The Transcriptome

• the exons of most genes are separated by much-longer introns
• between our genes lie vast amounts of DNA much of which appears to regulate the expression of our genes but is not transcribed and translated into a protein product. [More]

So even when the complete sequence of a genome is known, it is often difficult to spot particular genes (open reading frames or ORFs).

One approach to solving the problem is to examine a transcriptome of the organism. Most commonly this is defined as: All the messenger RNA (mRNA) molecules transcribed from the genome.

(Speaking strictly, one would define the transcriptome as all the RNA molecules — which includes a wide variety of untranslated, nonprotein-encoding RNA [Link to examples] — transcribed from the DNA of the genome. It is now thought that 76% of our DNA is transcribed into RNA although only 1.5% of this is messenger RNA for protein synthesis.)

It is "a" transcriptome, not "the" transcriptome, because what genes are transcribed in a cell depends on

• the kind of cell (e.g., liver cell vs. lymphocyte)
• what the cell is doing at that time, e.g.,
  • getting ready to divide by mitosis;
  • responding to the arrival of a hormone or cytokine;
  • getting ready to secrete a protein product.

Expressed Sequence Tags (ESTs)

The Procedure:

• Isolate the messenger RNA (mRNA) from a particular tissue (e.g., liver)
• Treat it with reverse transcriptase. Reverse transcriptase is a DNA polymerase that uses RNA as its template. Thus it is able to make genetic information flow in the reverse (RNA ->DNA) of its normal direction (DNA -> RNA).
• This produces complementary DNA (cDNA). Note that cDNA differs from the normal gene in lacking the intron sequences.
• Sequence 200–500 nucleotides at both the 5′ and 3′ ends of each cDNA.
• Examine the database of the organism's genome to find a matching sequence.
• That is the gene that was expressed.