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| Status |
Public on Aug 19, 2013 |
| Title |
Distinct Global Shifts in Genomic Binding Profiles of Limb Malformation Associated HOXD13 Mutations |
| Organism |
Gallus gallus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
We applied ChIP-seq to explore the effect of missense mutations in TFs on their genome wide binding profile. Using a retroviral expression system in chicken mesenchymal stem cells, we elucidated the mechanism underlying a novel missense mutation in HOXD13 (Q317K) associated with a complex hand and foot malformation phenotype. The glutamine at position 317 (position 50 of the homeodomain) is conserved in most homeodomains, a notable exception being bicoid-type homeodomains that have K at this position. Our results show that the mutation results in a shift in the binding profile of the mutant towards a bicoid/PITX1 motif. Gene expression analysis and functional assays using in vivo overexpression studies confirm that the mutation results in a partial conversion of HOXD13 into a TF with bicoid/PITX1 properties. A similar shift was not observed with the mutation Q317R, which is associated with brachysyndactyly, suggesting that the bicoid/PITX1-shift observed for Q317K might be related to the severe clinical phenotype.
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| Overall design |
For each wt or mutant transcription factor two independent biological replicates were used for ChIP-seq together with corresponding input DNA as reference samples. For expression analysis one RNA sample for each wt and mutant transcription factor was used and compared to the expression level of cells infected with empty vector by RNA-seq.
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| Contributor(s) |
Hansen P, Ibrahim DM, Hecht J, Rödelsperger C, Stiege A, Dölken S, Horn D, Jäger M, Janetzki C, Krawitz P, Leschik G, Wagner F, Scheuer T, Schmidt-von Kegler M, Seemann P, Timmermann B, Robinson PN, Mundlos S |
| Citation(s) |
23995701 |
| |
| Submission date |
Mar 01, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Hansen |
| E-mail(s) |
peter.hansen@charite.de
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| Phone |
+49 (0)30 450-569127
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| Organization name |
Charité-Universitätsmedizin Berlin
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| Department |
Institute for Medical Genetics and Human Genetics
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| Lab |
Computational Biology Group
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| Street address |
Augustenburger Platz 1
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| City |
Berlin |
| ZIP/Postal code |
13353 Berlin |
| Country |
Germany |
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| Platforms (1) |
| GPL13797 |
Illumina Genome Analyzer IIx (Gallus gallus) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA192680 |
| SRA |
SRP019231 |
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