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Related Concept Videos

RNA Splicing01:32

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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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RNA Editing02:23

RNA Editing

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Next-generation Sequencing03:00

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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
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RNA-seq03:21

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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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Exon Recombination02:32

Exon Recombination

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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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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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Alternative Splicing, RNA Editing, and the Current Limits of Next Generation Sequencing.

Manuela Piazzi1,2, Alberto Bavelloni3, Sara Salucci4

  • 1"Luigi Luca Cavalli-Sforza" Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 40136 Bologna, Italy.

Genes
|July 29, 2023
PubMed
Summary

Next-generation sequencing (NGS) revolutionized gene expression analysis but has limitations. Understanding RNA binding proteins and processing is crucial for accurate cancer research and effective therapeutic strategies.

Keywords:
RNA editingRNA-seqWGS/WESadenosine deaminationcancercytidine deaminationspliceosomesplicing factors

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Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology
  • Cancer Research

Background:

  • Next-generation sequencing (NGS) has transformed gene expression analysis in various diseases.
  • Global gene expression analysis aids in identifying novel pathways, therapeutic targets, and disease profiles.

Purpose of the Study:

  • To highlight limitations of current NGS technologies in cancer research.
  • To discuss the impact of RNA binding proteins and RNA processing on NGS data interpretation.
  • To emphasize how overlooking these limitations may hinder long-term therapeutic strategies.

Main Methods:

  • Perspective piece analyzing current NGS methodologies.
  • Discussion of data availability and deposition in public databases.
  • Focus on the role of RNA binding/modifying proteins and RNA processing.

Main Results:

  • Significant caveats exist in current NGS data analysis, preventing a complete understanding.
  • Incomplete or outdated public databases limit the utility of deposited scientific data.
  • RNA binding/modifying proteins and RNA processing introduce complexities not fully addressed by current NGS.

Conclusions:

  • Current NGS approaches may provide an incomplete picture of gene expression in cancer.
  • Limitations in data management and understanding RNA biology can negatively impact therapeutic development.
  • A deeper appreciation of RNA-related factors is essential for advancing cancer therapies using NGS.