 and H3K9
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-
?
additional information
?
-
-
LSD1 demethylates mono- and dimethylated H3K4 and H3K9, but does not alter trimethylated H3K4 and H3K9
-
-
?
additional information
?
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no activity with histone H3 N6,N6,N6-dimethyl-L-lysine4
-
-
?
additional information
?
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no activity with histone H3 N6,N6,N6-dimethyl-L-lysine4
-
-
?
additional information
?
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the bifunctional enzyme catalyzes the demethylation of H3K4me2/me1 and H3K9me2/me1 (EC 1.14.11.65)
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-
?
additional information
?
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the bifunctional enzyme catalyzes the demethylation of H3K9me2/me1 (EC 1.14.11.65) and H3K4me2/me1
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
histone H3 N6-methyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 L-lysine4 + succinate + formaldehyde + CO2
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2
[histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2
[histone H3]-N6,N6-dimethyl-L-lysine4 + 2 2-oxoglutarate + 2 O2
[histone H3]-L-lysine4 + 2 succinate + 2 formaldehyde + 2 CO2
[histone H3]-N6,N6-methyl-L-lysine4 + 2-oxoglutarate + O2
[histone H3]-L-lysine4 + succinate + formaldehyde + CO2
-
demethylation of H3K4 is critical for establishing the DNA methylation imprints during oogenesis
-
-
?
[histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2
[histone H3]-L-lysine 4 + succinate + formaldehyde + CO2
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
-
?
histone H3 N6,N6-dimethyl-L-lysine4 + 2-oxoglutarate + O2
histone H3 N6-methyl-L-lysine4 + succinate + formaldehyde + CO2
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2
[histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2
[histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine4 + 2 2-oxoglutarate + 2 O2
[histone H3]-L-lysine4 + 2 succinate + 2 formaldehyde + 2 CO2
-
-
-
-
?
[histone H3]-N6,N6-dimethyl-L-lysine4 + 2 2-oxoglutarate + 2 O2
[histone H3]-L-lysine4 + 2 succinate + 2 formaldehyde + 2 CO2
-
demethylation of H3K4 is critical for establishing the DNA methylation imprints during oogenesis
-
-
?
[histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2
[histone H3]-L-lysine 4 + succinate + formaldehyde + CO2
-
-
-
?
[histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2
[histone H3]-L-lysine 4 + succinate + formaldehyde + CO2
-
-
-
?
additional information
?
-
-
amine oxidase flavin-containing domain 1, AOF1, also called lysine demethylase 1B , KDM1B, is a protein related to the lysine demethylase KDM1or LSD1, it functions as a H3K4 demethylase and is required for de novo DNA methylation of some imprinted genes in oocytes
-
-
?
additional information
?
-
-
p53 directly interacts with LSD1 to alter chromatin structure and confer developmental repression of the tumor marker alpha-fetoprotein, AFP, p53 and LSD1 cooccupy a p53 response element, concomitant with dimethylated histone H3 lysine 4 demethylation and postnatal repression of AFP transcription, overview
-
-
?
additional information
?
-
-
the enzyme is organized in histone demethylase complexes containing LSD1, RE1 silencing transcription factor corepressor, CoREST, histone deacetylase 1, HDAC1, and histone deacetylase 2 in erythroleukemia and T cell leukemia cells. the Complex interacts with TAL, a critical transcription factor required for hematopoiesis, overview. The enzymatic domain of LSD1 plays an important role in repressing the TAL1-directed transcription, overview. TAL1-associated LSD1 and HDM activity are dynamically regulated during hematopoiesis
-
-
?
additional information
?
-
LSD1 demethylates mono- and dimethylated H3K4 and H3K9, but does not alter trimethylated H3K4 and H3K9
-
-
?
additional information
?
