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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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Methods to Study Long Noncoding RNA Expression and Dynamics in Zebrafish Using RNA Sequencing.

Samatha Mathew1,2, Ambily Sivadas2,3, Paras Sehgal1,2

  • 1Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India.

Methods in Molecular Biology (Clifton, N.J.)
|January 13, 2019
PubMed
Summary
This summary is machine-generated.

Researchers discovered novel long noncoding RNAs (lncRNAs) in zebrafish using advanced RNA sequencing and computational analysis. This study details methods for identifying and validating these crucial gene-regulating molecules in a key model organism.

Keywords:
Long noncoding RNANoncoding RNARNA sequencingTranscriptomeZebrafish

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Area of Science:

  • Genomics
  • Molecular Biology
  • Developmental Biology

Background:

  • Long noncoding RNAs (lncRNAs) are RNA transcripts that do not code for proteins.
  • Next-generation sequencing (NGS) has enabled comprehensive genome-scale annotation of transcripts.
  • LncRNAs play roles in epigenetic, transcriptional, and posttranscriptional gene regulation.

Purpose of the Study:

  • To describe experimental methods for discovering lncRNAs in zebrafish (Danio rerio).
  • To present a computational analysis pipeline for identifying novel lncRNA transcripts.
  • To detail validation assays for putative novel lncRNA transcripts.

Main Methods:

  • RNA sequencing of zebrafish transcriptome.
  • Development and application of a computational analysis pipeline for lncRNA discovery.
  • Qualitative and quantitative assays for lncRNA validation.

Main Results:

  • Identification of novel lncRNA transcripts in zebrafish.
  • Establishment of a robust computational pipeline for lncRNA identification.
  • Validation of newly discovered lncRNAs in the model organism.

Conclusions:

  • The study provides a framework for lncRNA discovery in zebrafish.
  • The described methods facilitate the identification and validation of novel lncRNAs.
  • This research contributes to understanding the functional roles of lncRNAs in gene regulation.