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3 Information: genes and genomes

Table 3.2 The sizes of a sample of genomes from a range of prokaryotic and eukaryotic species

Organism

Genome size (haploid* genome) in base pairs

Estimated number of protein-coding genes

Number of chromosomes

0.58 × 10 6

Mycoplasma genitalium (smallest known cellular genome)

Prokaryotes

470

1

4.6 × 10 6 12.0 × 10 6

Escherichia coli

4300 6600

1

Saccharomyces cerevisiae (‘baker’s’ yeast, a single-celled eukaryote) Caenorhabditis elegans (a nematode worm with about 1000 cells) Arabidopsis thaliana (a cress plant often used as a model organism by plant geneticists as it has one of the smallest genomes known in the plant kingdom) Drosophila melanogaster (fruit fly)

Eukaryotes

16

100 × 10 6

20,000

6 pairs

140 × 10 6 140 × 10 6

14,000 27,000

4 pairs 5 pairs

3.2 × 10 9 150 × 10 9

Homo sapiens

21,000

23 pairs 20 pairs

Paris japonica (a herb plant, which has the largest known genome)

Unknown

* The cells of most eukaryotic organisms are diploid (see Chapter 4). That is, they contain two copies of the genome. The size of a single copy of the genome is given in the table.

Percentage 0 10

20 30

40

50

60

70

80

90 100

LINEs

SINEs

Introns

Retrotransposons

Protein-coding exons

DNA-only transposons

Genes

Transposon-derived

Non-repetitive DNA that is in neither introns nor exons

Simple repeats Segment duplications

Repeated sequences

Unique sequences

Figure 3.11 Composition of the human genome. Half of the genome is made up of repetitive sequences, many of which derive from transposable elements or transposons. The main classes of transposons (LINEs, SINEs, other retrotransposons, and DNA-only transposons) are described in the text. Non-transposon repeats include simple repeats, also described in the text, and segment duplications, which are large blocks of sequence (1000–200,000 base pairs) that are found at two or more places in the genome. The non-repetitive unique sequences that are not introns or exons include genes that encode functional RNAs (such as tRNA and rRNA) and regulatory sequences, as well as sequences with no known function. Source : Matylla-Kulinska, K., Tafer, H., Weiss, A. and Schroeder, R. (2014) Functional repeat-derived RNAs often originate from retrotransposon-propagated ncRNAs. WIREs RNA , 5: 591–600. https://doi.org/10.1002/wrna.1243

Some retrotransposons within the human genome have sequence similarities to retroviruses , but retrotransposons can only repro duce their DNA and move around within the genome of the cell, they cannot become fully infectious viral particles. Reproduction and movement of transposable elements have played a major role in the evolution of the human genome, but most of the transposons in our present-day genome have under gone mutations that mean they are no longer mobile. The small proportion that can still move around contribute to human genome variation and occasionally cause disease by ‘jumping’ into the mid dle of protein-coding genes or into gene regulatory sequences.

that can (or could in the past) move from one part of the chro mosome to another. These transposable elements, or transposons , popularly known as ‘jumping genes’, are classified according to the mechanism by which they move around. DNA transposons are those in which the sequence is cut out of the chromosome and inserted in a new position. This type of transposon is also found in bacterial genomes. Retrotransposons are found only in eukary otes. They are not cut out of the DNA, but instead replicate by being transcribed into RNA copies, which are then copied back into DNA by a retrotransposon encoded enzyme, reverse transcriptase . The DNA copies insert themselves into new positions in the genome.

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