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A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiae

ABSTRACT: A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiae

PROVIDER: PRJNA669988 | ENA |

REPOSITORIES: ENA

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A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiae

Project description:This study investigates the suitability of neochromosomes as orthogonal expression platforms for rewiring native cellular processes and implementing new functionalities.

2020-11-09 | GSE159524 | GEO

A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiae.

Project description:The construction of microbial cell factories for sustainable production of chemicals and pharmaceuticals requires extensive genome engineering. Using Saccharomyces cerevisiae, this study proposes synthetic neochromosomes as orthogonal expression platforms for rewiring native cellular processes and implementing new functionalities. Capitalizing the powerful homologous recombination capability of S. cerevisiae, modular neochromosomes of 50 and 100 kb were fully assembled de novo from up to 44 transcriptional-unit-sized fragments in a single transformation. These assemblies were remarkably efficient and faithful to their in silico design. Neochromosomes made of non-coding DNA were stably replicated and segregated irrespective of their size without affecting the physiology of their host. These non-coding neochromosomes were successfully used as landing pad and as exclusive expression platform for the essential glycolytic pathway. This work pushes the limit of DNA assembly in S. cerevisiae and paves the way for de novo designer chromosomes as modular genome engineering platforms in S. cerevisiae.

| S-EPMC7897487 | biostudies-literature

Saccharomyces cerevisiae CEN.PK113-7D breed:Synthetic chromosome

Project description:A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiae

| PRJNA596648 | ENA

Modular structure and function of the XIST RNP in X chromosome inactivation

Project description:Long noncoding RNAs (lncRNAs) are an important class of transcripts that regulate gene expression on many levels, yet their mechanisms of action remain poorly understood. Previous studies have indicated that these RNAs can serve as modular scaffolds to recruit a variety of protein complexes and coordinate their distinct functions. XIST, a founding member of the lncRNA family, controls the inactivation of an entire X chromosome in placental mammals. Here we develop and integrate several orthogonal structure-interaction analysis methods to demonstrate that XIST RNA-protein complex folds into a modular architecture that is conserved in evolution. The discrete XIST RNA domains interact with distinct sets of effector proteins to orchestrate the X chromosome inactivation (XCI). The modular architecture plays an essential role, in addition to the sequence motifs, in determining the specificity of RBP binding and m6A modification. Together, this work builds a comprehensive structure-function model for the XIST RNA-protein complex, and establishes a paradigm for mechanistic studies of lncRNA functions.

2020-04-23 | GSE126715 | GEO

Expression data of sandwich cultured primary rat hepatocytes incubated to piperazine designer drugs

Project description:The piperazine derivatives most frequently consumed for recreational purposes are 1-benzylpiperazine (BZP), 1-(3,4-methylenedioxybenzyl)piperazine (MDBP), 1-(3-trifluoromethylphenyl)piperazine (TFMPP), and 1-(4-methoxyphenyl)piperazine (MeOPP). Currently it is unclear whether piperazine designer drugs induce mechanisms of hepatotoxicity and, if so, whether they act by a common mechanism. We performed a gene array study with rat hepatocytes incubated with the four designer drugs for 24 h in order to detail the global programme of gene expression Primary rat hepatocytes were cultured in collagen sandwich and incubated with the piperazine designer drugs. After 24 h, the RNA was extracted and the Affymetrix microarray analysis was performed.

2015-05-13 | E-GEOD-68785 | biostudies-arrayexpress

Modular structure and function of the XIST RNP in X chromosome inactivation

Project description:Modular structure and function of the XIST RNP in X chromosome inactivation

| PRJNA523034 | ENA

Deep functional analysis of synII, a 770 kb synthetic yeast chromosome

Project description:Here we report the design, construction and characterization of a 770 Kb synthetic yeast chromosome II (synII). With the UPLC-MS method, we demonstrated synII maintains a nearly wild-type phenotype and fitness despite hundreds of designer editing to it. Our phenomics, transcriptomics, proteomics data futher supports the identity of synII and wild one.

2016-10-13 | MTBLS296 | MetaboLights

A designer peptide against the EAG2-Kvβ2 potassium channel targets the interaction of cancer cells and neurons to treat glioblastoma

Project description:This dataset includes the raw single-cell RNAseq data from Xenograft GBM tumor (G411)-bearing NSG mice model treated with either control peptide K59-78TAT or designer peptide K90-114TAT and raw bulk RNAseq data from GBM cell (G411)-neuron coculture model treated with either control peptide K59-78TAT or designer peptide K90-114TAT. In this project, we focused on transcriptomic alteration caused by designer peptide in tumor cells.

2023-06-25 | GSE231577 | GEO

Expression data of sandwich cultured primary rat hepatocytes incubated to piperazine designer drugs

2015-05-13 | GSE68785 | GEO

Principles of Meiotic Chromosome Assembly

Project description:During meiotic prophase, chromosomes organise into a series of chromatin loops emanating from a proteinaceous axis, but the mechanisms of assembly remain unclear. Here we elucidate how this elaborate three-dimensional chromosome organisation is underpinned by genomic sequence in Saccharomyces cerevisiae. Entering meiosis, strong cohesin-dependent grid-like Hi-C interaction patterns emerge, reminiscent of mammalian interphase organisation, but with distinct regulation. Meiotic patterns agree with simulations of loop extrusion limited by barriers, yet are patterned by convergent transcription rather than binding of the mammalian interphase factor, CTCF, which is absent in S. cerevisiae—thereby both challenging and extending current paradigms of local chromosome organisation. While grid-like interactions emerge independently of meiotic chromosome synapsis, synapsis itself generates additional compaction that matures differentially according to telomere proximity and chromosome size. Collectively, our results elucidate fundamental principles of chromosome assembly and demonstrate the essential role of cohesin within this evolutionarily conserved process.

2019-09-04 | GSE127940 | GEO

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