Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864
Letunic et al. (2012) Nucleic Acids Res , doi:10.1093/nar/gkr931

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CHROMO Chromatin organization modifier domain

SMART accession number:	SM00298
Description:
Interpro abstract (IPR000953):	The CHROMO (CHRromatin Organization MOdifier) domain [(PUBMED:1982376), (PUBMED:1708124), (PUBMED:7667093), (PUBMED:7501439)] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting. Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain, with weak but significant sequence similarity to the N-terminal chromo domain,[(PUBMED:7667093)], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1). The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigen and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1. Functional dissections of chromo domain proteins suggests a mechanistic role for chromo domains in targeting chromo domain proteins to specific regions of the nucleus. The mechanism of targeting may involve protein-protein and/or protein/nucleic acid interactions. Hence, several line of evidence show that the HP1 chromo domain is a methyl-specific histone binding module, whereas the chromo domain of two protein components of the drosophila dosage compensation complex, MSL3 and MOF, contain chromo domains that bind to RNA in vitro [(PUBMED:11574148)]. The high resolution structures of HP1-family protein chromo and chromo shadow domain reveal a conserved chromo domain fold motif consisting of three beta strands packed against an alpha helix. The chromo domain fold belongs to the OB (oligonucleotide/oligosaccharide binding)-fold class found in a variety of prokaryotic and eukaryotic nucleic acid binding protein [(PUBMED:11574148)].
GO component:	nucleus (GO:0005634)
Family alignment:	View or CHROMA formatCLUSTALW formatMSF formatFASTA formatPIR format

There are 3904 CHROMO domains in 3091 proteins in SMART's nrdb database.

Click on the following links for more information.

• Evolution (species in which this domain is found)

• Click on to expand nodes. To display all proteins with a CHROMO domain in a specific node, click on it.

  This tree shows only several representative species. The complete taxonomic breakdown of all proteins with CHROMO domain is also avaliable.

  Useful shortcuts: Expand all nodes or Collapse tree
  Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes

• Cellular role (predicted cellular role)

• Cellular role: chromatin
  

• Literature (relevant references for this domain)

• Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

  • Singh PB et al.
  • A sequence motif found in a Drosophila heterochromatin protein is conserved in animals and plants.
  • Nucleic Acids Res. 1991; 19: 789-94
  • Display abstract

  • Modifiers of position-effect-variegation in Drosophila encode proteins that are thought to modify chromatin, rendering it heritably changed in its expressibility. In an attempt to identify similar modifier genes in other species we have utilized a known sequence homology, termed chromo box, between a suppressor of position-effect-variegation, Heterochromatin protein 1 (HP1), and a repressor of homeotic genes, Polycomb (Pc). A PCR generated probe encompassing the HP1 chromo box was used to clone full-length murine cDNAs that contain conserved chromo box motifs. Sequence comparisons, in situ hybridization experiments, and RNA Northern blot analysis suggest that the murine and human sequences presented in this report are homologues of the Drosophila HP1 gene. Chromo box sequences can also be detected in other animal species, and in plants, predicting a strongly conserved structural role for the peptide encoded by this sequence. We propose that epigenetic (yet heritable) changes in gene expressibility, characteristic of chromosomal imprinting phenomena, can largely be explained by the action of such modifier genes. The evolutionary conservation of the chromo box motif now enables the isolation and study of putative modifier genes in those animal and plant species where chromosomal imprinting has been described.

  • Paro R
  • Imprinting a determined state into the chromatin of Drosophila.
  • Trends Genet. 1990; 6: 416-21
  • Display abstract

  • The Polycomb gene of Drosophila melanogaster is a member of a class of genes involved in the clonal transmission of the repressed state of bomeotic regulatory genes through development. Genetic evidence, and the finding of a molecular similarity between the Polycomb protein and a heterochromatin-associated protein of Drosophila, suggest that this mechanism of repression might be imprinted in the structure of the chromatin, rather than being sustained through the action of diffusible regulatory factors.

• Metabolism (metabolic pathways involving proteins which contain this domain)

• Click the image to view the interactive version of the map in iPath

  % proteins involved KEGG pathway ID Description 42.86 map00310 Lysine degradation 28.57 map04310 Wnt signaling pathway 28.57 map00230 Purine metabolism This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with CHROMO domain which could be assigned to a KEGG orthologous group, and not all proteins containing CHROMO domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

• Structure (3D structures containing this domain)

