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RNA-seq analysis for E.coli dnd and dam derivatives

ABSTRACT: To get a global view of PT modification’s function in ∆dam mutant, we did an RNA-seq to compare the gene expression change after dam knocks out and test whether PT could restore the changes.

ORGANISM(S): Escherichia coli BW25113 Escherichia coli K-12

PROVIDER: GSE135938 | GEO | 2020/05/21

REPOSITORIES: GEO

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RNA-seq analysis for E.coli dnd and dam derivatives

Project description:RNA-seq analysis for E.coli dnd and dam derivatives

| PRJNA560689 | ENA

Basal gene expression in dam, dam mutS, and mutS mutant E. coli strains

Project description:We determined the global gene expression profiles of wildtype, dam, dam mutS, and mutS mutant E. coli strains. Keywords: Basal gene expression comparison

2005-07-14 | GSE2928 | GEO

Dam-specific RNA-seq

Project description:Dam-specific RNA-seq

| PRJEB25687 | ENA

Dam-specific RNA-seq

Project description:To determine the transcription start site and the abundance of dam mRNA, we conducted mRNA-specific RNA-Seq experiments. Essentially two strategies were tested. First strategy: We obtained the cDNA with a specific RT-PCR in order to get the mRNA from our dam construct (see DNA-seq of DamID reporter cassette). An enrichment, in which we used a Biotinylated dam oligo and Streptavidin magnetic beads, was needed. Then, similar to SHAPE-seq, the ssDNA ligation was performed with CircLigase. The last step was the PCR reaction in order to prepare the cDNA libraries to be sequenced. Second strategy: Similar to the first one, but the specificity was introduced at the PCR, not at the RT. Thereby, busk cDNA was prepared with random hexamers. The enrichment step was not needed.

2018-03-22 | E-MTAB-5363 | biostudies-arrayexpress

ChIP-seq study on Dnd proteins

Project description:Tto get the DNA PT modification proteins binding regions on the genome, ChIP with anti-Flag antibody followed by Illumina sequencing was applied.

2020-05-21 | GSE135768 | GEO

DNA adenine methyltransferase (Dam) overexpression impairs Photorhabdus luminescens motility and virulence

Project description:Dam, the most described bacterial DNA-methyltransferase, is widespread in gamma-proteobacteria. Dam DNA methylation can play a role in various genes expression and is involved in pathogenicity of several bacterial species. In the entomopathogenic bacterium Photorhabdus luminescens, a dam ortholog was identified. Overexpression of dam in P. luminescens did not impair growth ability in vitro. In contrast, compared to a control strain harboring an empty plasmid, a significant decrease in motility was observed in the dam-overexpressing strain. In addition, the dam-overexpressing P. luminescens strain showed a delayed virulence compared to that of the control strain after injection in larvae of the lepidopteran Spodoptera littoralis. These results reveal that Dam plays a major role during P. luminescens insect infection.

2017-10-04 | GSE100650 | GEO

Mapping PT modifications in bacteria

Project description:One microbial organism always contains multiple DNA modification systems as defense strategies or epigenetic controls. Here, we describe crosstalk between two distinct DNA modifications with different target sequence motif: DNA phosphorothioation (PT, GPSAAC/GPSTTC by DndACDE proteins) and N6-methyl-adenine methylation (m6A, G6mATC by Dam protein). By using a newly developed DNA modification sequencing method PT nick-seq, we found that half of PT modifications change from GAAC/GTTC to GATC sites after bacteria have lost Dam.

2020-05-21 | GSE135910 | GEO

DamID of Dam::LMN-1 and Dam::EMR-1 in Caenorhabditis elegans adult worms

Project description:Laminopathies are caused by mutations in components of the nuclear envelope (NE). While most NE components are widely expressed, laminopathies affect only a subset of tissues. However, the understanding of the molecular mechanisms that explain this phenomenon is still elusive. Here we have performed a genome wide DamID analysis in adult C. elegans nematodes comparing the DNA association profile of two components of the NE, Lamin/LMN-1 and Emerin/EMR-1. Although both proteins were associated to silent DNA, EMR-1 showed a predominant role in the anchoring of muscle and neuronal promoters to the nuclear periphery. Deletion of either EMR-1 or LEM-2, another integral NE protein, caused local changes in nuclear architecture with both increased and decreased LMN-1 association. Comparison of Dam::LMN-1 and Dam::EMR-1 DNA assotiation in wild type strains and Dam::LMN-1 DNA association in wild type, lem-2(tm1582) and emr-1(gk119) mutant backgrounds.

2013-12-02 | E-GEOD-44188 | biostudies-arrayexpress

Cisplatin-induced gene expression in DNA adenine methyltransferase (dam) and mismatch repair deficient E. coli

Project description:We used Affymetrix microarrays to determine the cisplatin-induced gene expression changes in E. coli deficient in dam and mismatch repair (dam, dam mutS, and mutS mutant strains). E. coli deficient in dam are hypersensitive to cisplatin. However introducing an additional mutation in mismatch repair (i.e., a mutation in mutS or mutL) abrogates this sensitivity and essentially restores wildtype levels of resistance. Keywords: Drug-induced expression

2005-07-27 | GSE2999 | GEO

Neisseria gonorrhoeae drg::cm versus wild type and Neisseria gonorrhoeae drg::dam versus wild type

Project description:Transcriptional profiling of N. gonorrhoeae comparing wild type cells to cells with inactivated by chloramphenicol cassette (cm) dam replacing gene (drg) or wild type cells comparing to cells with inserted dam gene. The Goal was to study the role of drg or dam presence in overall expression profile.

2017-02-09 | GSE60347 | GEO

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