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| Status |
Public on Dec 31, 2017 |
| Title |
Genome-wide changes in DNase-hypersensitivity during osteoblastogenesis reveal differential usage of DNA motifs and define novel cis-regulatory regions that control gene expression during differentiation [ChIP-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Gene regulation during the process of osteoblastogenesis has been well-described, yet the discovery of novel regulatory regions has been limited by how we currently predict the locations of functional cis-regulatory modules. Historically, the de novo identification of sequences critical for the control of gene expression relied primarily on sequence conservation in promoters. Queries for binding motifs were based on position weight matrices of known transcription factors and the identification of disease-causing, non-coding mutations near critical genes. However, we now must consider that regulatory elements also rely on 3-dimensional chromosomal interactions between far-distal regions, epigenetic chromosomal modifications, and RNA:DNA interactions. Traditionally, DNaseI-hypersensitivity assays have been used for the identification of regulatory regions via preferential digestion at chromatin depleted or displaced of nucleosomes, as a result of transcription factor occupancy. We probed DNase hypersensitivity on a genome-wide scale to determine whether osteogenic differentiation and/or bone-related gene regulation is marked by the presence of commonly utilized DNA motifs within active cis-regulatory modules. We thus sought to evaluate the gain or loss of motif representation within hypersensitive regions during osteoblastogenesis, from day-0 (growth-phase) to day-28 (mineralizing) MC3T3 cultures. We find that differentiation is marked by an increased enrichment of NFkB-p65, MEF2, and bHLH/E-box motifs within hypersensitive regions, while CTCF, NF1, TEAD, and AP1 motifs decrease. Furthermore, grouping hypersensitive regions based on genomic positioning (promoters, introns, exons, and far-distal regions) reveals significant differences in motif abundance in first introns versus other genomic positions. This finding suggests that the regulation conferred within first intron sequences may be somewhat distinct. Interestingly, the majority of motifs that were enriched, regardless of genomic position or differentiation time-point, were not completely matched to currently known transcription factor motifs (curated in the JASPAR database). Taken together, the changes in DNase-hypersensitive regions during osteoblastogenesis and the enrichment of distinct motifs within these regions indicate that osteoblasts utilize unique sets of motif rules for transcription factor binding or that regulatory control operates through undiscovered factors.
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| Overall design |
To identiy the genome-wide occupancy of Ctcf, DNA bound by Ctcf at the prolieration, matrix deposition, and mineralization stages were recovered by Ctcf ChIP. Libraries of purified DNA were generated using Illumina SR adapters (Illumina) following manufacturer’s manual, and were selected for the inserted fragments of 200 ± 50 bp, and sequenced 36 bases on an Illumina Genome Analyzer II. Base calls and sequence reads were generated by Illumina CASAVA software (version 1.6, Illumina). Two independent biological repeats of Ctcf ChIP-Seq libraries were prepared for each time point, and two Input libraries were prepared with sonicated DNA from day 9 MC3T3-E1 cells.
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| Contributor(s) |
Wu H, Tai PW, Gordon JA, Whitfield TW, van Wijnen AJ, Stein JL, Stein GS, Lian JB |
| Citation(s) |
25120271 |
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| Submission date |
Feb 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jonathan AR Gordon |
| E-mail(s) |
Jonathan.A.Gordon@uvm.edu
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| Organization name |
University of Vermont
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| Department |
Biochemistry
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| Street address |
89 Beaumont Ave Given E209
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| City |
Burlington |
| State/province |
VT |
| ZIP/Postal code |
05405 |
| Country |
USA |
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| Platforms (1) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
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| Samples (4)
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| GSM1328459 |
MC3T3-E1 cells_Input DNA (for ChIP-Seq) |
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| This SubSeries is part of SuperSeries: |
| GSE55047 |
Genome-wide changes in DNase-hypersensitivity during osteoblastogenesis reveal differential usage of DNA motifs and define novel cis-regulatory regions that control gene expression during differentiation |
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| Relations |
| BioProject |
PRJNA238322 |
| SRA |
SRP037980 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE55045_RAW.tar |
1.5 Gb |
(http)(custom) |
TAR (of BED, BIGWIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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