-
-
LSD1 demethylates mono- and dimethylated H3K4 and H3K9, but does not alter trimethylated H3K4 and H3K9
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3-((1S,2R)-2-(cyclobutylamino)cyclopropyl)-N-(5-methyl-1,3,4-thiadiazol-2-yl)benzamide
compound increases H3K4 methylation in the brain without causing hematological side effects. Compound increases brain H3K4 methylation and partially restores learning function in mice with NMDA receptor hypofunction. Compound has minimal impact on the LSD1-GFI1B complex in human TF-1alpha erythroblasts
Phenelzine
inhibitor targets both the flavin adenine dinucleotide and CoREST binding domains of LSD1. Treatment reduces nuclear demethylase activity and increases transcription and expression of M1-like signatures both in vitro and in a murine triple-negative breast cancer model
[histone H3 peptide 21mer]-L-lysine4
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the demethylated peptide, product of the LSD2 reaction, inhibits LSD2
-
additional information
-
in p53-null mice, LSD1 binding is depleted, H3K4me2 is increased, and H3K9me2 remains unchanged compared to those of the wild type
-
additional information
-
TAL1-associated LSD1, HDAC1, and their enzymatic activities are coordinately down-regulated during the early phases of erythroid differentiation
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0125
[histone H3 peptide 21mer P16A]-N6-methyl-L-lysine4
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.0066
[histone H3 peptide 21mer]-N6,N6-dimethyl-L-lysine4-dimethyl-L-lysine9
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.0705
[histone H3 peptide 21mer]-N6-methyl-L-lysine4-acetyl-L-lysine9
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.0081
[histone H3 peptide 21mer]-N6-methyl-L-lysine4-methyl-L-arginine17
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.009
[histone H3 peptide 21mer]-N6-methyl-L-lysine4-methyl-L-lysine9
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.0051
[histone H3 peptide 30mer]-N6-methyl-L-lysine4
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.0113
[histone H3 peptide 21mer]-N6-methyl-L-lysine4
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.092
[histone H3 peptide 21mer]-N6-methyl-L-lysine4
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0043
[histone H3 peptide 21mer P16A]-N6-methyl-L-lysine4
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.0222
[histone H3 peptide 21mer]-N6,N6-dimethyl-L-lysine4-dimethyl-L-lysine9
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.0058
[histone H3 peptide 21mer]-N6-methyl-L-lysine4-acetyl-L-lysine9
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.005
[histone H3 peptide 21mer]-N6-methyl-L-lysine4-methyl-L-arginine17
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.004
[histone H3 peptide 21mer]-N6-methyl-L-lysine4-methyl-L-lysine9
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.0068
[histone H3 peptide 30mer]-N6-methyl-L-lysine4
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.0046
[histone H3 peptide 21mer]-N6-methyl-L-lysine4
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.033
[histone H3 peptide 21mer]-N6-methyl-L-lysine4
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.046
[histone H3 peptide 21mer]-L-arginine4
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.002
[histone H3 peptide 21mer]-L-glutamine4
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.033
[histone H3 peptide 21mer]-L-lysine4
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.00015
[histone H3 peptide 21mer]-L-methionine4
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.058
[histone H3 peptide 21mer]-N6,N6,N6-trimethyl-L-lysine4
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
0.0066
[histone H3 peptide 21mer]-N6-methyl-L-lysine9
-
pH 8.0, 25°C, recombinant wild-type LSD2
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
the highest expression of LSD1 occurs in postmitotic retinal cells during the peak period of rod photoreceptor differentiation. LSD1 appears to be absent at the outer margin of the retina, enzyme distribution, overview
KDM1/LSD1 shows relatively higher levels of expression in mouse testis and related tissues, complementing the observed lower levels of H3K4me2 in these tissues
additional information
additional information
large scale transcriptome analysis of C57BL/6J (GDS868)
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
additional information
-
genome-wide mapping and cellular localization studies of LSD1, transcriptional corepressor LSD1 is enriched at the promoter regions of highly expressed genes in ES cells
-
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
metabolism
physiological function
additional information
malfunction
-
