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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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Before mRNAs are exported to the cytoplasm, it is crucial to check each mRNA for structural and functional integrity. Eukaryotic cells use several different mechanisms, collectively known as mRNA surveillance, to look for irregularities in mRNAs. Irregular or aberrant mRNA are rapidly degraded by various enzymes. If a defective mRNA escapes the surveillance, it would be translated into a protein which would either be non-functional or not function properly. One of the primary irregularities in...
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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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Predicting nonsense-mediated mRNA decay from splicing events in sepsis using RNA-sequencing data.

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Alternative splicing (AS) and nonsense-mediated mRNA decay (NMD) are key gene expression regulators. A new NMD pipeline reveals higher NMD rates in sepsis patients, indicating aberrant splicing linked to critical illness and mortality.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Computational Biology

Background:

  • Alternative splicing (AS) and nonsense-mediated mRNA decay (NMD) are crucial conserved mechanisms regulating gene expression.
  • Understanding the interplay between AS and NMD is vital for comprehending cellular responses to disease states.

Purpose of the Study:

  • To introduce and validate a novel computational pipeline (NMD pipeline) for analyzing AS events and predicting NMD rates.
  • To investigate the role of AS and NMD in sepsis using whole-blood RNA-sequencing data from critically ill patients.

Main Methods:

  • Development of the NMD pipeline based on AS data from Whippet.
  • Analysis of deep RNA-sequencing data from sepsis patients, control groups, and survival groups.
  • Statistical analysis for differential gene expression (adjusted P < 0.05, |log2 fold change| > 2) and AS (probability ≥0.9, |DeltaPsi| > 0.1).

Main Results:

  • The NMD pipeline demonstrated a higher rate of NMD in sepsis and deceased patient groups compared to control and survived groups.
  • Aberrant splicing, particularly a predominance of non-exon skipping events, was associated with disease severity and mortality in sepsis.
  • The pipeline identified proteins potentially associated with sepsis.

Conclusions:

  • The NMD pipeline is a valuable tool for studying AS-NMD interactions and differential gene expression.
  • Aberrant splicing and elevated NMD rates may be significant indicators of altered physiology in critical illness like sepsis.
  • This approach aids in uncovering disease-associated proteins and understanding disease mechanisms.