• 3D Structures of CHROMO domains in PDB

  PDB code	Main view	Title
  1ap0		Structure of the chromatin binding (chromo) domain from mouse modifier protein 1, nmr, 26 structures
  1dz1		Mouse hp1 (m31) c terminal (shadow chromo) domain
  1g6z		Solution structure of the clr4 chromo domain
  1guw		Structure of the chromodomain from mouse hp1beta in complex with the lysine 9-methyl histone h3 n-terminal peptide, nmr, 25 structures
  1kna		Chromo domain of hp1 complexed with histone h3 tail containing dimethyllysine 9.
  1kne		Chromo domain of hp1 complexed with histone h3 tail containing trimethyllysine 9
  1pdq		Polycomb chromodomain complexed with the histone h3 tail containing trimethyllysine 27.
  1pfb		Structural basis for specific binding of polycomb chromodomain to histone h3 methylated at k27
  1q3l		Chromodomain of hp1 complexed with histone h3 tail containing monomethyllysine 9.
  1s4z		Hp1 chromo shadow domain in complex with pxvxl motif of caf-
  1wgs		Solution structure of the tudor domain from mouse hypothetical protein homologous to histone acetyltransferase
  1x32		Three dimensional solution structure of the chromo1 domain of cpsrp43
  1x3p		3d solution structure of the chromo-3 domain of cpsrp43
  1x3q		3d solution structure of the chromo-2 domain of cpsrp43
  2b2t		Tandem chromodomains of human chd1 complexed with histone h3 tail containing trimethyllysine 4 and phosphothreonine 3
  2b2u		Tandem chromodomains of human chd1 complexed with histone h3 tail containing trimethyllysine 4 and dimethylarginine 2
  2b2v		Crystal structure analysis of human chd1 chromodomains 1 and 2 bound to histone h3 resi 1-15 mek4
  2b2w		Tandem chromodomains of human chd1 complexed with histone h3 tail containing trimethyllysine 4
  2b2y		Tandem chromodomains of human chd1
  2bud		The solution structure of the chromo barrel domain from the males-absent on the first (mof) protein
  2d9u		Solution structure of the chromo domain of chromobox homolog 2 from human
  2dnt		Solution structure of rsgi ruh-064, a chromo domain from human cdna
  2dnv		Solution structure of rsgi ruh-055, a chromo domain from mus musculus cdna
  2dy7		Solution structure of the first chromodomain of yeast chd1
  2dy8		Solution structure of the second chromodomain of yeast chd1
  2ee1		Solution structures of the chromo domain of human chromodomain helicase-dna-binding protein 4
  2efi		Solution structure of the chromo domain of mortality factor 4-like protein 1 from human
  2eko		Solution structure of ruh-073, a pseudo chromo domain from human cdna
  2epb		Solution structure of chromo domain 2 in chromodomain- helicase-dna-binding protein 6
  2f5k		Crystal structure of the chromo domain of human mrg15
  2fmm		Crystal structure of emsy-hp1 complex
  2h1e		Tandem chromodomains of budding yeast chd1
  2hug		3d solution structure of the chromo-2 domain of cpsrp43 complexed with cpsrp54 peptide
  2k1b		Solution nmr structure of the chromo domain of the chromobox protein homolog 7
  2k28		Solution nmr structure of the chromo domain of the chromobox protein homolog 4
  2k3x		Solution structure of eaf3 chromo barrel domain
  2k3y		Solution structure of eaf3 chromo barrel domain bound to histone h3 with a dimethyllysine analog h3k36me2
  2rnz		Solution structure of the presumed chromodomain of the yeast histone acetyltransferase, esa1
  2ro0		Solution structure of the knotted tudor domain of the yeast histone acetyltransferase, esa1
  3deo		Structural basis for specific substrate recognition by the chloroplast signal recognition particle protein cpsrp43
  3dep		Structural basis for specific substrate recognition by the chloroplast signal recognition particle protein cpsrp43
  3dm1		Crystal structure of the complex of human chromobox homolog (cbx3) with peptide
  3e9f		Crystal structure short-form (residue1-113) of eaf3 chromo domain
  3e9g		Crystal structure long-form (residue1-124) of eaf3 chromo domain
  3f2u		Crystal structure of human chromobox homolog 1 (cbx1)
  3fdt		Crystal structure of the complex of human chromobox homolog (cbx5) with h3k9(me)3 peptide
  3g7l		Chromodomain of chp1 in complex with histone h3k9me3 peptide
  3gv6		Crystal structure of human chromobox homolog 6 (cbx6) with h3k9 peptide
  3h91		Crystal structure of the complex of human chromobox homolog (cbx2) and h3k27 peptide
  3i3c		Crystal structural of cbx5 chromo shadow domain
  3i8z		Crystal structure of human chromobox homolog 4 (cbx4)
  3i90		Crystal structure of human chromobox homolog 6 (cbx6) with h3k27 peptide
  3i91		Crystal structure of human chromobox homolog 8 (cbx8) with h3k9 peptide

• Links (links to other resources describing this domain)

• PFAM	chromo
  INTERPRO	IPR000953
  PROSITE	CHROMO_2

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