Effects of renal ischemia-reperfusion injury in Azin1 A-to-I locked and uneditable mice
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE253286 | GEO | 2024/01/20
REPOSITORIES: GEO
Similar Datasets
Project description:Time course experiments involving bilateral renal ischemia reperfusion injury (IRI) in C57BL/6J mice (0 hr control, 20 min bilateral ischemia without reperfusion, 4, 16, 24, 36, 48, and 72 hrs post IRI). This dataset also includes IRI at 48 hrs and 72 hrs in Azin1 A-to-I locked and Azin1 A-to-I uneditable mice.
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Project description:Adenosine-to-inosine (A-to-I) RNA editing plays a vital role in many biological processes. Our previous study has demonstrated that the hematopoietic stem and progenitor cells (HSPCs) deficient in RNA editing cannot reconstitute the irradiated recipients in vivo. However, the overall profile of RNA editome in hematopoiesis has not been established and the underlying mechanism is poorly understood. Here, we sorted 12 murine adult hematopoietic cell populations, and performed deep RNA and DNA sequencing. We depicted the first landscape of RNA editing in hematopoietic cells and identified 30,796 editing sites in total. Although total editing frequency was stable across the 12 hematopoietic populations, we identified stage-specific and group-specific editing genes, and uncovered multiple famous hematopoietic regulators were dynamically edited. By charactering group specific editing genes, we found that the Azin1 (antizyme inhibitor 1) was highly edited in HSPCs, which was required for HSPCs differentiation. A-to-I editing of Azin1 transcript resulted in serine-to-glycine substitution at residue 367 of AZIN1, induced its translocation from cytoplasm to nucleus, enabled its higher binding affinity with DDX1 (DEAD box polypeptide 1) in nucleus further to alter the chromatin distribution of DDX1, resulting in multiple hematopoietic regulators expression change. Collectively, this study provided the first landscape of RNA editing in hematopoietic cascade and uncovered the mechanism of A-to-I editing of Azin1 in regulating HSPCs function.
2020-09-29 | GSE142216 | GEO
Project description:Effects of renal ischemia-reperfusion injury in Azin1 A-to-I locked and uneditable mice
| PRJNA1064974 | ENA
Project description:We report the discovery of a simple environmental sensing mechanism for biofilm formation in the bacterium Bacillus subtilis that operates without the involvement of a dedicated RNA or protein. Certain serine codons, the four UCN codons, in the gene for the biofilm repressor SinR caused a lowering of SinR levels under biofilm-inducing conditions. Synonymous substitutions of these UCN codons with AGC or AGU impaired biofilm formation and gene expression. Conversely, switching AGC or AGU to UCN codons upregulated biofilm formation. Genome-wide ribosome profiling showed that ribosomes paused longer at UCN codons than at AGC or AGU during biofilm formation. Serine starvation recapitulated the effect of biofilm-inducing conditions on ribosome pausing and SinR production. As serine is one of the first amino acids to be exhausted at the end of exponential phase growth, ribosome pausing at serine codons may be exploited by other microbes in adapting to stationary phase. 4 samples for ribosome profiling and 2 samples for total mRNA profiling
2013-10-22 | E-GEOD-50870 | biostudies-arrayexpress
Project description:We report the discovery of a simple environmental sensing mechanism for biofilm formation in the bacterium Bacillus subtilis that operates without the involvement of a dedicated RNA or protein. Certain serine codons, the four TCN codons, in the gene for the biofilm repressor SinR caused a lowering of SinR levels under biofilm-inducing conditions. Synonymous substitutions of these TCN codons with AGC or AGT impaired biofilm formation and gene expression. Conversely, switching AGC or AGT to TCN codons upregulated biofilm formation. Genome-wide ribosome profiling showed that ribosome density was higher at UCN codons than at AGC or AGU during biofilm formation. Serine starvation recapitulated the effect of biofilm-inducing conditions on ribosome occupancy and SinR production. As serine is one of the first amino acids to be exhausted at the end of exponential phase growth, reduced translation speed at serine codons may be exploited by other microbes in adapting to stationary phase.
2013-10-22 | GSE50870 | GEO
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Project description:bvgS phase-locked mutant derivatives of B. bronchiseptica RB50, B. pertussis GMT-1, and B. pertussis Tohama I were grown at 37 degrees C in the absence of modulator and harvested at mid-log phase. Comparison of gene expression profiles identified a set of genes in each strain that were regulated by BvgAS.
2006-03-31 | E-TABM-31 | biostudies-arrayexpress
Project description:Streptococcus pneumoniae (pneumococcus) is a leading human pathogen that can cause serious localized and invasive diseases. Pneumococci can undergo a spontaneous and reversible phase variation that is reflected in colony opacity, which allows the population to adapt to different host environments. Generally, transparent variants are adapted for nasopharyngeal colonization whereas opaque variants are associated with invasive disease. In recent work, colony phase variation was shown to occur by means of recombination events to generate multiple alleles of the hsdS targeting domain of a DNA methylase complex, which mediates epigenetic changes in gene expression. A panel of isogenic strains were created in the well-studied S. pneumoniae TIGR4 background that are “locked” in the transparent (n=4) or opaque (n=2) colony phenotype. The strains had significant differences in colony size which were stable over multiple passages in vitro and in vivo. While there were no significant differences in adherence for the phase-locked mutant strains to immortalized epithelial cells, biofilm formation and viability was reduced for opaque variants in static assays. Nasopharyngeal colonization was stable for all strains, but the mortality rate differed between them. Transcript profiling by RNA-seq analyses revealed that expression of certain virulence factors were increased in a phase-specific manner. As epigenetic regulation of phase variation (often referred to as phasevarion) is emerging as a common theme for mucosal pathogens, these studies serve as a model for future studies of host-pathogen interactions.
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