Bioinformatics Definitions
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4 months ago
joe_genome ▴ 10

Hello,

I'm starting to switch to the field of genetics and have the need for some clarification on some definitions that come up constantly. I have googled of course but I get different interpretations, with this what would the difference between the following be concluded as:

  1. Genome
  2. Transcriptome
  3. Transcript
  4. Exome
  5. DNA Methylation

Sorry for the very naive question but would rather a direct answer be fulfuilled.

genome • 373 views
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Have you read the wikipedia articles on these or checked any text book? Either of those will give you correct definitions.

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I think maybe my largest confusion is if the transcript and transcriptome are ultimately referring to the same thing?

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Transcriptome is the collection of all transcripts from genes in a genome.

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More in general, the 'ome' of something is the collection of all smaller parts:

protein -> proteome
exon -> exome

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An over-simplified overview:

The genome is the polymeric molecule(s) made of deoxyribonucleic acid (DNA) which is used as the template for the process of transcription. Those portions of the genome from which a corresponding ribonucleic acid (RNA) molecule can be transcribed that--when translated--produces a protein molecule would correspond to "genes". Thus the genome can be considered a "collection" of genes.

The aforementioned RNAs are "transcripts" (products of transcription), and the collection of all transcripts produced from the genome at any given time represents the transcriptome (at that point in time). The transcripts are linear sequences (in that the molecule is a polymer comprised of a "chain" of monomers) that can be parsed by the ribosomes to manufacture proteins.

However, not all parts of the raw transcript produced by transcription can be "read": those that can be read by the ribosome are the exons, and those that cannot be are the introns. As such, the introns are excised out of the transcripts before they arrive at the ribosomes, making the transcript a collection of exons only (more or less). These exons also correspond to specific portions of the genome (by virtue of having been derived from them). The exome would thus be the set of all "exonic" regions in the genome.

As for DNA methylation, it is the process of adding methyl groups to DNA nucleotides. It can happen naturally (e.g., because of epigenetic mechanisms) or artificially (e.g., humans wish to experiment with the genome).

(Others please correct me wherever I am wrong.)

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