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| Status |
Public on Jul 05, 2016 |
| Title |
Shox2/TALE ChIP-Seq |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
ChIP-Sequencing on Shox2-HA E12.5 and E13.5 Limb and Palate, as well as Pbx on E12.5 limb .
Abstract:
Vertebrate appendage patterning is programmed by Hox-TALE factors-bound regulatory elements. However, it remains enigmatic which cell lineages are commissioned by Hox-TALE factors to generate regional specific pattern and whether other Hox-TALE co-factors exist. In this study, we investigated the transcriptional mechanisms controlled by the Shox2 transcriptional regulator in limb patterning. Harnessing an osteogenic lineage-specific Shox2 inactivation approach we show that despite widespread Shox2 expression in multiple cell lineages, lack of the stylopod observed upon Shox2 deficiency is a specific result of Shox2 loss of function in the osteogenic lineage. ChIP-Seq revealed robust interaction of Shox2 with cis-regulatory enhancers clustering around skeletogenic genes that are also bound by Hox-TALE factors, supporting a lineage autonomous function of Shox2 in osteogenic lineage fate determination and skeleton patterning. Pbx ChIP-Seq further allowed the genome-wide identification of cis-regulatory modules exhibiting co-occupancy of Pbx, Meis, and Shox2 transcriptional regulators. Integrative analysis of ChIP-Seq and RNA-Seq data and transgenic enhancer assays indicate that Shox2 patterns the stylopod as a repressor via interaction with enhancers active in the proximal limb mesenchyme and antagonizes the repressive function of TALE factors in osteogenesis.
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| Overall design |
Shox2/TALE
For ChIP-Seq, the list of libraries below, including controls, were generated [listed in the format of (antibody)-target-tissue-stage]: (α-HA)-Shox2-Limb-E12.5, (α-HA)-Shox2-Limb-E13.5, (α-HA)-Shox2-Palate-E12.5, (α-HA)-Shox2-Limb/Palate-E12.5, (α-Pbx)-Pbx-Limb-E12.5, Input (control), (α-HA)-Mixed Limb/Palate from Shox2+/+ mice-E12.5 (control).
*The attached signal tracks(*.bigwig) were generated by –bdgcmp (MACS2) to filter out background signal(by filtering against the signal track obtained from (α-HA)-Mixed Limb/Palate from Shox2+/+ mice-E12.5 (control)) and subsequently convert to bigwig for analysis and visualization.
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| Web link |
http://www.ncbi.nlm.nih.gov/pubmed/27287812
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| Contributor(s) |
Ye W, Chen Y |
| Citation(s) |
27287812 |
| BioProject |
PRJNA321628 |
| Submission date |
May 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yiping Chen |
| E-mail(s) |
ychen@tulane.edu
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| Organization name |
Tulane University
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| Department |
CMB
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| Street address |
6400 Freret
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| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70118 |
| Country |
USA |
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| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (7)
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| Relations |
| SRA |
SRP075214 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE81897_RAW.tar |
3.4 Gb |
(http)(custom) |
TAR (of BED, BIGWIG) |
| GSE81897_Shox2-Pbx-co-occupy.bed.gz |
83.1 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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