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Related Concept Videos

Experimental RNAi02:15

Experimental RNAi

RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
Ribosome Profiling02:24

Ribosome Profiling

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 helps...
RNA-seq03:21

RNA-seq

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 microarray-based...
RNA Interference01:23

RNA Interference

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.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
RNA Interference01:23

RNA Interference

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.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
siRNA - Small Interfering RNAs02:30

siRNA - Small Interfering RNAs

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 ATP-dependent...

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Related Experiment Video

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Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library
08:40

Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library

Published on: April 6, 2012

A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens.

Frederic D Sigoillot1, Susan Lyman, Jeremy F Huckins

  • 1Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.

Nature Methods
|February 21, 2012
PubMed
Summary

Off-target effects in RNA interference (RNAi) screens can be identified using a new bioinformatics method called genome-wide enrichment of seed sequence matches (GESS). This approach helps improve the accuracy and validation of RNAi screening results.

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Last Updated: May 24, 2026

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Published on: April 6, 2012

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay
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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Off-target effects complicate the interpretation and validation of RNA interference (RNAi) screening data.
  • Accurate identification of targeted transcripts is crucial for reliable experimental outcomes.

Purpose of the Study:

  • To develop a bioinformatics method for identifying candidate off-targeted transcripts in RNAi screening data.
  • To improve the validation rate of RNAi screens by addressing off-target effects.

Main Methods:

  • Development of a bioinformatics method named genome-wide enrichment of seed sequence matches (GESS).
  • Application of GESS analysis to primary RNAi screening data to detect off-targeted transcripts.
  • Specific analysis of MAD2 (MAD2L1) as a prominent off-targeted transcript in spindle assembly checkpoint screens.

Main Results:

  • The GESS method successfully identified candidate off-targeted transcripts in RNAi screening data.
  • MAD2 (MAD2L1) was identified as a significant off-targeted transcript across multiple screens, including those for spindle assembly checkpoint genes.
  • GESS analysis provides valuable insights into potential off-target activities.

Conclusions:

  • The genome-wide enrichment of seed sequence matches (GESS) method is effective in identifying off-targeted transcripts.
  • Implementing GESS analysis can enhance the validation rate and reliability of RNAi screens.
  • This bioinformatics approach aids in the precise interpretation of RNAi screening data.