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DLX6 (distal-less homeobox 6)

Written2014-03Yorick Gitton, Giovanni Levi
Evolution des Regulations Endocriniennes, CNRS, UMR7221, Museum National d'Histoire Naturelle, Paris, France

Abstract DLX6 belongs to the six-member family of DLX genes characterized by a homeobox related to that found in the insect Distal-less (Dll) gene. The six DLX genes are organized as three bigenic pairs with a tail-to-tail orientation (Zerucha et al., 2000), and located on chromosomes where HOX clusters are also found (DLX5/DLX6; 7q21.3, syntenic to the HOXA cluster), (DLX1/DLX2; 2q32 syntenic to the HOXD cluster) and (DLX3/DLX4; 17q21.33 syntenic to the HOXB cluster). During embryonic development DLX genes are involved in the control of appendage and craniofacial morphogenesis and in the differentiation of reproductive organs; in the adult they play a role in bone homeostasis and in the maintenance of tissue integrity.

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Identity

Alias_namesdistal-less homeo box 6
Other alias
HGNC (Hugo) DLX6
LocusID (NCBI) 1750
Atlas_Id 52195
Location 7q21.3  [Link to chromosome band 7q21]
Location_base_pair Starts at 96635290 and ends at 96640352 bp from pter ( according to hg19-Feb_2009)  [Mapping DLX6.png]
Local_order Forward strand of human chromosome 7, from 96634860 to 96640352 - see Figure 1 below. DLX6 forms a bigenic cluster with DLX5 at 7q21.31.
 
  Figure 1. Genomic context of the human DLX5/DLX6 bigenic locus.

DNA/RNA

 
  Figure 2. The four known human DLX6 transcripts.
Description In contrast to DLX5, no intragenic mutations have been found for DLX6. It is considered that disruption of distant regulatory elements is most usually responsible for DLX5/DLX6-related disorders in human. Breakpoint analyses of genomic deletions and chromosomal rearrangements in the congenital split-hand/split-foot malformation (SHFM type 1D, OMIM #220600), have shown that positional effect and disrupted regulatory elements controlling DLX5/DLX6 activity are involved in the pathogenesis of this developmental disorder (see further "dysmorphologies"). In-depth sequencing of the candidate regions has shown that the expression of DLX6 depends upon the activity of conserved regulatory elements shared with DLX5, and located both within the DLX5/DLX6 intergenic territory and outside of the locus (see Figure 1; Lango Allen et al., 2014). Furthermore these enhancers have been identified in all examined species - including in mouse where transgenic analyses have allowed the functional characterization of their tissue-specificity.
The status of parental imprinting of the DLX5/DLX6 locus has recently gained strong interest as these genes have been considered to be putative methylation targets of the methyl-CpG binding protein-2 (MECP2), and thus might be indirectly involved in the aetiology of the Rett syndrome, a severe X-linked neurodevelopmental disorder afflicting girls with MECP2 mutation (see further "Rett syndrome").
Transcription Transcription from DLX6 yields four splice variants, one transcript being untranslated (see Figure 2). The three coding ones range from 666 b to 2304 b (major isoform) due to alternative splicing sites throughout the precursor transcript. Furthermore, two antisense non-coding transcripts have been characterized - one of which, Evf2 (Dlx6as/Dlx6os1; HNGC#37151), has been demonstrated to regulate transactivation from an intergenic enhancer of Dlx5/Dlx6 (Feng et al., 2006; Berghoff et al., 2013).
DLX6 sequence analysis of one sporadic SHFM patient (Ferro et al., 2001) has led to the discovery of a longer transcript endowing the N-terminus of DLX6 with an unusual dual poly-glutamine/poly-proline stretch, 11-20 CAG/CCG repeat long, which has been found to be conserved in mouse (Pfeffer et al., 2001; see further "trinucleotide repeats"). The functional consequences of these expansions upon DLX6 activity remain to be determined.

