Bioinformatics of RNA Notes

RNA Bioinformatics

The RNA story differs from DNA. While RNA is linked to proteins due to encoding, protein-encoding RNAs make up only 5% of transcripts. Non-coding RNAs are more frequent.

  • Examples of RNA molecules that are transcribed but not translated:
    • tRNA
    • Ribosomal RNA
    • Small interfering RNA
    • MicroRNA
  • Ribosomal RNA and tRNA combined make up almost 85% of transcribed RNA.

Encoding Gene RNA

Protein-encoding gene RNA represents less than 5% of the total generated transcript. This small number is sufficient due to the ability of the same RNA copy to generate multiple peptides simultaneously via the ribosomal and translation machinery.

  • Roles of other RNA types:
    • Translation machinery: ribosomal RNA and tRNA.
    • Post-transcriptional gene regulation: microRNA and small interfering RNA.
    • Splicing: some RNAs are involved in RNA processing (splicing).
  • Eukaryotic genes consist of exons and introns.
  • Splicing is an important step in eukaryotic systems where intronic sequences are removed before translation.
  • RNA splicing is controlled by other transcribed but non-translated RNAs.

RNA and Level

The main objective is to elucidate methods for exploring RNA sequence, structure, and quantity. RNA quantity is perhaps the most crucial information. Identifying RNA sequence can be achieved through sequencing, even by sequencing the same region at the genomic level.

  • Gene expression is correlated with the level of transcription.
  • Gene expression happens when a gene is transcribed.
  • The level of transcription of a particular gene is correlated with the level of expression.
  • There isn't always a correlation between RNA expression and protein translation levels.
  • Increased RNA expression increases the likelihood of protein identification.

RNA to DNA

Non-coding RNAs are important for regulation and gene expression. The central dogma of molecular biology initially stated information flow was from DNA to protein, not protein to DNA. The flow from RNA to DNA was also considered impossible. The discovery of reverse transcriptase activity showed that some bacteria can move from RNA to DNA, converting RNA genomes into DNA (as seen in viruses).

  • Information transferred into proteins cannot move back out.
  • Crick's discussion on the central dogma:
    • Transfer of information from nucleic acids to nucleic acids or from nucleic acids to protein may be possible.
    • Transfer of information from protein to protein or protein to nucleic acid is impossible.
  • Crick and Watson discovered the double helix structure of DNA and the base pairing rules.

Isolate The RNA

RNA can be purified from DNA and proteins.

RNA and DNA

Key differences between RNA and DNA: RNA is single-stranded, while DNA is double-stranded (though single-stranded DNA is possible). RNA contains uracil in place of thymine.

Have Different Sugars

RNA and DNA have different sugars: at the two prime position of the sugar, DNA has a hydrogen atom, whereas RNA has a hydroxyl group. DNA is called deoxyribose because it lacks a hydroxyl group at the two prime position.

DNA and RNA

RNA can be isolated from DNA and proteins. DNA, especially in eukaryotes, is associated with proteins at the genomic level. Density gradient centrifugation and sedimentation coefficients were used to specify molecular weight. Svedberg units (S) are used to attribute size or molecular weight.

  • Examples:
    • 23S23S: large bacterial ribosomal subunit RNA.
    • 16S16S: small bacterial ribosomal subunit RNA.
  • 23S and 16S RNAs in ribosomes represent almost 85% of RNA.
  • tRNA and ribosomal RNA represent more than 90% of total RNA.
  • mRNA, corresponding to protein encoding genes, accounts for less than 5%.