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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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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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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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Eukaryotic RNA Polymerases

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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
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RNA Structure

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The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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Transcriptome Studies in Trypanosoma cruzi Using RNA-seq.

Gonzalo Greif1, Luisa Berná1, Florencia Díaz-Viraqué1

  • 1Laboratory of Host Pathogen Interactions-UBM, Institut Pasteur de Montevideo, Montevideo, Uruguay.

Methods in Molecular Biology (Clifton, N.J.)
|March 15, 2019
PubMed
Summary
This summary is machine-generated.

This chapter details RNA sequencing (RNA-seq) protocols for Trypanosoma cruzi, enabling the study of gene regulation and RNA stability. It also presents a bioinformatic pipeline for analyzing RNA-seq data, including differential gene expression.

Keywords:
Bioinformatic pipelineDifferential expressionGene expressionRNA-seqTrypanosoma cruzi

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • RNA sequencing (RNA-seq) is a key technology for transcriptome analysis.
  • Understanding gene regulation and RNA stability is crucial in various biological contexts.
  • Trypanosoma cruzi presents unique challenges for molecular studies.

Purpose of the Study:

  • To describe robust RNA sequencing library preparation protocols for Trypanosoma cruzi.
  • To present a comprehensive bioinformatic analysis pipeline for RNA-seq data.
  • To facilitate the study of gene expression and regulation in Trypanosoma cruzi.

Main Methods:

  • Development of directional and nondirectional RNA-seq library preparation methods.
  • Implementation of a bioinformatic pipeline involving read trimming and alignment to the Trypanosoma cruzi reference genome.
  • Application of differential gene expression analysis.

Main Results:

  • Established and validated protocols for RNA-seq library preparation in Trypanosoma cruzi.
  • A functional bioinformatic pipeline for processing and analyzing RNA-seq data from Trypanosoma cruzi.
  • The methodology allows for detailed investigation of transcriptome dynamics.

Conclusions:

  • The described RNA-seq protocols and bioinformatic pipeline are effective for studying gene regulation in Trypanosoma cruzi.
  • This work provides a valuable resource for researchers investigating the biology of Trypanosoma cruzi.
  • The methodology supports in-depth transcriptome analysis, including differential expression studies.