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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.
The technique...
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RNA Interference01:23

RNA Interference

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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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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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siRNA - Small Interfering RNAs02:30

siRNA - Small Interfering RNAs

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Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the...
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piRNA - Piwi-interacting RNAs02:57

piRNA - Piwi-interacting RNAs

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PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...
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A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
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Mining diverse small RNA species in the deep transcriptome.

Kasey C Vickers1, Leslie A Roteta1, Holli Hucheson-Dilks2

  • 1Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.

Trends in Biochemical Sciences
|December 2, 2014
PubMed
Summary

High-throughput sequencing reveals diverse small RNAs (sRNA). Analyzing all sRNA types, not just microRNAs, is crucial for discovering their biological functions and physiological relevance.

Keywords:
RNA sequencingdata analysishigh-throughput sequencinglong-noncoding RNAmicroRNAsmall RNAtranscriptome

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transcriptomes exhibit remarkable diversity across species.
  • High-throughput sequencing is increasingly used to analyze non-protein-coding RNAs, specifically small RNAs (sRNA).
  • Current sRNA sequencing studies often focus narrowly on microRNAs, neglecting other sRNA species.

Purpose of the Study:

  • To advocate for the comprehensive analysis of all sRNA species in sequencing datasets.
  • To highlight the potential for discovering novel biological functions and physiological relevance of understudied sRNAs.
  • To encourage a broader approach in sRNA research.

Main Methods:

  • Utilizing high-throughput sequencing data.
  • Quantifying diverse small RNA species.
  • Bioinformatic analysis of transcriptomic data.

Main Results:

  • Existing datasets contain a wealth of unanalyzed sRNA species.
  • Focusing solely on microRNAs limits the scope of discovery.
  • A comprehensive approach is feasible with current technologies.

Conclusions:

  • Analyzing the full spectrum of small RNAs is essential for a complete understanding of their roles.
  • Expanding analytical scope in sRNA sequencing will accelerate the discovery of biological functions.
  • This approach enhances the physiological relevance derived from transcriptomic studies.