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| Status |
Public on Dec 16, 2021 |
| Title |
Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation [DNA-Seq] |
| Organisms |
Mus musculus; Rattus norvegicus |
| Experiment type |
Other
|
| Summary |
Precise Hox gene expression is crucial for embryonic patterning. Local transcription factor binding and distal enhancer elements have emerged as the major regulatory modes controlling the initiation and maintenance of Hox gene expression. However, quantifying their relative contributions has remained elusive. Here, we introduce ‘synthetic regulatory reconstitution’, a novel conceptual framework for studying gene regulation and apply it to the mammalian HoxA cluster. To measure the HoxA intrinsic regulatory potential and distal enhancer contributions, we de novo synthesized and delivered variant rat HoxA clusters (130-170 kilobases each) to an ectopic location in the mouse genome. We find that a minimal HoxA cluster lacking distal enhancers induces the appropriate gene set and establishes distinct chromatin domains in response to patterning signals, while distal enhancers are required for full transcriptional output. These results suggest that the genomically compact Hox clusters contain all the information to decode patterning signals and maintain positional information
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| Overall design |
DNA-Seq was used to verify the identity of large synthetic constructs at all stages of the build and delivery pipeline from yeast to bacteria and mESCs
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| Contributor(s) |
Pinglay S, Bulajić M, Rahe DP, Huang E, Brosh R, German S, Cadley J, Rieber L, Easo N, Mahony S, Maurano MT, Holt LJ, Mazzoni EO, Boeke JD |
| Citation missing |
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| Submission date |
Dec 14, 2021 |
| Last update date |
Dec 18, 2021 |
| Contact name |
Jef Boeke |
| E-mail(s) |
jef.boeke@nyulangone.org
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| Organization name |
NYU School of Medicine
|
| Street address |
435 E 30th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10036 |
| Country |
USA |
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| Platforms (3) |
| GPL20084 |
Illumina NextSeq 500 (Rattus norvegicus) |
| GPL30020 |
Illumina NovaSeq 6000 (Mus musculus; Rattus norvegicus) |
| GPL31094 |
Illumina NextSeq 500 (Mus musculus; Rattus norvegicus) |
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| Samples (20)
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| GSM5733560 |
DNA sequencing of 134kb SynHoxA 1-14 half assemblon purified from E.coli |
| GSM5733561 |
DNA sequencing of 134kb SynHoxA 15-28 half assemblon purified from E.coli |
| GSM5733562 |
DNA sequencing of Source BAC CH230-79B14 purified from E.coli |
| GSM5733563 |
DNA sequencing of Source BAC CH230-454G2 purified from E.coli |
| GSM5733564 |
DNA sequencing of 134kb SynHoxA assemblon purified from E.coli |
| GSM5733565 |
DNA sequencing of 170kb Enhancers + SynHoxA assemblon purified from E.coli |
| GSM5733566 |
DNA sequencing of 130kb RARE∆ SynHoxA assemblon purified from E.coli |
| GSM5733567 |
DNA sequencing of 166kb Enhancers + RARE∆ SynHoxA assemblon purified from E.coli |
| GSM5733568 |
Whole Genome Sequencing of Parental WT A17iCre mESCs |
| GSM5733569 |
Whole Genome Sequencing of HoxA -/- A17iCre mESCs |
| GSM5733570 |
Capture Sequencing of 134kb SynHoxA assemblon delivered to WT mESC |
| GSM5733571 |
Capture Sequencing of 170kb Enhancers + SynHoxA assemblon delivered to WT mESC |
| GSM5733572 |
Capture Sequencing of 134kb SynHoxA assemblon delivered to Hoxa -/- mESC |
| GSM5733573 |
Capture Sequencing of 170kb Enhancers + SynHoxA assemblon delivered to Hoxa -/- mESC |
| GSM5733574 |
Capture Sequencing of HoxA -/- A17iCre mESCs |
| GSM5733575 |
Capture Sequencing of Parental WT A17iCre mESCs |
| GSM5733576 |
Capture Sequencing of 130kb RARE∆ SynHoxA assemblon delivered to Hoxa -/- mESC |
| GSM5733577 |
Capture Sequencing of 130kb RARE∆ SynHoxA assemblon delivered to WT mESC |
| GSM5733578 |
Capture Sequencing of 166kb Enhancers + RARE∆ SynHoxA assemblon delivered to Hoxa -/- mESC |
| GSM5733579 |
Capture Sequencing of 166kb Enhancers + RARE∆ SynHoxA assemblon delivered to WT mESC |
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| This SubSeries is part of SuperSeries: |
| GSE190906 |
Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation |
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| Relations |
| BioProject |
PRJNA788891 |
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