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Comparison of gene expression after induction of DNA endonuclease

ABSTRACT: Investigating the induction of the SOS response after the introduction of a single dsDNA break per genome by expressing an endonuclease. The endonuclease is under the control of a xylose-inducible promoter.

ORGANISM(S): Bacillus subtilis

PROVIDER: GSE13544 | GEO | 2008/11/21

SECONDARY ACCESSION(S): PRJNA113939

REPOSITORIES: GEO

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Comparison of gene expression after induction of DNA endonuclease in strains either containing a cut site or not

Project description:Investigating the induction of the SOS response after the introduction of a single dsDNA break per genome by expressing the SceI endonuclease. The endonuclease is under the control of a xylose-inducible promoter.

2008-11-21 | GSE13545 | GEO

Merging candidate gene approach with high throughput systems biology technology for the development of xylose utilising S. cerevisiae strains

Project description:Though highly efficient at fermenting hexose sugars, the ethanologenic yeast Saccharomyces cerevisiae has limited ability to ferment five-carbon sugars. As a significant portion of sugars found in cellulosic biomasses is the five carbon sugar xylose, S. cerevisiae must be engineered to metabolize pentose sugars. Here we combined classical candidate gene approach with systems biology to develop xylose-utilising S. cerevisiae strains. The introduction of an exogenous xylose isomerase (XYLA) and an additional copy of the endogenous xylulokinase gene (XKS1) results in the significant improvement of xylose consumption. Microarray studies reveal that the introduction of XYLA and XKS1 results in the dramatic transcriptional remodelling of the cell under both glucose and xylose conditions. To further investigate the cellular processes impacted by the introduction of XYLA and XKS1, using genome-wide chemical and synthetic lethal screens we identified greater than 40 deletion mutants that impact xylose utilization. We identified four genes, ALP1, ISC1, RPL20B and BUD21, that when individually deleted allow S. cerevisiae to utilize xylose as the sole carbon source. When these mutants are combined with XYLA and XKS1, it results in strains with significant improvement in xylose consumption. We have demonstrated that systems biology techniques combined with candidate gene approaches can successfully lead to novel genetic strategies for the improvement of xylose utilization

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Merging candidate gene approach with high throughput systems biology technology for the development of xylose utilising S. cerevisiae strains

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Project description:We described endonuclease enrichment TAPS (eeTAPS), which utilizes dihydrouracil (DHU)-sensitive endonuclease digestion after TAPS to enrich methylated CpG (mCpG). eeTAPS can accurately detect 87% of methylated CpGs in the mouse genome with a sequencing depth comparable to 4x whole genome sequencing. In comparison, reduced representation TAPS (rrTAPS) detected less than 4% of methylated CpGs with 2.5x sequencing depth. Our results demonstrate eeTAPS to be a new strategy for cost-effective genome-wide methylation analysis at single-CpG resolution that can fill the gap between whole-genome and reduced representation sequencing.

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A damage independent role for 53BP1 that impacts break order and Igh architecture during CSR

Project description:During Class Switch Recombination (CSR) B cells replace the Igh CÎ¼/Î´ exons with another downstream constant region exon (CH), altering the antibody isotype. CSR occurs through the introduction of AID-mediated double strand break (DSBs) in switch regions and subsequent ligation of broken ends. Here we developed an assay to investigate the dynamics of DSB introduction in individual cells. We demonstrate that the upstream switch region SÎ¼ is always targeted first during recombination and that the mechanism underlying this control relies on 53BP1. Surprisingly, regulation of break order occurs through residual binding of 53BP1 to chromatin before the introduction of damage and independent of its established role in DNA repair. Using chromosome conformation capture we show that 53BP1 mediates changes in chromatin architecture that affect break order. Finally, our results explain how changes in Igh architecture in the absence of 53BP1 could promote inversional rearrangements that compromise CSR. High Resolution 4C was performed in resting and activated B cells using a bait on the EÎ¼ enhancer

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Project description:Thermoanaerobacter pseudethanolicus 39E was grown on 10, 50 and 200 mM xylose in order to identify pathways and transporters responsible for xylose transport and conversion to ethanol.

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Comparison of Thermoanaerobacter sp. X514 grown on different xylose concentrations

Project description:Thermoanaerobacter sp. X514 was grown on 1, 10, 50 and 200 mM xylose in order to identify pathways and transporters responsible for xylose transport and conversion to ethanol.

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A damage independent role for 53BP1 that impacts break order and Igh architecture during CSR

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2016-06-16 | GSE81180 | GEO

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