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    PKL chromatin remodeling factor CHD3 (PICKLE) [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 817055, updated on 18-Sep-2024

    Summary

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    Official Symbol
    PKL
    Official Full Name
    chromatin remodeling factor CHD3 (PICKLE)
    Primary source
    TAIR:AT2G25170
    Locus tag
    AT2G25170
    See related
    Araport:AT2G25170
    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
    AT2G25170.1; CHD3; CHD3 PROTEIN; CHR6; CKH2; CYTOKININ-HYPERSENSITIVE 2; ENHANCED PHOTOMORPHOGENIC 1; EPP1; GYM; GYMNOS; PICKLE; SSL2; SUPPRESSOR OF SLR 2
    Summary
    Encodes a SWI/SWF nuclear-localized chromatin remodeling factor of the CHD3 group. Involved in post-germination repression of embryonic development. Acts with GA to establish repression of embryonic genes upon germination. Protein preferentially accumulates in differentiating tissues. Loss of function alleles are associated with expression of embryonic traits in adult plants and derepression of embryonic genes such as PHEROS1. Is an extragenic suppressor of slr2 (SSL2). Mutations in PKL (SSL2) restores lateral root formation in the slr2 mutant slr-1. It was proposed that PKL/SSL2-mediated chromatin remodeling negatively regulates auxin-mediated LR formation in Arabidopsis.
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    Genomic context

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    See PKL in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    33
    Sequence:
    Chromosome: 2; NC_003071.7 (10713807..10724106)

    Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene HXXXD-type acyl-transferase family protein Neighboring gene cytochrome P450, family 82, subfamily F, polypeptide 1 Neighboring gene uncharacterized protein Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene response regulator 12 Neighboring gene Defensin-like (DEFL) family protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003071.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The CHD3 remodeler PICKLE associates with genes enriched for trimethylation of histone H3 lysine 27. Zhang H, et al. Plant Physiol, 2012 May. PMID 22452853, Free PMC Article
    2. PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis. Ogas J, et al. Proc Natl Acad Sci U S A, 1999 Nov 23. PMID 10570159, Free PMC Article
    3. LWR1 and LWR2 are required for osmoregulation and osmotic adjustment in Arabidopsis. Verslues PE, et al. Plant Physiol, 2004 Sep. PMID 15347788, Free PMC Article
    4. PICKLE acts during germination to repress expression of embryonic traits. Li HC, et al. Plant J, 2005 Dec. PMID 16359393, Free PMC Article
    5. PICKLE is required for SOLITARY-ROOT/IAA14-mediated repression of ARF7 and ARF19 activity during Arabidopsis lateral root initiation. Fukaki H, et al. Plant J, 2006 Nov. PMID 17010112