Protein

 
  Figure 3. Structure of the three DLX6 protein isoforms. Sequence below belongs to the longest isoform. Note the N-terminal series of poly-residue stretches.
Description DLX6 is a 175 AA helix-turn-helix homeodomain transcription factor (19.7 kDa and pI 9.9). The homeodomain spans AA 49-108 across exons 2 and 3 (see Figure 3).
Function During mouse craniofacial morphogenesis, Dlx6 acts as transactivator of the helix-loop-helix dHand gene through a regulatory element, [ATTA/TAAT], which does not bind other Dlx factors. Noticeably, this binding is a specifically endothelin-1 signaling-dependent mechanism. Thus, despite sharing regulatory elements and subsequent expression patterns with Dlx5, the Dlx6 factor appears to be competent to exert selective roles depending upon specific cellular signalling contexts. As other DLX factors, DLX6 modulates target genes expression through a domain which is distinct from the DNA-binding homeodomain, and in association within transactivating complexes which include MSX. Composition biases in DLX6 include one poly-Gly and one-His stretches (see Figure 3).
Of note, DLX6 encodes for one long isoform endowed with a contiguous series of residue stretches including glutamine, proline, alanine and histidine (see Figure 3).
 
  Figure 4. NCBI/COBALT alignment of DLX homeoproteins. Note the disposition according to the DLX 1/4/6 versus DLX 2/3/5 clades. Indicated by a yellow box is the ultraconserved Glutamine featured by most homeoproteins at position 50 of the homeodomain.
Homology With regards to other members of the DLX family, DLX6 belongs to the DLX1/4/6 clade based on sequence homology (see Figure 4). It shares a lack of N-terminal DLL-like domain specific to the other clade constituted by DLX2/3/5. The homeodomain remains close to all other DLX proteins.

Implicated in

Note
  
Entity Lung cancers
Note Neoplastic processes often result from combinatorial activity of developmental genes (Abate-Shen, 2002). Dysregulated expression of homeobox-containing genes of the distal-less family, arranged as three bigenic pairs in mammals (DLX1/2, DLX3/4 and DLX5/6; Kraus and Lufkin, 2006), has been reported to correlate with distinct oncogenic mechanisms.
DLX6 along with DLX5 is a direct MYC oncogene inducer, responsible for neoplastic initiation in many cancers, including lymphoma and lung cancers (Xu and Testa, 2009).
  
  
Entity Breast cancers and their bone metastases
Note DLX6, together with DLX5, is upregulated in lung and bone metastatic cells derived from primary breast tumors in human - a pattern associated with tumour agressivity and thus, poor prognosis and increased relapses (Morini et al., 2010). Transcriptional profiling in search for prognosis markers has identified DLX6 as an upregulated candidate for high-grade astrocytomas (Phillips et al., 2006).
  
