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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. 
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A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then...
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Metabolic Labeling of Newly Transcribed RNA for High Resolution Gene Expression Profiling of RNA Synthesis, Processing and Decay in Cell Culture
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Transcriptome profiling of expression changes during neuronal death by RNA-Seq.

Dharmendra Sharma1, Min Soo Kim2, Santosh R D'Mello3

  • 1Department of Biological Sciences, Southern Methodist University, Dallas, TX 75272, USA.

Experimental Biology and Medicine (Maywood, N.J.)
|September 27, 2014
PubMed
Summary
This summary is machine-generated.

This study used RNA-sequencing to comprehensively analyze gene expression changes in dying cerebellar granule neurons (CGNs). It identified thousands of altered genes, revealing new insights into neuronal death mechanisms relevant to neurodegenerative diseases.

Keywords:
Cerebellar granule neuronsRNA-sequencingapoptosispotassium withdrawal

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Area of Science:

  • Neuroscience
  • Molecular Biology
  • Genomics

Background:

  • Neuronal death mechanisms are not fully understood.
  • Cultured cerebellar granule neurons (CGNs) are a model for studying apoptosis.
  • Previous studies used DNA microarrays, which have limitations in detecting low-abundance transcripts.

Purpose of the Study:

  • To conduct a comprehensive gene expression analysis in CGNs undergoing apoptosis using RNA-sequencing.
  • To identify novel genes and pathways involved in neuronal death.
  • To provide a more sensitive and detailed understanding compared to microarray analysis.

Main Methods:

  • Utilized RNA-sequencing (RNA-seq) for global gene expression profiling.
  • Induced apoptosis in CGNs by switching from high potassium (HK) to low potassium (LK) medium.
  • Analyzed significant gene expression alterations, including up-regulation and down-regulation.

Main Results:

  • Observed significant alterations in 4334 genes (2199 up-regulated, 2135 down-regulated) in LK-treated CGNs.
  • Identified key affected functional categories: cell death/survival, growth/proliferation, molecular transport, and nervous system development/function.
  • Detected deregulation in pathways such as mitochondrial dysfunction and oxidative phosphorylation.

Conclusions:

  • RNA-seq provides a more sensitive and comprehensive view of gene expression during neuronal death than microarrays.
  • Identified numerous genes potentially mediating neuronal death, including those relevant to neurodegenerative diseases.
  • The findings offer new targets for understanding and potentially treating neurodegenerative disorders.