How can there be so few functional genes?

Question 1

So few functional genes

Answer 1

How do we explain the fact that there are ~10,000 – 30,000 genes in vertebrate genomes (each ~1,000 bp or so, in a genome that may be 2 billion bp long – so 1.97 billion bp = not genes), and so much phenotypic diversity both within and among species?

Question 2

Simplest and rarest: one gene coding one phenotype

Answer 2

Famous example: sickle-cell anaemia. This is where a single-base mutation in the gene coding for hemoglobin changes the morphology of the red blood cells, and results in the disease.
Remember mendelian genetics can tell us if a trait is behaving as a single locus e.g. pea colour

Question 3

The molecular genetic cause of Mendels pea colour:
the colour gene sgr or ‘stay green’
(Armstead et al. 2007)

Answer 3

Staygreen inhibits the opening of the chlorophyll ring which results in chlorophyll breakdown

So in the wildtype in the dark the green fades but knocking out this gene slows the process

Domestication often provides useful information on the genetics of phenotypic traits

Question 4

Another example: the ‘mirror’ phenotype in the carp
(Rohner et al. 2009 Curr Biol 19, 1642–1647)

Answer 4

Known from breeding to be a single-locus effect, the details were found to entail mutations at fibroblast growth factor receptor 1 (fgfr1).

Exon 11 was truncated from 111bp to just 33bp in the mutant in addition to a point mutation

fgfr1 is an important developmental gene, but the loss of function is compensated for by a duplicate copy – a ‘paralog’ (present due to the whole genome duplication events in teleost fish

that led to modern fish see ‘genome evolution’ end)

this paralog is redundant in early development, but divergent function in the adult fish.

So fish develops normal physical form but lacks scales due to the mutation on the repeat

Question 5

Another example: Coat colour variation in old field mice (Hoekstra et al. (2007) PLoS Biol. 5(9): e219)

Answer 5

3 genes were identified that affected phenotypic colour – Agouti, Mc1r and Corin

Much of the variation in coat colour is explained by differences in two genes (Agouti & Mc1r):

Infact Mc1r affects coat colouration in many species

Question 6

Another example: test to see if flies learn which test tubes are electrified and then avoid them

Answer 6

Wild-type would learn which tubes were electrified and retain this knowledge for ~24hrs

Mutations in genes – especially in Dunce gene affected learning

Question 7

Pathways can be very complex

Answer 7

involving scores of loci, and a small change can affect many aspects of the process.

e.g. ‘knocking out’ the hypoxanthine-guanine phosphoribosyltransferase (HPRT) locus changes expression at a range of loci (Song & Friedman 2007 Mol. Ther. 15, 1432–1443). [left of blocks wildtype, right – HPRT deficient]

Question 8

The expression of a gene can be controlled

Answer 8

Either by determining the level of transcription
or just turning the gene on or off

– this is mediated by e.g. ‘transcription factors’ and the micro-RNA ‘switches’

Question 9

Example of gene expression control: Sticklebacks
(Jones et al 2012)

Answer 9

Stickleback adaptation to marine or freshwater environment is dominated by regulatory changes probably including micro-RNA switches

Question 10

Pleiotropy

Answer 10

Means one gene with many functions i.e. it codes for many traits e.g. EPO:
Erythropoietin is a cytokine (immune system gene) involved in inhibiting programmed cell death (apoptosis) but actually has multiple pleiotropic effects

Question 11

‘Quantitative Traits’ are ‘polygenic’

Answer 11

This means that multiple genes interact to generate the phenotype, and they can interact with each other in different ways:

Epistasis – the interaction between two or more genes to control a single phenotype (e.g. when the genotype at one locus masks the effects of genotype at another locus).

Additive – each relevant gene has an independent effect on the phenotype and work together

Question 12

Heritability

Answer 12

Phenotype (P) is determined by genotype (G) and Environment (E; especially developmental environment)

If we consider the variance of the distribution of values:

VP (phenotype) = VG (genotype) + VE (environment)

But ‘VG’ can be broken down into components of additive (A), dominance (D) and interaction (I) variance, so:

VP = VA + VD + VI + VE

(Where VD and VI are non-additive)

Question 13

Heritability can be quantified in two ways:
broad and narrow sense heritability

Answer 13

Broad sense heritability:

H = VG / VP

Or, because additive genetic variance explains much of the differences among phenotypic traits;

‘Narrow sense heritability’:

H squared = VA (additive) / VP (phenotypic)

Question 14

Example of attempt to assess heritability:

Galapagos ground finch (Geospiza fortis; Boag 1983 Evol. 37, 877-894

Answer 14

Weight is highly heritable whereas bill length appears to be more environmentally influenced

(on the graph the two lines show before/ after a selective event see paper)

Question 15

Summary so far

Answer 15

1)Most often genes function as part of a pathway or through interactions among genes (e.g. transcription factors, epistasis), meaning that traits tend to be polygenic.

