Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA307274 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3067723.fastq.gz | Fastqsanger.gz | |||
| SRR3067724.fastq.gz | Fastqsanger.gz | |||
| SRR3067725.fastq.gz | Fastqsanger.gz | |||
| SRR3067726.fastq.gz | Fastqsanger.gz | |||
| SRR3067727.fastq.gz | Fastqsanger.gz |
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Project description:Transfer RNAs (tRNAs) carry abundant chemical modifications, and growing evidence shows dysregulation of chemical modifications on human tRNAs causes an expanding number of diseases including cancers, diabetes, neurological diseases, and mitochondrial disorders. Sensitive and robust detection and quantification of chemical modifications are critical to discovering functionally relevant and regulatory tRNA chemical modifications. Here we report a method “MapID-tRNA-seq” deploying a recently evolved processive reverse transcriptase to map modifications in human tRNAs and MapID-based data processing pipeline for de novo modification identification and tRNA expression quantification. MapIDs refer to consolidated sequences of human tRNA genes with reduced redundancy and annotations of genetic variation sites. MapID-based data processing largely improved the accuracy of modification detection and expression quantification by tRNA-seq, which otherwise got compromised from reads mis- and multi-alignment to the highly redundant human tRNA genome. “MapID-tRNA-seq” robustly detected the occurrence and stoichiometries of N1-methyladenosines, providing insights into the function and biosynthesis of N1-methyladenosine in human tRNAs. Our data revealed unique signatures of the evolved reverse transcriptase against N1-methyladenosine and four other types of chemical modifications. “MapID-tRNA-seq” provides a generalizable platform for de novo identification and quantitation of chemical modifications in human tRNAs to elucidate their functions in biology and diseases.
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Project description:Purpose: High-throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, such those derived from tRNAs. Also recent advances in high-throughput RNA sequencing has revealed the complex RNA modification landscape and the complex role these nucleosides modifactions have in cell signalling, stem cell biology, development and cancer. The goal of this study is to establish how m5C-tRNA methylation and tRNA-derived small RNAs can affect stem cell fucntion in cancer. Methods: four replicates of tRNAs and RNA buisulphite sequencing of wild-type (WT) and NSun2 -/- mouse skin squamous tumours were generated by deep sequencing, using Illumina HiSeq platform. Results: Our analyses reveal that inhibition of post-transcriptional cytosine-5 methylation locks stem cells in this distinct translational inhibition programme that results in tumour progression but that also sentizes cancer cells to genotoxic stress. Transfer RNA (tRNA) sequencing and RNA Bisulphite sequencing of wild-type (WT) and NSun2 -/- mouse skin squamous tumours
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