  
Entity Dysmorphologies
Note DLX6 is often regarded as a functional substitute of DLX5 and autonomous regulation as been seldom observed; one rare such situation being the Endothelin-1→Endothelin-Ra→Dlx6→Hand2 signalling cascade which specifies lower jaw identity in the mouse embryo (Charité et al., 2001). As such, malformations described for DLX5 are commonly regarded as involving DLX6. In most mouse mutant models, severe phenotypes result from dual invalidation of Dlx5 and Dlx6. Malformative processes implying DLX6 will thus be simultaneously described on the DLX5 gene card.
Split hand-foot malformation (SHFM) type 1 with sensory-neural hearing loss (SHFM1D; MIM:220600). This malformative syndrome affects hands and feet alike, resulting in moderate to severe median ray deficiency with syndactily. Among the described six non-syndromic SHFM loci, one spans the DLX5/DLX6 bigenic cluster (Scherer et al., 1994; Crackower et al., 1996). Numerous reported mutations spare DLX5 or DLX6 open reading frames, suggesting it may rather be their common regulatory elements which is impacted (Robledo et al., 2002 ; Lo Iacono et al., 2008). However recently, two rare familial cases of SHFM1 have been demonstrated to result, with highest probability, from intragenic missense mutations of two critical glutamine residues in the third helix of the DLX5 homeodomain (Q178P reported in Shamseldin et al., 2012; and Q186H characterized in Wang et al., 2014). In the first case, a causal link between defective DLX5/DLX6 expression and the pathogenic mechanism impairing limb development remains to be elucidated. In the second case, the mutated DLX5 has been demonstrated to fail at transactivating its bona fide MYC target. Such an observation is not unexpected as the mutation affects Q50, the most conserved residue of all homeoproteins (see diagram), which numerous biochemical studies have demonstrated to be responsible for the specificity of the DNA recognition at the TAATT homeo-element (for review, Galliot et al., 1999).
Other pathogenetic processes: on a further note, SHFM cases have often been reported to include hearing loss, a trait consistent with a developmental role demonstrated for Dlx5/Dlx6 during ear formation in mouse embryogenesis (Acampora et al., 1999; Merlo et al., 2002; Robledo and Lufkin, 2006; Chatterjee et al., 2010; Frenz et al., 2010). Moreover, both genes are major targets of two regulator genes whose deficiencies are responsible for a related pathogenic condition, the auriculo-condylar syndrome (ACS, Rieder et al., 2012).
Anorectal malformation associated with SHFM has been reported in a family with a missense mutation in the P63 gene, a known direct upstream regulator of DLX5/DLX6 during morphogenesis (Su et al., 2013). Whether DLX5/DLX6 expression is dysregulated in this condition, and whether this trait can be functionaly associated with the phenotype, remains to be elucidated.
  
  
Entity Trinucleotide repeats
Note The first DLX6 exon harbours a trinucleotide repeat region of 11 to 20 CAG triplets in normal, heterozygous subjects. This CAG repeat is highly polymorphic (Pfeffer et al., 2001). While no obvious phenotype was associated with this newly discovered polymorphism in the investigated cohort, such repeat length variations are critical determinants of colon carcinogenesis and neurodegenerative disorder when occurring in the androgen receptor and huntingtin genes, respectively.
  
  
Entity Rett syndrome
Note DLX6 and DLX5 (OMIM #600028) have been controversial candidates for neurodevelopmental defects progressively afflicting young girls suffering of Rett syndrome (OMIM #312750). This late onset disorder features fatal motor abnormalities, seizures, autism and mental retardation. While the genomic sequence of the DLX5/DXL6 locus remains unaffected in all reported cases, it is a direct target of the transcriptional regulator methyl-CpG-binding protein 2 (MeCP2), which has been strongly associated to this syndrome by linkage analysis (Horike et al., 2005). While still debated (Horike et al., 2005; Schüle et al., 2007; LaSalle, 2007; Miyano et al., 2008), initial MeCP2 deficiency is considered as causing defective neurogenesis through dysregulated expression of DLX5/DLX6, due to altered chromatin state at this target locus (Horike et al., 2005; Lilja et al., 2013). Mouse mutagenesis has substantiated this hypothesis by pinpointing GABA (γ-aminobutyric acid)-releasing neurons as a major cellular target expressing Dlx5 and Dlx6, whose deficiency impairs neurogenesis in MeCP2 null mutant (Chao et al., 2010).
  
  
Entity Osteoporosis
Note Mouse mutational studies have demonstrated a role for Dlx5 and Dlx6 as a major determinant of chondrogenesis and chondrocyte hypertrophy in the endochondral skeleton, throughout embryogenesis and adulthood (Samee et al., 2007; Samee et al., 2008; Samee et al., 2009). These observations pave the way for a better understanding of human osteoporosis, in particular in patients with dysfunctional regulation of bone-remodeling hormonal levels (Prall et al., 2013).
  
  
Entity Reproductive tract
Note Dlx5 and Dlx6 are involved in the development and function of the reproductive tract. The dual mouse mutant for Dlx5 and Dlx6 displays abnormal urethra formation (Suzuki et al., 2008), reduced testicular steroidogenesis with feminization (Nishida et al., 2008), and early ovarian follicular depletion (Bouhali et al., 2011). A human mutation in a genomic region including DLX5 and DLX6 has been associated to a case of familial premature ovarian failure (Caburet et al., 2012).
  