dysregulation of the enzyme action, in balance with the H3K4 methylation, may be a major cause for vascular inflammation and metabolic memory associated with diabetic complications, overview
malfunction
-
in p53-null mice, LSD1 binding is depleted, H3K4me2 is increased, and H3K9me2 remains unchanged compared to those of the wild type. Partial hepatectomy of wild-type mouse liver and induces a regenerative response, which leads to a loss of p53, increases H3K4me2, and decreases LSD1 interaction at AFP chromatin, in parallel with reactivation of AFP expression
malfunction
-
oocytes from KDM1B-deficient females show a substantial increase in H3K4 methylation and fail to set up the DNA methylation marks at four out of seven imprinted genes examined
malfunction
-
Cre-induced deletion of SALL4 in gene-targeted BM progenitors results in a remarkable decrease of SALL4-bound and LSD1-bound EBF1, accompanied by a 750fold increase of Lys4-dimethylated histon H3. Knockdown of LSD1 in bone marrow hematopoietic stem and progenitor cells leads to altered SALL4 downstream gene expression and increased cellular activity
malfunction
-
LSD1 knockdown by RNA interference or its displacement from the chromatin by antineoplastic agents caused an increase in the levels of a subset of LSD1 target genes
malfunction
pharmacological inhibition of LSD1 in retinal explants cultured from PN1 to PN8 has three major effects. It prevents the normal decrease in expression of genes associated with progenitor function, it blocks rod photoreceptor development, and it increases expression of genes associated with other retinal cell types, e.g. genes Gnat2, Otop3, Pde6c, and Gnb3. Enzyme inhibition blocks rhodopsin expression in PN1 retinal explants, changes in rhodopsin expression caused by trans-2-phenylcyclopropylamine are not secondary to changes in cell proliferation or cell death. LSD1 enzyme inhibition changes the expression of many genes, but does not change the expression levels of these key regulators of retina development, microarrays, detailed overview
malfunction
a KDM1 mutant is embryonic lethal, analysis of demethylase developmental expression patterns and mutant/knockdown phenotypes, overview
malfunction
depletion of LSD1 in an immortalized olfactory-placode-derived cell line (OP6) results in multigenic and multiallelic odorant receptor (OR) transcription per cell, while not seemingly disrupting the ability of these cells to activate new OR genes during clonal expansion. LSD1 depletion does not seem to alter OR representation in OP6 cell populations. Apparent systematic accumulation of H3K4me2 (and possibly H3K9me2) in LSD1-depleted cell populations
metabolism
hyperglycemia/hyperinsulinemia induces changes in expression of chromatin modifying genes and their regulation by histone modifications, overview. Crosstalk between these histone modifications under hyperinsulinemic/hyperglycemic conditions: no change in H3K9me1 levels at the coding regions of histone H3K9 demethylase (Jmjd2b) and H3K4 demethylase (Aof1), and decreased H3K4me1 levels at Myst4 and Jmjd2b, and increased H3K4me1 levels at Set and Aof1. Levels of H3K9me1 are only changed at histone acetylase (Myst4) and deacetylase (Set), highlighting the role of this modification in regulating histone acetylation only. The chromatin remodelling genes Myst4, Jmjd2b, Set, and Aof1 show similar pattern of change for H3Ac and H3K4me1 on Myst4, Jmjd2b, Aof1 and Set gene promoter regions under both low glucose and high glucose condition after insulin stimulation
metabolism
the enzyme is involved in patterns of specific lysine methyl modifications achieved by a precise lysine methylation system, consisting of proteins that add, remove and recognize the specific lysine methyl marks. KDM1/LSD1 is linked to an ERalpha-mediated gene activation program in a ligand-dependent manner, with approximately 58% of ERalpha + promoters also exhibiting KDM1/LSD1 recruitment. H3K27me3 and H3K4me3 demethylation are likely to be coupled, the demethylases are also likely to be involved in the developmentally programmed silencing of PcG targets
physiological function
-
amine oxidase flavin-containing domain 1, AOF1, is required for de novo DNA methylation of some imprinted genes in oocytes
physiological function
-
LSD1 is targeted to chromatin by p53, likely in a gene-specific manner, and define a molecular mechanism by which p53 mediates transcription repression in vivo during differentiation
physiological function
-
LSD1 plays, together with H3K4 methylation, a functional role in inflammation in vascular smooth muscle cells, overview
physiological function
-
