CLF SET domain-containing protein [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: CLF
Official Full Name: SET domain-containing protein
Primary source: TAIR:AT2G23380
Locus tag: AT2G23380
See related: Araport:AT2G23380
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: CURLY LEAF; F26B6.3; F26B6_3; ICU1; INCURVATA 1; SDG1; SET1; SETDOMAIN 1; SETDOMAIN GROUP 1
Summary: Similar to the product of the Polycomb-group gene Enhancer of zeste. Required for stable repression of AG and AP3. Putative role in cell fate determination. Involved in the control of leaf morphogenesis. mutants exhibit curled, involute leaves. AGAMOUS and APETALA3 are ectopically expressed in the mutant.
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Genomic context

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See CLF in Genome Data Viewer

Location:: chromosome: 2

Exon count:: 17

Sequence:: Chromosome: 2; NC_003071.7 (9955092..9960386)

Chromosome 2 - NC_003071.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003071.7

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CURLY LEAF modulates apoplast liquid water status in Arabidopsis leaves.
Title: CURLY LEAF modulates apoplast liquid water status in Arabidopsis leaves.
Arabidopsis CURLY LEAF functions in leaf immunity against fungal pathogens by concomitantly repressing SEPALLATA3 and activating ORA59.
Title: Arabidopsis CURLY LEAF functions in leaf immunity against fungal pathogens by concomitantly repressing SEPALLATA3 and activating ORA59.
The complexity of PRC2 catalysts CLF and SWN in plants.
Title: The complexity of PRC2 catalysts CLF and SWN in plants.
CURLY LEAF Regulates MicroRNA Activity by Controlling ARGONAUTE 1 Degradation in Plants.
Title: CURLY LEAF Regulates MicroRNA Activity by Controlling ARGONAUTE 1 Degradation in Plants.
It s reported that the RNA binding protein FCA interacts with the PRC2 subunit CURLY LEAF (CLF) and binds nascent COOLAIR transcripts to allow deposition of H3K27me3 at FLC. [CLF]
Title: PRC2 recruitment and H3K27me3 deposition at FLC require FCA binding of COOLAIR.
The phenotype of the dwarfed grapevine plants was similar to that of clf mutants of A. thaliana and orthologues of the known targets of CLF in A. thaliana were differentially expressed in the dwarfed plants. This suggests that CLF, a major developmental regulator in A. thaliana, also controls shoot development in grapevine
Title: Dissecting the control of shoot development in grapevine: genetics and genomics identify potential regulators.
AG-incRNA4 can associate with CLF to repress AG expression in leaf tissues through histone H3 lysine 27methylation 3-mediated repression and to autoregulate its own expression level.
Title: A noncoding RNA transcribed from the AGAMOUS (AG) second intron binds to CURLY LEAF and represses AG expression in leaves.
Ultraviolet-B light downregulates the expression of MSI1 and CLF, two of the components of the polycomb repressive complex 2, which in consequence drives a decrease in H3K27me3 histone methylation of MIR156 and FLC genes. [CLF]
Title: UV-B radiation delays flowering time through changes in the PRC2 complex activity and miR156 levels in Arabidopsis thaliana.
A novel mechanism of the CLF-mediated epigenetic regulation of FT protein activation in photoperiod-induced flowering.
Title: Temporal-Specific Interaction of NF-YC and CURLY LEAF during the Floral Transition Regulates Flowering.
CLF represses a large number of genes in embryos at the mature-green stage.CLF regulates gene sets coordinating seed size and lipid biosynthesis.
Title: CURLY LEAF Regulates Gene Sets Coordinating Seed Size and Lipid Biosynthesis.

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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_001335847.1

Supported by ESTs:

NM_127902.6

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables histone H3K27 trimethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K27 trimethyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA-mediated transformation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within callus formation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within epigenetic programming in the endosperm	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within leaf morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression, epigenetic	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of flower development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of leaf senescence	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within response to abscisic acid	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within transcription initiation-coupled chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within vegetative to reproductive phase transition of meristem	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within vernalization response	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of PcG protein complex	IEA Inferred from Electronic Annotation more info
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: SET domain-containing protein

NP_179919.1

CURLY LEAF (CLF); FUNCTIONS IN: protein binding, sequence-specific DNA binding transcription factor activity; INVOLVED IN: in 7 processes; LOCATED IN: chloroplast; EXPRESSED IN: 15 plant structures; EXPRESSED DURING: 7 growth stages; CONTAINS InterPro DOMAIN/s: SET domain (InterPro:IPR001214); BEST Arabidopsis thaliana protein match is: SET domain-containing protein (TAIR:AT4G02020.1); Has 5951 Blast hits to 5285 proteins in 534 species: Archae - 0; Bacteria - 530; Metazoa - 2584; Fungi - 730; Plants - 989; Viruses - 16; Other Eukaryotes - 1102 (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

NC_003071.7 Reference assembly

Range

9955092..9960386

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_127902.6 → NP_179919.1 SET domain-containing protein [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_179919.1

Status: REVIEWED

UniProtKB/Swiss-Prot

O80455, P93831

UniProtKB/TrEMBL

A0A5S9X0G8

Conserved Domains (2) summary

smart00317
Location:759 → 869

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

pfam03638
Location:689 → 720

TCR; Tesmin/TSO1-like CXC domain, cysteine-rich domain
NM_001335847.1 → NP_001324816.1 SET domain-containing protein [Arabidopsis thaliana]

Status: REVIEWED

UniProtKB/TrEMBL

A0A1P8B187