  
Entity Teratology
Note With regards to pharmacologically-induced teratogenesis, dysregulation of Dlx5/Dlx6 gene expression has been demonstrated to be a major step during craniofacial embryopathy induced by two compounds :
i) retinoic acid, a vitamin A derivative found in the RoAccutane ® drug, which prevents the induction of Dlx5/Dlx6 in all animal models investigated (Vieux-Rochas et al., 2007; Vieux-Rochas et al., 2010); this discovery has given strong insight into the aetiology of teratologic impact of fetal exposure to RoAccutane medication in man. Analyses of retinoic acid-induced embryopathy in mouse neurulas have demonstrated that retinoic acid exposure prevents proper induction of both Dlx5 and Dlx6 by endothelin-1 signalling. This disruption has been found to be finely tuned during a surprisingly short timeframe spanning a critical period of neurulation. This exposure creates a functional invalidation of Dlx5/Dlx6-controlled cranio-facial morphogenesis (reviewed in Gitton et al., 2010);
ii) the food contaminant ochratoxin A, a fungal toxin demonstrated to prevent Dlx5 activation in exposed mouse embryos, which later develop craniofacial malformations (Wei and Sulik, 1993; Napoletano et al., 2010). Although a causal link between Dlx5, Dlx6 and the toxin remains to be functionally demonstrated, this observation may account for teratogenesis observed in human embryos maternally exposed to the toxin (Hope and Hope, 2012; Thrasher et al., 2012).
  

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Citation

This paper should be referenced as such :
Y Gitton, G Levi
DLX6 (distal-less homeobox 6)
Atlas Genet Cytogenet Oncol Haematol. 2014;18(11):817-823.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/DLX6ID52195ch7q21.html


