RGD Reference Report - Deletion of a conserved noncoding sequence in Plzf intron leads to Plzf down-regulation in limb bud and polydactyly in the rat. - Rat Genome Database

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Deletion of a conserved noncoding sequence in Plzf intron leads to Plzf down-regulation in limb bud and polydactyly in the rat.

Authors: Liska, F  Snajdr, P  Sedova, L  Seda, O  Chylikova, B  Slamova, P  Krejci, E  Sedmera, D  Grim, M  Krenova, D  Kren, V 
Citation: Liska F, etal., Dev Dyn. 2009 Mar;238(3):673-84.
RGD ID: 2312786
Pubmed: PMID:19191224   (View Abstract at PubMed)
DOI: DOI:10.1002/dvdy.21859   (Journal Full-text)

Lx mutation in SHR.Lx rat manifests in homozygotes as hindlimb preaxial polydactyly. It was previously mapped to a chromosome 8 segment containing the Plzf gene. Plzf (promyelocytic leukemia zinc finger protein) influences limb development as a direct repressor of posterior HoxD genes. However, the Plzf coding sequence is intact in the Lx mutants. Using linkage mapping in F2 hybrids, we downsized the segment containing Lx to 155 kb and sequenced conserved noncoding elements (CNEs) inside. A 2,964-bp deletion in Plzf intron 2, never detected in control animals, is the only candidate for Lx. The deletion removes the most deeply conserved CNE in the 155-kb segment, suggesting a regulatory influence on Plzf expression. Correspondingly, using in situ hybridization and quantitative real-time polymerase chain reaction, we found a decrease of Plzf expression in Lx/Lx limb buds with concomitant anterior expansion of expression domains of its targets, Hoxd10-13 genes, in the absence of ectopic Sonic hedgehog expression. Upstream regulation of Plzf in limb buds is currently unknown. We present here the first candidate Plzf cis-regulatory sequence.



RGD Manual Disease Annotations    Click to see Annotation Detail View

  
Object SymbolSpeciesTermQualifierEvidenceWithNotesSourceOriginal Reference(s)
SHR.PD-(D8Rat42-D8Arb23)/CubRatpolydactyly  IAGP  RGD 
ZBTB16Humanpolydactyly  ISOZbtb16 (Rattus norvegicus)DNA:deletion:intron (rat)RGD 
Zbtb16Ratpolydactyly  IAGP DNA:deletion:intron (rat)RGD 
Zbtb16Mousepolydactyly  ISOZbtb16 (Rattus norvegicus)DNA:deletion:intron (rat)RGD 
Zbtb16LxRatpolydactyly  IAGP  RGD 

Gene Ontology Annotations    Click to see Annotation Detail View

Biological Process

  
Object SymbolSpeciesTermQualifierEvidenceWithNotesSourceOriginal Reference(s)
Zbtb16Ratembryonic digit morphogenesis  IMP  RGD 
Zbtb16Ratembryonic hindlimb morphogenesis  IMP  RGD 
Zbtb16Ratprotein localization to nucleus  IDA recruits Epn1 to nucleusRGD 

Molecular Function

  
Object SymbolSpeciesTermQualifierEvidenceWithNotesSourceOriginal Reference(s)
Zbtb16Ratprotein domain specific binding  IPIEpn1 (Rattus norvegicus) RGD 

Phenotype Annotations    Click to see Annotation Detail View

Mammalian Phenotype

Object SymbolSpeciesTermQualifierEvidenceWithNotesSourceOriginal Reference(s)
SHR.PD-(D8Rat42-D8Arb23)/CubRatpreaxial polydactyly  IAGP  RGD 
Zbtb16Ratpreaxial polydactyly  IAGP  RGD 
Zbtb16LxRatpreaxial polydactyly  IAGP  RGD 
Objects Annotated

Genes (Rattus norvegicus)
Zbtb16  (zinc finger and BTB domain containing 16)
Zbtb16Lx  (zinc finger and BTB domain containing 16, Lx mutant)

Genes (Mus musculus)
Zbtb16  (zinc finger and BTB domain containing 16)

Genes (Homo sapiens)
ZBTB16  (zinc finger and BTB domain containing 16)

Objects referenced in this article
Gene Epn1 Epsin 1 Rattus norvegicus

Additional Information