Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Unintended side effects of transformation are very rare

ABSTRACT: Received wisdom in the field of fungal biology holds that the process of editing a genome by transformation and homologous recombination is inherently mutagenic. However, that belief is based only on circumstantial evidence. We provide the first direct measurement of the effects of transformation on the genome by sequencing the genomes of 29 transformants and 30 untransformed controls to high coverage. Contrary to the received wisdom, our results show that transformation of DNA flanked by long targeting sequences, followed by homologous recombination and selection on a drug marker, is extremely safe. Gene deletion may select for a few mutations that occur after transformation, but even then we found fewer than two point mutations per gene deletion strain. We also tested these strains for changes in gene expression and found only a few genes that were consistently differentially expressed between wild types and strains with a drug resistance marker inserted. As part of this process, we provide the first published genome sequence of the commonly used laboratory strain Cryptococcus neoformans var. grubii strain KN99.

ORGANISM(S): Cryptococcus neoformans

PROVIDER: GSE104198 | GEO | 2017/09/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

comparative proteomics studies of the wild strain SC1401 and the tfoX deficient strain

Project description:Natural transformation, as one of the horizontal gene transfer (HGT) modes of bacteria, allows bacteria to actively uptake foreign DNA under natural conditions and integrate it into their genome through homologous recombination. Natural transformation plays an vital role in the rapid spread of pathogen virulence factors and resistance genes, resulting in the emergence of multidrug resistant or highly pathogenic strains.To investigate the mechanism by which tfoX regulates the natural transformation process of Glaesserella parasuis, comparative proteomics studies were performed on the parent wild strain SC1401 and the tfoX deficient strain.

2022-03-17 | PXD032382 | iProX

A Study of Hansoh (HS)-10502 in Patients With Advanced Solid Tumors

Project description:HS-10502 is a Poly(ADP-ribose) polymerase 1 (PARP1)-specific selective inhibitor. The purpose if this study is to assess the safety, tolerability, pharmacokinetics (PK), and efficacy of HS-10502 in subjects with homologous recombination repair (HRR) gene mutant or homologous recombination deficiency (HRD) positive advanced solid tumors.

| 9330 | ecrin-mdr-crc

A Study to Evaluate Rucaparib in Participants With Solid Tumors and With Deleterious Mutations in HRR Genes

Project description:A Phase 2, open-label, single-arm trial to evaluate the response of rucaparib in participants with various solid tumors and with deleterious mutations in Homologous Recombination Repair (HRR) genes.

| 2322588 | ecrin-mdr-crc

RecG Directs DNA Synthesis During Double-Strand Break Repair [Chromosomal marker frequency analysis]

Project description:In the bacterium Escherichia coli, RecG directs DNA synthesis during the repair of DNA double-strand breaks by homologous recombination. Chromosomal marker frequency analysis (MFA) following induction of a DSB in the absence and presence of RecG

2016-05-19 | E-GEOD-77183 | biostudies-arrayexpress

Genome wide expression analysis of psaA and psbA tobacco mutant plants.

Project description:Transcriptome analysis in tobacco mutant plants using tomato Genechip Genome array Tobacco (Nicotiana tabacum cv. Petit Havanna) psaA and psbA deletion mutants were constructed through a targeted deletion of 767 and 1152 nucleotides of coding regions, respectively with two gene cassettes: psbAproR:uidA:psbterR and rrnR:aadA:rbcLterR coding for GUS reporter and spectinomycin selectable marker genes, respectively. Standard established procedures were followed for chloroplast transformation to generate the psaA and psbA deletion mutants based on the homologous recombination. Gene expression profiles in psaA and psbA tobacco mutant plants were analyzed using tomato Genechip Genome array to study the global changes in the expression of genome.

2011-08-02 | GSE23626 | GEO

Effect of deletion of trkA on gene expression of Porphyromonas gingivalis W83

Project description:To investigate the comprehensive function of trkA in Porphyromonas gingivalis W83, we established isogenic trkA deletion strain via homologous recombination and compared the transcriptional alteration between mutant and wild type group through RNA sequencing.

2022-11-07 | GSE210663 | GEO

Leishmania infantum: Alba20 null mutant Vs wild type

Project description:Transcriptome analysis of an LiAlba20 (LinJ.34.2410) null mutant strain versus Wild type. Experiments were run with promastigotes and axenic amastigotes independently. Null mutant was produced by homologous recombination, replacing both alleles with Hygromycin phosphotransferase and Puromycin.

2014-12-31 | GSE49825 | GEO

Accelerated growth in the absence of DNA replication origins

Project description:DNA replication initiates at defined sites called origins, which serve as binding sites for initiator proteins that recruit the replicative machinery. Origins differ in number and structure across the three domains of life1 and their properties determine the dynamics of chromosome replication. Bacteria and some archaea replicate from single origins, whilst most archaea and all eukaryotes replicate using multiple origins. Initiation mechanisms that rely on homologous recombination operate in some viruses. Here we show that such mechanisms also operate in archaea. We have used deep sequencing to study replication in Haloferax volcanii. Four chromosomal origins of differing activity were identified. Deletion of individual origins resulted in perturbed replication dynamics and reduced growth. However, a strain lacking all origins has no apparent defects and grows significantly faster than wild-type. Origin-less cells initiate replication at dispersed sites rather than at discrete origins and have an absolute requirement for the recombinase RadA, unlike strains lacking individual origins. Our results demonstrate that homologous recombination alone can efficiently initiate the replication of an entire cellular genome. This raises the question of what purpose replication origins serve and why they have evolved. Measurement of replication dynamics (marker frequency analysis; MFA) for Haloferax volcanii strains, including wild-type, the laboratory strain, individual and combinations of replication origin deletions.

2013-11-03 | E-GEOD-41961 | biostudies-arrayexpress

Genome wide expression analysis of psaA and psbA tobacco mutant plants.

2011-08-01 | E-GEOD-23626 | biostudies-arrayexpress

Comparison between GT and ntcA-overexpressing strains of cyanobacteria [nitrogen-depleted conditions]

Project description:NtcA regulates primary in a unicelluar cyanobacterium Synechocystis sp. PCC6803. We constructed an ntcA-overexpressing strain, named NOX10, by introducing the ntcA genes fusing psbAII promoter by homologous recombination. The transcript profiles of parental wild-type strain GT and NOX10 were compared by microarray CyanoChip (Takrara bio.). Experiments were performed two times with biologically independent RNA.

2014-07-01 | GSE54487 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data