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| Status |
Public on May 06, 2017 |
| Title |
Lmx1b ChIP-seq dataset in embryonic day 12.5 (e12.5) wild type mouse limb buds |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Lmx1b is a homeodomain transcription factor responsible for limb dorsalization. Despite striking double-ventral (loss-of-function) and double-dorsal (gain-of-function) limb phenotypes, no direct downstream gene targets in the limb have been confirmed. To determine direct targets of Lmx1b during limb dorsalization (E12.5), we performed chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). Nearly 84% (n=617) of the Lmx1b-bound genomic fragments or intervals (LBIs) identified by two Lmx1b-ChIP-seqs overlap with chromatin regulatory marks indicative of potential cis-regulatory modules (PCRMs). In addition, 73 LBIs mapped to known cis-regulatory modules (CRMs) active during limb development. We compared Lmx1b-bound PCRMs to genes differentially expressed by Lmx1b at E12.5 and found 292 PCRMs within 1 Mb of 254 Lmx1b-regulated genes. Gene ontology analysis of these associated genes suggests that Lmx1b mediates dorsalization through the regulation of extracellular matrix production, bone/joint formation, axonal guidance, vascular development, cell proliferation and cell movement. We validated the functional activity of 2 PCRMs associated to Lmx1b-regulated genes, demonstrating activity and overlap with the associated gene during limb development. This is the first report to describe the genome-wide distribution of Lmx1b binding during limb development, directly linking Lmx1b to targets that accomplish limb dorsalization.
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| Overall design |
pooled limbs from embryonic day 12.5 (both fore and hind limbs - 2 runs,48 limb buds each
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| Contributor(s) |
Haro E, Watson BA, Feenstra JM, Tegeler L, Pira CU, Mohan S, Oberg KC |
| Citation(s) |
28455377 |
| Submission date |
Jul 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kerby C Oberg |
| E-mail(s) |
koberg@llu.edu
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| Phone |
909 558-7212
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| Organization name |
Loma Linda University
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| Department |
Pathology
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| Lab |
Molecular Embryopathy
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| Street address |
24785 Stewart St
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| City |
Loma Linda |
| State/province |
CA |
| ZIP/Postal code |
92354 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA327925 |
| SRA |
SRP077965 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE84064_RAW.tar |
458.0 Mb |
(http)(custom) |
TAR (of BED, BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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