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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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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Alternative RNA Splicing02:18

Alternative RNA Splicing

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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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Ribosome Profiling02:24

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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.
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Pre-mRNA Processing: Modification of pre-mRNA Ends01:35

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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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In-situ Hybridization02:31

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In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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Intron Retention as a Mode for RNA-Seq Data Analysis.

Jian-Tao Zheng1, Cui-Xiang Lin1, Zhao-Yu Fang2

  • 1Hunan Provincial Key Lab on Bioinformatics, Center for Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China.

Frontiers in Genetics
|August 1, 2020
PubMed
Summary
This summary is machine-generated.

Intron retention (IR), once overlooked, is now recognized for regulating gene expression and its links to diseases like Alzheimer's. This review covers IR functions, disease associations, and detection methods.

Keywords:
RNA-seqalternative splicingdisease associationgene regulationintron retention

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Intron retention (IR) is an alternative splicing event where introns remain in mature mRNA.
  • Historically dismissed as splicing errors, IR's regulatory roles are now gaining attention.
  • IR is increasingly linked to gene expression regulation and complex diseases.

Purpose of the Study:

  • To review the functional roles of intron retention in biological processes.
  • To summarize the association of intron retention with various diseases.
  • To describe current methods for detecting intron retention and discuss future challenges.

Main Methods:

  • Review of existing literature on intron retention.
  • Analysis of transcriptomic data applications.
  • Description of RNA-seq analysis tools like IRFinder and iREAD.

Main Results:

  • Intron retention plays roles in neuron differentiation and CD4+ T cell activation.
  • Associations between intron retention and diseases such as Alzheimer's disease and cancers are noted.
  • Current IR detection tools like IRFinder and iREAD have specific advantages and limitations.

Conclusions:

  • Intron retention is a significant regulatory mechanism in gene expression.
  • Further development of accurate IR detection methods is crucial for understanding its biological and pathological roles.
  • Improved IR detection will enhance transcriptomic data analysis and disease research.