External links

Nomenclature
HGNC (Hugo)DLX6   2919
Cards
AtlasDLX6ID52195ch7q21
Entrez_Gene (NCBI)DLX6  1750  distal-less homeobox 6
Aliases
GeneCards (Weizmann)DLX6
Ensembl hg19 (Hinxton)ENSG00000006377 [Gene_View]  chr7:96635290-96640352 [Contig_View]  DLX6 [Vega]
Ensembl hg38 (Hinxton)ENSG00000006377 [Gene_View]  chr7:96635290-96640352 [Contig_View]  DLX6 [Vega]
ICGC DataPortalENSG00000006377
TCGA cBioPortalDLX6
AceView (NCBI)DLX6
Genatlas (Paris)DLX6
WikiGenes1750
SOURCE (Princeton)DLX6
Genetics Home Reference (NIH)DLX6
Genomic and cartography
GoldenPath hg19 (UCSC)DLX6  -     chr7:96635290-96640352 +  7q21.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)DLX6  -     7q21.3   [Description]    (hg38-Dec_2013)
EnsemblDLX6 - 7q21.3 [CytoView hg19]  DLX6 - 7q21.3 [CytoView hg38]
Mapping of homologs : NCBIDLX6 [Mapview hg19]  DLX6 [Mapview hg38]
OMIM600030   
Gene and transcription
Genbank (Entrez)AK094086 BC069363 BC103688 BC103689 BC103690
RefSeq transcript (Entrez)NM_005222
RefSeq genomic (Entrez)NC_000007 NC_018918 NT_007933 NW_004929332
Consensus coding sequences : CCDS (NCBI)DLX6
Cluster EST : UnigeneHs.249196 [ NCBI ]
CGAP (NCI)Hs.249196
Alternative Splicing GalleryENSG00000006377
Gene ExpressionDLX6 [ NCBI-GEO ]   DLX6 [ EBI - ARRAY_EXPRESS ]   DLX6 [ SEEK ]   DLX6 [ MEM ]
Gene Expression Viewer (FireBrowse)DLX6 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1750
GTEX Portal (Tissue expression)DLX6
Protein : pattern, domain, 3D structure
UniProt/SwissProtP56179   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP56179  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP56179
Splice isoforms : SwissVarP56179
PhosPhoSitePlusP56179
Domaine pattern : Prosite (Expaxy)HOMEOBOX_1 (PS00027)    HOMEOBOX_2 (PS50071)   
Domains : Interpro (EBI)Homeobox_CS    Homeobox_dom    Homeobox_metazoa    Homeodomain-like    HTH_motif   
Domain families : Pfam (Sanger)Homeobox (PF00046)   
Domain families : Pfam (NCBI)pfam00046   
Domain families : Smart (EMBL)HOX (SM00389)  
Conserved Domain (NCBI)DLX6
DMDM Disease mutations1750
Blocks (Seattle)DLX6
SuperfamilyP56179
Human Protein AtlasENSG00000006377
Peptide AtlasP56179
HPRD02493
IPIIPI00980746   IPI01025022   IPI00942734   
Protein Interaction databases
DIP (DOE-UCLA)P56179
IntAct (EBI)P56179
FunCoupENSG00000006377
BioGRIDDLX6
STRING (EMBL)DLX6
ZODIACDLX6
Ontologies - Pathways
QuickGOP56179
Ontology : AmiGOskeletal system development  transcription factor activity, sequence-specific DNA binding  nucleus  regulation of transcription, DNA-templated  nervous system development  embryonic limb morphogenesis  epithelial cell differentiation  inner ear morphogenesis  sequence-specific DNA binding  anatomical structure formation involved in morphogenesis  positive regulation of epithelial cell proliferation  palate development  head development  
Ontology : EGO-EBIskeletal system development  transcription factor activity, sequence-specific DNA binding  nucleus  regulation of transcription, DNA-templated  nervous system development  embryonic limb morphogenesis  epithelial cell differentiation  inner ear morphogenesis  sequence-specific DNA binding  anatomical structure formation involved in morphogenesis  positive regulation of epithelial cell proliferation  palate development  head development  
NDEx NetworkDLX6
Atlas of Cancer Signalling NetworkDLX6
Wikipedia pathwaysDLX6
Orthology - Evolution
OrthoDB1750
GeneTree (enSembl)ENSG00000006377
Phylogenetic Trees/Animal Genes : TreeFamDLX6
HOVERGENP56179
HOGENOMP56179
Homologs : HomoloGeneDLX6
Homology/Alignments : Family Browser (UCSC)DLX6
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerDLX6 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)DLX6
dbVarDLX6
ClinVarDLX6
1000_GenomesDLX6 
Exome Variant ServerDLX6
ExAC (Exome Aggregation Consortium)DLX6 (select the gene name)
Genetic variants : HAPMAP1750
Genomic Variants (DGV)DLX6 [DGVbeta]
DECIPHER (Syndromes)7:96635290-96640352  ENSG00000006377
CONAN: Copy Number AnalysisDLX6 
Mutations
ICGC Data PortalDLX6 
TCGA Data PortalDLX6 
Broad Tumor PortalDLX6
OASIS PortalDLX6 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICDLX6  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDDLX6
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch DLX6
DgiDB (Drug Gene Interaction Database)DLX6
DoCM (Curated mutations)DLX6 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)DLX6 (select a term)
intoGenDLX6
NCG5 (London)DLX6
Cancer3DDLX6(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600030   
Orphanet
MedgenDLX6
Genetic Testing Registry DLX6
NextProtP56179 [Medical]
TSGene1750
GENETestsDLX6
Huge Navigator DLX6 [HugePedia]
snp3D : Map Gene to Disease1750
BioCentury BCIQDLX6
ClinGenDLX6 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1750
Chemical/Pharm GKB GenePA27374
Clinical trialDLX6
Miscellaneous
canSAR (ICR)DLX6 (select the gene name)
Probes
Litterature
PubMed21 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineDLX6
EVEXDLX6
GoPubMedDLX6
iHOPDLX6
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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