Biology Reference
In-Depth Information
BOX 4.3 Model Organisms Commonly used in Studies of GRNs
Escherichia coli:
Advantages:
l
Disadvantages:
l
Large genome (~23 300 protein-coding genes, including
somewhere between ~420 and ~620 predicted sequence-
specific TFs; ~814 Mb
[169]
; ~93% non-coding; ~30 kb
average intergenic distance)
Small, compact genome (K-12 strain
[162]
: 4288 protein-
coding genes, including ~270 sequence-specific TFs [163];
4.6 Mb; 11.2% non-coding)
l
Short generation time (~20 min doubling time in optimal
conditions)
l
Relative ease of gene targeting and site-directedmutagenesis
Disadvantages:
l
Slow generation time (~1 year) impedes genetic studies and
development of transgenic lines
l
More cumbersome gene targeting and site-directed muta-
genesis (less efficient homologous recombination)
l
Unicellular
Mouse:
Advantages:
l
Mammal; major non-primate model organism for human
l
Many available inbred strains that have been bred selec-
tively to carry human disease traits or other phenotypes of
biomedical importance
l
RNAi knockdown of gene expression
Disadvantages:
l
Saccharomyces cerevisiae (budding yeast):
Advantages:
l
Small, compact genome (S288C strain: 5885 protein-coding
genes
[164]
, including ~200 sequence-specific TFs
[12]
;
12 Mb; ~30% non-coding)
Short generation time (~90 min doubling time in optimal
conditions)
l
Facile gene targeting and site-directed mutagenesis (highly
efficient homologous recombination)
Disadvantages:
Large genome (~22 000 protein-coding genes
[170]
,
including ~1600 sequence-specific TFs
[171]
; ~2.5 Gb
euchromatic portion of the genome; ~97.9% non-coding)
l
Unicellular, although there are different cell types accord-
ing to mating type (a, alpha) and growth form (filamentous,
non-filamentous)
Slow generation time (~12 weeks)
l
l
More cumbersome gene targeting and site-directed muta-
genesis (less efficient homologous recombination)
l
Caenorhabditis elegans (nematode worm):
Advantages:
l
Human cell lines:
Advantages:
l
Moderate-sized genome (~20 000 protein-coding genes
[165]
, including ~940 sequence-specific TFs
[107,157]
;97
Mb; ~73% non-coding)
Relative ease of growth in lab conditions depending on cell
type
l
RNAi knockdown of gene expression
Disadvantages:
l
Large genome (~22 300 protein-coding genes
[172,173]
,
including ~1400 sequence-specific TFs
[11,26]
; ~3.08 Gb, of
which ~2.88 Gb is euchromatin (2.85 Gb of which is in the
sequenced portion of the genome); ~98.1% non-coding)
l
Transformed or otherwise immortalized cell lines are
'cancer-like' and not truly representative of the primary cells
from which they have been derived
l
More cumbersome gene targeting and site-directed muta-
genesis (less efficient homologous recombination)
Arabidopsis thaliana (thale cress):
Advantages:
l
Relatively short generation time (3 days
in optimal
l
conditions)
RNAi knockdown of gene expression
l
Moderate efficiency in genomic incorporation of
trans-
l
formed DNA
Disadvantages:
l
More cumbersome gene targeting and site-directed muta-
genesis (no homologous recombination)
Drosophila melanogaster (fruit fly):
Advantages:
l
Moderate-sized genome (~13 600 protein-coding genes
[166]
, including ~750 sequence-specific TFs
[167]
; ~180
Mb, of which 120 Mb is euchromatin; ~80% non-coding)
Small genome (diploid) relative to other plants, many of
which are polyploid (~25500 protein-coding genes,
including ~1700 sequence-specific TFs; ~125 Mb, of which
~115 Mb is sequenced; ~70% non-coding
[174]
)
Relatively short generation time (9 days
in optimal
l
conditions)
RNAi knockdown of gene expression
Disadvantages:
l
l
Relatively short generation time (~6 weeks in optimal
conditions)
l
More cumbersome gene targeting and site-directed muta-
genesis (inefficient homologous recombination)
Many inbred strains have been bred selectively to carry
specific traits
Disadvantages:
l
l
Strongylocentrotus purpuratus (sea urchin):
Advantages:
l
More cumbersome gene targeting and site-directed muta-
genesis (plants preferentially utilize non-homologous end-
joining instead of homologous recombination in DNA end
repair)
Highly efficient (although random) genomic incorporation
of DNA injected into eggs
Morpholino knockdown of transcripts
[168]
l