the enzymatic domain of LSD1 plays an important role in repressing the TAL1-directed transcription. TAL1 recruits LSD1 to the silenced p4.2 promoter in undifferentiated, but not in differentiated, murine erythroleukemia cells. LSD1 negatively regulates TAL1-mediated transcription and suggest that the dynamic regulation of TAL1-associated LSD1/HDAC1 complex determines the onset of erythroid differentiation programs
physiological function
-
histone demethylase LSD1 is involved in SALL4 mediated transcriptional repression in hematopoietic stem cells, SALL4 and LSD1 co-occupy the same regions of GATA1, CEBPA, and TNF promoters, and SALL4 does dynamically recruit LSD1 to its target genes. LSD1 also appears to act as a central regulator for hematopoietic stem and progenitor cell proliferation and differentiation
physiological function
-
LSD1 is regulated in a cell cycle-dependent manner, overview. Histone demethylase LSD1, a component of the CoREST (corepressor for element 1-silencing transcription factor) corepressor complex, plays an important role in the downregulation of gene expression during development, correlation between the genomic levels of LSD1/H3K4me2 and gene expression, including many highly expressed ES cell genes, mechanisms underlying these two distinct functions of LSD1, overview. Cell cycle-dependent association and dissociation of LSD1 with chromatin mediates short-time-scale gene expression changes during embryonic stem cell cycle progression
physiological function
LSD1 is an enzyme active at key stages of development in a number of tissues, including the central nervous system. LSD1-mediated demethylation of H3K4me2 is required for the transition from late progenitor to differentiated mouse rod photoreceptor. LSD1 acts in concert with a series of nuclear receptors to modify chromatin structure and repress progenitor genes as well as to inhibit ectopic patterns of gene expression in the differentiating postmitotic retinal cells
physiological function
function of the mammalian olfactory system depends on specialized olfactory sensory neurons (OSNs) that each express only one allele of one odorant receptor (OR) gene (monogenic). The lysine-specific demethylase-1 (LSD1) has a role in silencing additional OR alleles in the immortalized olfactory-placode-derived cell line (OP6) cellular context. LSD1 protein removes activating H3K4 or silencing H3K9 methylation marks in a variety of developmental contexts
physiological function
histone demethylases play important roles in epigenetic regulation of gene expression, regulatory mechanisms that modulate demethylase recruitment and activity, overview. Modulation of demethylase activity involves regulation at multiple levels, including gene expression, recruitment, coordination with other epigenetic marks, and post translational modifications. Conserved role for KDM1 in meiosis and germ cell development. Demethylase activity can be modulated by DNA-binding transcription factors, and the local chromatin environment regulates demethylase accessibility. Non-coding RNAs might also play roles in recruiting H3K4 demethylase complexes to establish locus specific epigenetic patterns
physiological function
LSD1 is a nuclear amine oxidase that utilizes oxygen as an electron acceptor to reduce methylated lysine to form lysine. It demethylates H3K4m1 and H3K4m2, as well as H3K9m1 and H3K9m2 as a removal of the active methylation mark. LSD1 is associated with co-repressor complexes and promotes suppression or activation of gene expression, e.g. LSD1 might be associated to cooperative recruitment to the NFkappaB p65 site for activation in hyperglycemia
physiological function
the inhibition of LSD1 activates energy-expenditure genes by transcriptional and epigenetic mechanisms in adipocytes. Disruption of LSD1 function results in the derepression of these genes leading to the activation of mitochondrial respiration and lipolysis in adipocytes. LSD1-mediated tranxadscriptional repression is FAD-dependent, and the disruption of cellular FAD synthesis exerts similar effects on the metabolic gene expression as the LSD1 inhibition. The expression of LSD1-target genes is markedly repressed in high fat-exposed white adipose tissue, and can be reverted by LSD1 inhibition
additional information
LSD1 has no DNA-binding domain, LSD1 may interact with nuclear receptors NR2E1/ NR2E3 to bind to specific loci around progenitor genes and its promoters and that this binding is developmentally regulated
additional information
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LSD1 has no DNA-binding domain, LSD1 may interact with nuclear receptors NR2E1/ NR2E3 to bind to specific loci around progenitor genes and its promoters and that this binding is developmentally regulated
additional information
KDM1/LSD1-mediated H3K4me2 demethylation and epigenetic regulation model. Model for demethylase regulation by expression, interacting proteins and local chromatin environment
