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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Ribosome Profiling02:24

Ribosome Profiling

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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.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Types of RNA01:23

Types of RNA

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Overview
Three main types of RNA are involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). These RNAs perform diverse functions and can be broadly classified as protein-coding or non-coding RNA. Non-coding RNAs play important roles in the regulation of gene expression in response to developmental and environmental changes. Non-coding RNAs in prokaryotes can be manipulated to develop more effective antibacterial drugs for human or animal use.
RNA...
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Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
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RNA Stability01:53

RNA Stability

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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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Translational Regulation01:29

Translational Regulation

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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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Related Experiment Video

Updated: Dec 4, 2025

Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA
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Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA

Published on: January 22, 2018

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Structured RNA Contaminants in Bacterial Ribo-Seq.

Brayon J Fremin1, Ami S Bhatt2,3

  • 1Department of Genetics, Stanford University, Stanford, California, USA.

Msphere
|October 22, 2020
PubMed
Summary
This summary is machine-generated.

Ribosome profiling (Ribo-Seq) data from bacteria often contain noncoding RNA (ncRNA) fragments. These fragments are protected by RNA structure, not ribosomes, offering insights into in vivo RNA secondary structures.

Keywords:
RNA structuremetagenomicsmetatranscriptomicsmicrobiome

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Ribosome profiling (Ribo-Seq) is a key technique for studying bacterial translation.
  • Ribo-Seq libraries frequently contain reads from noncoding RNAs (ncRNAs), which are not expected to be translated.
  • These ncRNA fragments persist through Ribo-Seq library preparation, including nuclease digestion and size selection.

Purpose of the Study:

  • To investigate the origin and nature of noncoding RNA (ncRNA) fragments in bacterial Ribosome Profiling (Ribo-Seq) data.
  • To determine whether RNA structure or ribosome binding explains the presence of these ncRNA fragments.
  • To explore the potential of using these 'contaminant' reads for inferring in vivo RNA secondary structures.

Main Methods:

  • Analysis of Ribosome Profiling (Ribo-Seq) data from bacterial experiments, focusing on reads mapping to noncoding RNAs (ncRNAs).
  • Bioinformatic analyses to correlate ncRNA fragment distribution with predicted RNA secondary structures.
  • Examination of ncRNA fragment survival through micrococcal nuclease (MNase) treatment and size selection steps.

Main Results:

  • A significant overlap was observed between ncRNA fragments in Ribo-Seq data and predicted structured regions of ncRNAs.
  • Evidence suggests that RNA secondary structures, rather than ribosome occupancy, protect ncRNAs from degradation during Ribo-Seq library preparation.
  • These ncRNA fragments are resistant to micrococcal nuclease (MNase) digestion, indicating structural protection.

Conclusions:

  • Caution is advised when interpreting Ribo-Seq signal as indicative of translation, as ncRNA fragments can be misinterpreted.
  • ncRNA fragments in Ribo-Seq data can serve as a valuable resource for inferring in vivo RNA secondary structures.
  • Reanalysis of existing Ribo-Seq data holds potential for large-scale elucidation of RNA structure-function relationships in bacteria.