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Manipulating the 3D organization of the largest synthetic yeast chromosome [RNAseq]

ABSTRACT: Manipulating the 3D organization of the largest synthetic yeast chromosome [RNAseq]

PROVIDER: PRJNA999663 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25449039_1.fastq.gz	Fastqsanger.gz
	SRR25449039_2.fastq.gz	Fastqsanger.gz
	SRR25449040_1.fastq.gz	Fastqsanger.gz
	SRR25449040_2.fastq.gz	Fastqsanger.gz
	SRR25449041_1.fastq.gz	Fastqsanger.gz

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Manipulating the 3D organization of the largest synthetic yeast chromosome

Project description:Manipulating the 3D organization of the largest synthetic yeast chromosome

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Manipulating the 3D organization of the largest synthetic yeast chromosome [WGS]

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Manipulating the 3D organization of the largest synthetic yeast chromosome [HiC]

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Manipulating the 3D organization of the largest synthetic yeast chromosome [RNAseq]

Project description: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.

2023-08-04 | GSE239534 | GEO

Manipulating the 3D organization of the largest synthetic yeast chromosome [HiC]

2023-08-04 | GSE239532 | GEO

Manipulating the 3D organization of the largest synthetic yeast chromosome [WGS]

2023-08-04 | GSE239535 | GEO

Manipulating the 3D organization of the largest synthetic yeast chromosome

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-08-04 | GSE239536 | GEO

Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization.

Project description:Synthetic genome evolution provides a dynamic approach for systematically and straightforwardly exploring evolutionary processes. Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is an evolutionary system intrinsic to the synthetic yeast genome that can rapidly drive structural variations. Here, we detect over 260 000 rearrangement events after the SCRaMbLEing of a yeast strain harboring 5.5 synthetic yeast chromosomes (synII, synIII, synV, circular synVI, synIXR and synX). Remarkably, we find that the rearrangement events exhibit a specific landscape of frequency. We further reveal that the landscape is shaped by the combined effects of chromatin accessibility and spatial contact probability. The rearrangements tend to occur in 3D spatially proximal and chromatin-accessible regions. The enormous numbers of rearrangements mediated by SCRaMbLE provide a driving force to potentiate directed genome evolution, and the investigation of the rearrangement landscape offers mechanistic insights into the dynamics of genome evolution.

| S-EPMC10202648 | biostudies-literature

Metaphase-Chromosome-Organization

Project description:Metaphase-Chromosome-Organization

| PRJEB4743 | ENA

Metaphase-Chromosome-Organization

Project description:Mitotic chromosomes are among the most recognizable structures in the cell, yet for over a century their internal organization remains largely unsolved. We applied chromosome conformation capture methods, 5C and Hi-C, across the cell cycle and revealed two alternative three-dimensional folding states of the human genome. We show that the highly compartmentalized and cell-type-specific organization described previously for non-synchronous cells is restricted to interphase. In metaphase, we identify a homogenous folding state, which is locus-independent, common to all chromosomes, and consistent among cell types, suggesting a general principle of metaphase chromosome organization. Using polymer simulations, we find that metaphase Hi-C data is inconsistent with classic hierarchical models, and is instead best described by a linearly-organized longitudinally compressed array of consecutive chromatin loops.

2013-11-05 | E-MTAB-1948 | biostudies-arrayexpress

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