additional information
transient hyperglycemia induces recruitment of LSD1 to gene regulation sites/promoters
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). KDM1A_MOUSE
853
0
92851
Swiss-Prot
Secretory Pathway (Reliability: 4)
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
Aof1 hetero- or homozygous mutants, phenotypes, overview. Oocytes from KDM1B-deficient females show a substantial increase in H3K4 methylation and fail to set up the DNA methylation marks at four out of seven imprinted genes examined. KDM1B deficiency results in H3K4me2 elevation in oocytes and maternal-effect embryonic lethality
additional information
-
construction of two N-terminally truncated mutants, DELTA25 and DELTA257
additional information
-
overexpression of Flag-tagged p53 or LSD1 in U2OS cells, which express endogenous p53, does not cause a generalized decrease in cellular H3K4me2 levels
additional information
-
shRNA-mediated knockdown of LSD1 in murine erythroleukemia cells cells resulted in derepression of the TAL1 target gene accompanied by increasing dimeH3K4 at the promoter region
additional information
-
siRNA downregulation of LSD1 leads to significantly increased inflammatory gene expression and enhanced vascular smooth muscle cell-monocyte binding in nondiabetic mouse vascular smooth muscle cells, while overexpression in diabetic db/db mice vascular smooth muscle cells inhibits their enhanced inflammatory gene expression, phenotypes, overview
additional information
-
hairpin RNA enzyme LSD1 knockdown, RNAi rescue experiments by expressing the human LSD1 cDNA
additional information
RNAi knockdown of LSD1 expression leads to undetectable levels in about 90% of olfactory-placode-derived cell line (OP-6) cells in culture, modeling. Apparent systematic accumulation of H3K4me2 (and possibly H3K9me2) in LSD1-depleted cell populations, overview
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
LSD1 in the histone demethylase complex also containing CoREST, HDAC1, and HDAC2
-
recombinant Flag-tagged wild-type KDM1B and mutant KDM1B from HEK 293T cells to near homogeneity
-
recombinant His6-tagged wild-type LSD2 and truncated mutants from Escherichia coli strain BL21(DE3) by nickel affinity and anion exchange chromatography, followed by ultra- and gel filtration
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
coexpression of HA-tagged SALL4 and FLAG-tagged LSD1 in HEK-293 cells, coexpression of LSD1 and SALL4 proteins in mouse bone marrow hematopoietic stem and progenitor cells
-
determination of expression of Aof1 wild-type and hetero- or homozygous mutants during development. Functional expression of Flag-tagged wild-type KDM1B and mutant KDM1B in nuclei of HEK 293T cells and NIH 3T3 cells
-
LSD1 genome-wide mapping and expression analysis, LSD1 genomic regions overlap H3K4me2 regions, transcriptional corepressor LSD1 is enriched at the promoter regions of highly expressed genes in ES cells
-
LSD2, DNA and amino acid sequence determination and analysis, expression of the His6-tagged wild-type enzyme and two truncated mutants in Escherichia coli strain BL21(DE3)
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
TAL1-associated LSD1, HDAC1, and their enzymatic activities are coordinately down-regulated during the early phases of erythroid differentiation
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Lee, M.G.; Wynder, C.; Schmidt, D.M.; McCafferty, D.G.; Shiekhattar, R.
Histone H3 lysine 4 demethylation is a target of nonselective antidepressive medications
Chem. Biol.
13
563-567
2006
Mus musculus
Reddy, M.A.; Villeneuve, L.M.; Wang, M.; Lanting, L.; Natarajan, R.
Role of the lysine-specific demethylase 1 in the proinflammatory phenotype of vascular smooth muscle cells of diabetic mice
Circ. Res.
103
615-623
2008
Mus musculus
Karytinos, A.; Forneris, F.; Profumo, A.; Ciossani, G.; Battaglioli, E.; Binda, C.; Mattevi, A.
A novel mammalian flavin-dependent histone demethylase
J. Biol. Chem.
284
17775-17782
2009
Mus musculus
Tsai, W.W.; Nguyen, T.T.; Shi, Y.; Barton, M.C.
p53-targeted LSD1 functions in repression of chromatin structure and transcription in vivo
Mol. Cell. Biol.
28
5139-5146
2008
Mus musculus
Ciccone, D.N.; Su, H.; Hevi, S.; Gay, F.; Lei, H.; Bajko, J.; Xu, G.; Li, E.; Chen, T.
KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints
Nature
461
415-418
2009
Mus musculus
Hu, X.; Li, X.; Valverde, K.; Fu, X.; Noguchi, C.; Qiu, Y.; Huang, S.
LSD1-mediated epigenetic modification is required for TAL1 function and hematopoiesis
Proc. Natl. Acad. Sci. USA
106
10141-10146
2009
Mus musculus
Liu, L.; Souto, J.; Liao, W.; Jiang, Y.; Li, Y.; Nishinakamura, R.; Huang, S.; Rosengart, T.; Yang, V.; Schuster, M.; Ma, Y.; Yang, J.
