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Related Concept Videos

Transfer RNA Synthesis02:36

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One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
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Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
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An In Vitro Assay to Detect tRNA-Isopentenyl Transferase Activity
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tModBase: deciphering the landscape of tRNA modifications and their dynamic changes from epitranscriptome data.

Hao-Tian Lei1, Zhang-Hao Wang2, Bin Li1

  • 1MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P.R. China.

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tModBase is a new database for analyzing tRNA modifications, crucial for cellular processes and diseases. It reveals how these modifications change across tissues and in cancer, linking them to enzymes and genetic variations.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Transfer RNA (tRNA) molecules possess abundant modifications impacting their structure, stability, and function.
  • These tRNA modifications are influenced by environmental factors and are implicated in various physiological and pathological conditions.
  • Existing resources for analyzing dynamic tRNA modification profiles are limited.

Purpose of the Study:

  • To establish tModBase, a comprehensive database for exploring tRNA modification landscapes using epitranscriptome data.
  • To analyze tRNA modification profiles across species, tissues, and in relation to human diseases.
  • To develop tools for investigating the interplay between tRNA modifications, RNA modification enzymes, tsRNA expression, and DNA variations.

Main Methods:

  • Utilized 103 datasets from second- and third-generation sequencing technologies.
  • Analyzed tRNA modification profiles across ten species, including misincorporation and termination signals.
  • Integrated transcriptome data from 32 cancer types and genetic variation data.

Main Results:

  • Systematically demonstrated tRNA modification profiles across diverse tissues and cell lines.
  • Summarized characteristics of tRNA modifications associated with human diseases.
  • Developed novel analytical tools to explore relationships between tRNA modifications, enzymes, tsRNA expression, and DNA variations.

Conclusions:

  • tModBase provides a valuable resource for deciphering tRNA modification profiles and their biological significance.
  • The database offers new insights into the features of tRNA modifications and their roles in biological pathways.
  • Findings highlight the dynamic nature of tRNA modifications and their relevance in health and disease.