2)Changes in the genes in a pathway can alter the outcome in a variety of ways, meaning that the same set of genes can lead to a diversity of functions.

3)Individual genes may affect multiple traits (pleiotropy), often as part of one or more complex pathways.

4)Not all aspects of a trait are predictable based on genotype, since environmental factors also influence the heritability of a trait.

Question 16

In one version of pleiotropy a given gene can function in very different ways in different contexts known as ‘gene sharing’ or ‘moonlighting’.

Answer 16

E.g. neuroleukin found to be the same as PGI protein and since many of these have been observed
see Copley 2012 bioessays
or Jeffreys 2003 ‘one yeast protein two functions’

Question 17

Alternative splicing events

Answer 17

create alternative mRNA isoforms
(see notes for diagram from Wang et al 2008)

Question 18

Homeobox genes – developmental control

Answer 18

Epistasis genes

Consistent shape (80bp of 60 aminos)

Involved in early stages of embryo growth

Term comes from ‘homeotic mutations’ involved in major transformations

Small mutations have large phenotypic impact

Question 19

Features of homeobox genes

Answer 19

involved in developmental control, but also an important group involved in the early stages of embryogenesis, and 100s have been described.

The term ‘homeobox’ comes from the homeotic mutations that cause major transformations (e.g. antennapedia – antp causing legs to grow from a fly’s head), but not all homeobox genes have as major an effect.

The homeodomain (protein encoded for by the homeobox gene) is usually a transcription factor, regulating the transcription of other genes (figure shows the interaction of antp with its DNA binding site).

HOX genes are a sub-group of the homeobox genes that play an important role in development along the anterior-posterior (head to tail) axis of the body. These genes are often clustered, and in four clusters in mammals.

Another example are the PAX genes, which play a critical role in the formation of tissues and organs during development.

Question 20

Homeobox genes: body plan gene similarity in drosophila, mice and human embryos

Answer 20

Hox genes found to be clustered together on the chromosome in the same sequence as the fly body segments, it was then found that the same sequence appears in a diversity of other organisms with the same essential function

Question 21

Explanation of these body plan gene similarities?

Answer 21

This conservation is likely due to the fact that these genes are very important and this process of the ordering of the embryo and the generation of the adult is also very important

Because of this it has been conserved over a very long period of time – pretty much throughout metazoan live

Question 22

Impact of a single gene mutation

Answer 22

e.g. one gene for the hedgehog locus (a ligand) is involved in segment formation in drosophila.

See illustration in notes that shows part of the process required to maintain segment boundaries in Drosophila.

This involves a pathway where hedgehog binds to the trans-membrane protein ‘patch’.

That allows the production of cubitus interruptus (Ci) from smoother (smo) which turns the relevant target genes on (see Ayers & Therond 2010, Trends in Cell biology, 20, 287-298).

NOTE: the hedgehog gene like others has multiple functions beyond those studied

Question 23

Summary

Answer 23

Single gene effects (where one gene product is solely responsible for the phenotype) are rare.

Gene products are more often part of a pathway, and changing that pathway can change phenotypes in a diversity of ways.

Proteins encoded by genes often interact with other proteins in the pathway through inhibition or promotion, and can interact with DNA to promote or inhibit transcription (epistasis).

One gene may impact multiple traits (pleiotropy), and phenotypic traits are typically polygenic.

The polygenec ‘quantitative’ traits can involve genes with independent ‘additive’ effects, or the interaction between genes (epistasis).

Only part of the phenotype is typically down to the genotype, with the rest subject to environmental factors (defining heritability).

A single gene may have multiple roles, sometimes quite different or even opposite, depending on location of expression and context.

Alternative splicing during transcription can also lead to multiple functions for a given gene.

A set of developmental control genes (e.g. HOX) have a large effect on the developmental process, and therefore on phenotype, and these are typically associated with control of transcription.

This complexity means that although there are few genes compared to the size of genomes, they determine a much greater range of phenotypes than would be possible if one gene had one function.