Histone demethylase LSD1 is involved in SALL4 mediated transcriptional repression in hematopoietic stem cells
J. Biol. Chem.
288
34719-34728
2013
Mus musculus, Mus musculus C57/BL6J
Nair, V.D.; Ge, Y.; Balasubramaniyan, N.; Kim, J.; Okawa, Y.; Chikina, M.; Troyanskaya, O.; Sealfon, S.C.
Involvement of histone demethylase LSD1 in short-time-scale gene expression changes during cell cycle progression in embryonic stem cells
Mol. Cell. Biol.
32
4861-4876
2012
Mus musculus
Vyas, R.N.; Meredith, D.; Lane, R.P.
Lysine-specific demethylase-1 (LSD1) depletion disrupts monogenic and monoallelic odorant receptor (OR) expression in an olfactory neuronal cell line
Mol. Cell. Neurosci.
82
1-11
2017
Mus musculus (Q6ZQ88)
Popova, E.Y.; Pinzon-Guzman, C.; Salzberg, A.C.; Zhang, S.S.; Barnstable, C.J.
LSD1-mediated demethylation of H3K4me2 is required for the transition from late progenitor to differentiated mouse rod photoreceptor
Mol. Neurobiol.
53
4563-4581
2016
Mus musculus (Q6ZQ88), Mus musculus
Gupta, J.; Kumar, S.; Li, J.; Krishna Murthy Karuturi, R.; Tikoo, K.
Histone H3 lysine 4 monomethylation (H3K4me1) and H3 lysine 9 monomethylation (H3K9me1) distribution and their association in regulating gene expression under hyperglycaemic/hyperinsulinemic conditions in 3T3 cells
Biochimie
94
2656-2664
2012
Mus musculus (Q8CIG3)
Lan, F.; Nottke, A.C.; Shi, Y.
Mechanisms involved in the regulation of histone lysine demethylases
Curr. Opin. Cell Biol.
20
316-325
2008
Caenorhabditis elegans (Q9XWP6), Drosophila melanogaster (Q9VMJ7), Mus musculus (Q6ZQ88), Mus musculus C57BL/6J (Q6ZQ88)
Brasacchio, D.; Okabe, J.; Tikellis, C.; Balcerczyk, A.; George, P.; Baker, E.K.; Calkin, A.C.; Brownlee, M.; Cooper, M.E.; El-Osta, A.
Hyperglycemia induces a dynamic cooperativity of histone methylase and demethylase enzymes associated with gene-activating epigenetic marks that coexist on the lysine tail
Diabetes
58
1229-1236
2009
Homo sapiens (O60341), Homo sapiens, Mus musculus (Q6ZQ88), Mus musculus C57BL/6 (Q6ZQ88)
Tan, A.H.Y.; Tu, W.; McCuaig, R.; Hardy, K.; Donovan, T.; Tsimbalyuk, S.; Forwood, J.K.; Rao, S.
Lysine-specific histone demethylase 1A regulates macrophage polarization and checkpoint molecules in the tumor microenvironment of triple-negative breast cancer
Front. Immunol.
10
1351
2019
Mus musculus (Q6ZQ88), Mus musculus
Hino, S.; Sakamoto, A.; Nagaoka, K.; Anan, K.; Wang, Y.; Mimasu, S.; Umehara, T.; Yokoyama, S.; Kosai, K.; Nakao, M.
FAD-dependent lysine-specific demethylase-1 regulates cellular energy expenditure
Nat. Commun.
3
758
2012
Mus musculus (Q6ZQ88)
Matsuda, S.; Baba, R.; Oki, H.; Morimoto, S.; Toyofuku, M.; Igaki, S.; Kamada, Y.; Iwasaki, S.; Matsumiya, K.; Hibino, R.; Kamada, H.; Hirakawa, T.; Iwatani, M.; Tsuchida, K.; Hara, R.; Ito, M.; Kimura, H.
T-448, a specific inhibitor of LSD1 enzyme activity, improves learning function without causing thrombocytopenia in mice
Neuropsychopharmacology
44
1505-1512
2019
Mus musculus (Q6ZQ88)
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