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HRB2 enhances the light-induced expression of a B-box transcription factor gene, BBX21. BBX21 binds a T/G box in the ABI5 promoter and recruits HRB2 to modulate the chromatin structure at the ABI5 locus. [HRB2]
      Title: HRB2 and BBX21 interaction modulates Arabidopsis ABI5 locus and stomatal aperture.
    2. The Evening Complex and the Chromatin-Remodeling Factor PICKLE Coordinately Control Seed Dormancy by Directly Repressing DOG1 in Arabidopsis.
      Title: The Evening Complex and the Chromatin-Remodeling Factor PICKLE Coordinately Control Seed Dormancy by Directly Repressing DOG1 in Arabidopsis.
    3. The Chromatin-Remodeling Factor PICKLE Antagonizes Polycomb Repression of FT to Promote Flowering.
      Title: The Chromatin-Remodeling Factor PICKLE Antagonizes Polycomb Repression of FT to Promote Flowering.
    4. PKL activates FT transcription likely through facilitating access of CO to FT chromatin at dusk to synchronize flowering time in response to environmental cues.
      Title: The chromatin-remodelling factor PICKLE interacts with CONSTANS to promote flowering in Arabidopsis.
    5. The antagonistic functions of FIS1 and PKR2 in modulating endosperm development are similar to those of PICKLE (PKL) and CURLY LEAF (CLF), which antagonistically regulate root meristem activity.
      Title: Mutants in the imprinted PICKLE RELATED 2 gene suppress seed abortion of fertilization independent seed class mutants and paternal excess interploidy crosses in Arabidopsis.
    6. Pickle role in the vegetative growth and gibberellin signaling
      Title: Gibberellin Signaling Requires Chromatin Remodeler PICKLE to Promote Vegetative Growth and Phase Transitions.
    7. Plants lacking the CHD3 remodeler, PICKLE, exhibit various reproductive defects. These phenotypes result from loss of PICKLE in the maternal sporophyte.
      Title: Cross-Talk Between Sporophyte and Gametophyte Generations Is Promoted by CHD3 Chromatin Remodelers in Arabidopsis thaliana.
    8. data suggest that transcriptional regulation of LFY at the chromatin level by PKL may at least partially account for the late-flowering phenotype of pkl mutants
      Title: CHD3 chromatin-remodeling factor PICKLE regulates floral transition partially via modulating LEAFY expression at the chromatin level in Arabidopsis.
    9. EPP1 acts additively with SPA1 to repress seedling de-etiolation.
      Title: PICKLE is a repressor in seedling de-etiolation pathway.
    10. PKL physically interacts with HY5 to directly regulate hypocotyl cell elongation by repressing trimethylation of histone H3 Lys 27 (H3K27me3) on the regulatory regions of several cell elongation- related genes in response to changing light conditions.
      Title: Arabidopsis chromatin remodeling factor PICKLE interacts with transcription factor HY5 to regulate hypocotyl cell elongation.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001335976.1
    NM_001335977.1
    NM_001335978.1
    NM_128074.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables ATP hydrolysis activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables DNA helicase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within cell division IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within chromatin remodeling ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    acts_upstream_of_or_within cytokinin-activated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within intracellular water homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of abscisic acid-activated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of lateral root development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to auxin IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to gibberellin IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within response to water deprivation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within root development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    chromatin remodeling factor CHD3 (PICKLE)
    NP_565587.1
    • PICKLE (PKL); CONTAINS InterPro DOMAIN/s: Protein of unknown function DUF1087 (InterPro:IPR009463), Zinc finger, RING-type (InterPro:IPR001841), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, PHD-type (InterPro:IPR001965), Protein of unknown function DUF1086 (InterPro:IPR009462), Chromo domain (InterPro:IPR000953), SNF2-related (InterPro:IPR000330), DEAD-like helicase, N-terminal (InterPro:IPR014001), Chromo domain-like (InterPro:IPR016197), DNA/RNA helicase, C-terminal (InterPro:IPR001650), Zinc finger, FYVE/PHD-type (InterPro:IPR011011), Helicase, superfamily 1/2, ATP-binding domain (InterPro:IPR014021), Zinc finger, PHD-finger (InterPro:IPR019787); BEST Arabidopsis thaliana protein match is: chromatin remodeling factor, putative (TAIR:AT4G31900.1); Has 20234 Blast hits to 17178 proteins in 1958 species: Archae - 161; Bacteria - 5176; Metazoa - 5098; Fungi - 4334; Plants - 1876; Viruses - 134; Other Eukaryotes - 3455 (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_003071.7 Reference assembly

      Range
      10713807..10724106
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_128074.4 → NP_565587.1  chromatin remodeling factor CHD3 (PICKLE) [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_565587.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q0WNM8, Q9S775
      UniProtKB/TrEMBL
      A0A178VV87, A0A7G2ED44
      Conserved Domains (7) summary
      PLN03142
      Location:266 → 773
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18659
      Location:188 → 239
      CD2_tandem; repeat 2 of paired tandem chromodomains
      cd18660
      Location:96 → 170
      CD1_tandem; repeat 1 of paired tandem chromodomains
      pfam06461
      Location:919 → 1055
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:829 → 891
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08074
      Location:1068 → 1100
      CHDCT2; CHDCT2 (NUC038) domain
      cl22851
      Location:52 → 93
      PHD_SF; PHD finger superfamily

    2. NM_001335976.1 → NP_001324292.1  chromatin remodeling factor CHD3 (PICKLE) [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VV87, A0A1P8AZP2, A0A7G2ED44

    3. NM_001335977.1 → NP_001324293.1  chromatin remodeling factor CHD3 (PICKLE) [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178VV87, A0A1P8AZP6, A0A7G2ED44

    4. NM_001335978.1 → NP_001324291.1  chromatin remodeling factor CHD3 (PICKLE) [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q0WNM8, Q9S775
      UniProtKB/TrEMBL
      A0A178VV87, A0A7G2ED44
      Conserved Domains (7) summary
      PLN03142
      Location:266 → 773
      PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
      cd18659
      Location:188 → 239
      CD2_tandem; repeat 2 of paired tandem chromodomains
      cd18660
      Location:96 → 170
      CD1_tandem; repeat 1 of paired tandem chromodomains
      pfam06461
      Location:919 → 1055
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:829 → 891
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08074
      Location:1068 → 1100
      CHDCT2; CHDCT2 (NUC038) domain
      cl22851
      Location:52 → 93
      PHD_SF; PHD finger superfamily
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9S775.1

    Gene LinkOut

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