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Related Concept Videos

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.
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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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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. 
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Related Experiment Video

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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Transcribed-ultra conserved region expression profiling from low-input total RNA.

Paola Scaruffi1, Sara Stigliani, Simona Coco

  • 1Translational Paediatric Oncology, National Cancer Research Institute (IST), Largo R Benzi 10, Genoa, 16132, Italy. paola.scaruffi@istge.it

BMC Genomics
|March 5, 2010
PubMed
Summary

Researchers developed a new method using Ribo-SPIA amplification to accurately quantify Transcribed-Ultra Conserved Regions (T-UCRs) expression from small RNA samples. This technique enhances sensitivity and reliability for genome-wide noncoding gene profiling.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • Ultra Conserved Regions (UCRs) are noncoding genomic sequences.
  • Altered UCRs are observed in various cancers, suggesting a role in tumorigenesis.

Purpose of the Study:

  • To present a novel method for quantifying Transcribed-UCR (T-UCR) expression using minimal RNA quantities.
  • To assess the sensitivity, repeatability, and accuracy of this new quantification technique.

Main Methods:

  • Utilized Ribo-SPIA isothermal linear amplification for minute RNA quantities.
  • Employed quantitative PCR (qPCR) for T-UCR expression analysis.
  • Compared amplified and non-amplified cDNA in neuroblastoma cell lines.

Main Results:

  • Ribo-SPIA amplification increased sensitivity and repeatability in T-UCR quantification.
  • Analyzed all 481 T-UCRs using only 150 ng of RNA with minimal bias.
  • Relative expression magnitude was preserved, with high variability only in less abundant T-UCRs.

Conclusions:

  • The Ribo-SPIA-based quantification is an accurate and reliable technique for genome-wide noncoding gene profiling.
  • This method is crucial for transcription regulation studies using limited RNA from small samples.