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    LDL1 LSD1-like 1 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 842582, updated on 18-Sep-2024

    Summary

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    Official Symbol
    LDL1
    Official Full Name
    LSD1-like 1
    Primary source
    TAIR:AT1G62830
    Locus tag
    AT1G62830
    See related
    Araport:AT1G62830
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    ARABIDOPSIS LYSINE-SPECIFIC HISTONE DEMETHYLASE; ATLSD1; ATSWP1; F23N19.21; F23N19_21; LSD1; LSD1-like 1; LYSINE-SPECIFIC HISTONE DEMETHYLASE; SWP1
    Summary
    Encodes a homolog of human Lysine-Specific Demethylase1. Involved in H3K4 methylation of target genes including the flowering time loci FLC and FWA. Located in nucleus. Negatively regulates root elongation. Involved in repression of LRP1 via histone deacetylation.
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    Genomic context

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    See LDL1 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    1
    Sequence:
    Chromosome: 1; NC_003070.9 (23264486..23267221, complement)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene Calcium-binding EF-hand family protein Neighboring gene miscRNA Neighboring gene ankyrin repeat/KH domain protein (DUF1442) Neighboring gene ncRNA Neighboring gene Class I peptide chain release factor

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Characterization of a lysine-specific histone demethylase from Arabidopsis thaliana. Spedaletti V, et al. Biochemistry, 2008 Apr 29. PMID 18393445
    2. LSD1-LIKE1-Mediated H3K4me2 Demethylation Is Required for Homologous Recombination Repair. Hirakawa T, et al. Plant Physiol, 2019 Oct. PMID 31366719, Free PMC Article
    3. Involvement of KDM1C histone demethylase-OTLD1 otubain-like histone deubiquitinase complexes in plant gene repression. Krichevsky A, et al. Proc Natl Acad Sci U S A, 2011 Jul 5. PMID 21690391, Free PMC Article
    4. Regulation of root elongation by histone acetylation in Arabidopsis. Krichevsky A, et al. J Mol Biol, 2009 Jan 9. PMID 18835563, Free PMC Article
    5. The Arabidopsis LDL1/2-HDA6 histone modification complex is functionally associated with CCA1/LHY in regulation of circadian clock genes. Hung FY, et al. Nucleic Acids Res, 2018 Nov 16. PMID 30124938, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LSD1-LIKE1-Mediated H3K4me2 Demethylation Is Required for Homologous Recombination Repair.
      Title: LSD1-LIKE1-Mediated H3K4me2 Demethylation Is Required for Homologous Recombination Repair.
    2. Histone demethylases LDL1 and LDL2 interact with the histone deacetylase 6 ( HDA6) and co-regulate TOC1 by histone demetylation and deacetylaion.
      Title: The Arabidopsis LDL1/2-HDA6 histone modification complex is functionally associated with CCA1/LHY in regulation of circadian clock genes.
    3. LSD1, EDS1, and PAD4 participate in the regulation of various molecular and physiological processes that influence Arabidopsis fitness.
      Title: Lesion simulating disease1, enhanced disease susceptibility1, and phytoalexin deficient4 conditionally regulate cellular signaling homeostasis, photosynthesis, water use efficiency, and seed yield in Arabidopsis.
    4. AtSWP1 and AtCZS represent two main components of a co-repressor complex that fine tunes flowering and is unique to plants.
      Title: C2H2 zinc finger-SET histone methyltransferase is a plant-specific chromatin modifier.
    5. AtLSD1, similar to HsLSD1, has demethylase activity toward mono- and dimethylated Lys4 but not dimethylated Lys9 and Lys27 of histone 3. [LSD1]
      Title: Characterization of a lysine-specific histone demethylase from Arabidopsis thaliana.
    Submit: New GeneRIF Correction

    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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    NM_104961.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables histone H3K4 methyltransferase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within root development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast ISM
    Inferred from Sequence Model
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    LSD1-like 1
    NP_176471.1
    • LSD1-like 1 (LDL1); CONTAINS InterPro DOMAIN/s: Amine oxidase (InterPro:IPR002937), SWIRM (InterPro:IPR007526); BEST Arabidopsis thaliana protein match is: Flavin containing amine oxidoreductase family protein (TAIR:AT3G10390.1); Has 6747 Blast hits to 5826 proteins in 999 species: Archae - 53; Bacteria - 2706; Metazoa - 1658; Fungi - 565; Plants - 779; Viruses - 0; Other Eukaryotes - 986 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

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

    Reference assembly

    Genomic

    1. NC_003070.9 Reference assembly

      Range
      23264486..23267221 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_104961.4 → NP_176471.1  LSD1-like 1 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_176471.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q56WM3, Q8VXV7
      UniProtKB/TrEMBL
      A0A5S9WNW5
      Conserved Domains (1) summary
      PLN02328
      Location:1 → 844
      PLN02328; lysine-specific histone demethylase 1 homolog
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8VXV7.1

    Gene LinkOut

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