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Comparison of mitochondrial tRNA abundance profiling in wild type and mutant mitochondrial RNA polymerase overexpression flies.

ABSTRACT: Comparison of mitochondrial tRNA abundance profiling in wild type and mutant mitochondrial RNA polymerase overexpression flies.

PROVIDER: PRJNA689877 | ENA |

REPOSITORIES: ENA

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Comparison of mitochondrial tRNA abundance profiling in wild type and mutant mitochondrial RNA polymerase overexpression flies.

Project description:To investigate differential mitochondrial tRNA gene expression in wild type (WT) and mutant (E423P) mitochondrial RNA polymerase (POLRMT) overexpression flies, we performed Drsophila mitochondrial tRNA-seq according to the Hydro-tRNAseq method. tRNA-seq reads were subjected to 3' - adapter filtering , 3' - adapter trimming and quality control. The tRNAs expression levels were measured by tag count. For each tRNA sequence-based profile, the mapped reads number used to estimate the expression level of each tRNA. The tRNAs expression profiling was calculated based on uniquely mapped reads and including mapped reads, respectively. We found no difference in the relative abundance of mitochondrial individual tRNAs between WT and E423P overexpression flies.

2021-01-06 | GSE164324 | GEO

Comparison of mitochondrial transcription errors in wild type and mutant mitochondrial RNA polymerase overexpression flies

Project description:To determine the error rate of mitochondrial transcription, we ananlyzed 33 and 37 million reads respectively for wild type (WT) and mutant (E423P) mitochondrial RNA polymerase (POLRMT) overexpression flies and found that the error frequency of mitochondrial transcripts were over 5 fold higher in E423P flies than that of WT. To gain more insight into the molecular mechanisms that drive the error rate of transcription by POLRMT, we examined its distribution of errors along the mitochondrial genome. We also evaluated mitochondrial RNA processing by quantifying the frequency of a single read spanning two adjacent genes. There was no significant increase of unprocessed RNAs in E423P than that of WT. These observations concluded that overexpression of E423P POLRMT in adult flies leads to a statistically significant increase of mitochondrial transcripts errors.

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Comparison of mitochondrial unprocessed RNA frequency in wild type and mutant mitochondrial RNA polymerase overexpression flies.

Project description:The goal of this study is to compare the frequency of unprocessed preRNAs in mitochondria. Total mitochondrial RNA profiles of adult flies were generated in triplicates. We analyzed over 100 million reads for each group and used featureCounts to perform quantification allowing a read to be assigned to more than one gene. Using this analysis pipe line, we mapped about 30 million reads per sample to the Drosophila mitochondrial genome and identified a fequency of unprocessed preRNAs as 0.43% in PolrMT group, which is similar to that in PolrMT-E423P flies. These result revealed that overexpression of PolrMT-E423P does not contribute to pre-RNA processing.

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Comparison of mitochondrial transcription errors in wild type and mutant mitochondrial RNA polymerase overexpression flies

Project description:Comparison of mitochondrial transcription errors in wild type and mutant mitochondrial RNA polymerase overexpression flies

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Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments

Project description:The human genome encodes hundreds of tRNA genes but their individual contribution to the tRNA pool is not fully understood. Deep sequencing of tRNA transcripts (tRNA-Seq) can estimate tRNA abundance at single gene resolution, but tRNA structures and post-transcriptional modifications impair these analyses. Here we present a bioinformatics strategy to investigate differential tRNA gene expression and use it to compare tRNA-Seq datasets from cultured human cells and human brain. We find that sequencing caveats affect quantitation of only a subset of human tRNA genes. Unexpectedly, we detect several cases where the differences in tRNA expression among samples do not involve variations at the level of isoacceptor tRNA sets (tRNAs charged with the same amino acid but using different anticodons); but rather among tRNA genes within the same isodecoder set (tRNAs having the same anticodon sequence). Because isodecoder tRNAs are functionally equal in terms of genetic translation, their differential expression may be related to non-canonical tRNA functions. We show that several instances of differential tRNA gene expression result in changes in the abundance of tRNA-derived fragments (tRFs) but not of mature tRNAs. Examples of differentially expressed tRFs include: PIWI-associated RNAs, tRFs present in tissue samples but not in cells cultured in vitro, and somatic tissue-specific tRFs. Our data support that differential expression of tRNA genes regulate non-canonical tRNA functions performed by tRFs.

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Differential expression of human tRNA genes drives the abundance of tRNA-derived fragments

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Project description:Respiratory viruses such as SARS-CoV-2 are pathogens that can reach pandemic proportions. The early human response to respiratory viruses are in the nasal cavity and nasopharyngeal regions. Defining biomarkers of disease trajectory at the time of a positive test is important for opting for treatment and monitoring decisions. We hypothesize that the nasopharyngeal tRNA profiles can be used to predict symptom severity resulting from SARS-CoV-2 infection. We carried out multiplex small RNA sequencing (MSR-seq) on nasopharyngeal swaps to measure the human tRNA response to SARS-CoV-2 infection. Our result simultaneously measured full-length tRNA abundance, tRNA modifications, and tRNA fragmentation among individuals that went on to develop no/mild or severe symptoms. We identified distinct tRNA signatures that can predict the clinical outcome of SARS-CoV-2 infected individual at the time of a positive test. These results highlight the utility of using host tRNA properties as biomarkers for clinical applications.

2022-10-01 | GSE208612 | GEO

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