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| Status |
Public on Aug 04, 2023 |
| Title |
Manipulating the 3D organization of the largest synthetic yeast chromosome [RNAseq] |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Whether synthetic genomescan power life has attracted broad interest in the synthetic biology field, especially when the synthetic genomes are extensively modified with thousands of designer features. Here we reportde novosynthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bpSaccharomyces cerevisiaechromosome resulting from extensive genome streamlining and modification. During the construction ofsynIV, we developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction and facilitated chromosome debugging. In addition to the drastic sequence changes made to synIV by rewriting it, we further manipulated the three-dimensional structure of synIV in the yeast nucleus to explore spatial gene regulation within the nuclear space. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Lastly, we tethered synIV to the inner nuclear membrane via its hundreds of loxPsym sites and observed transcriptional repression of the entire chromosome, demonstrating chromosome-wide transcription manipulation without changing the DNA sequences. Our manipulation of the spatial structure of the largest synthetic yeast chromosome shed light on higher-order architectural design of the synthetic genomes.
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| Overall design |
For synIV multipoint tethering to the inner nuclar membrane assays, WT or synIV strains contain HEH1 and HEH2 serve as control, WT or synIV strains contain HEH1-ZF and HEH2-ZF are the experimental group. Two or three biological replicates were includes for each genotype.
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| Web link |
https://www.sciencedirect.com/science/article/pii/S1097276523008523?via%3Dihub
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| Contributor(s) |
Zhang W, Boeke JD |
| Citation(s) |
37944526 |
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| Submission date |
Jul 28, 2023 |
| Last update date |
Nov 10, 2023 |
| Contact name |
Weimin Zhang |
| E-mail(s) |
zhangweimindailab@gmail.com, weimin.zhang@nyulangone.org
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| Phone |
9175941528
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| Organization name |
NYU Langone Health
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| Department |
Institute for Systems Genetics
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| Lab |
Jef Boeke
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| Street address |
435 E 30th street
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platforms (1) |
| GPL26302 |
NextSeq 550 (Saccharomyces cerevisiae) |
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| Samples (30)
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| This SubSeries is part of SuperSeries: |
| GSE239536 |
Manipulating the 3D organization of the largest synthetic yeast chromosome |
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| Relations |
| BioProject |
PRJNA999663 |
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