Week 8: Evolution of Gene Regulation + Chromosome Evolution

How to measure changes in gene regulation?

Use RNA sequencing

1. Isolate mRNA from tissue of interest

2. Sequence all mRNA in a sample

3. Count number of sequences mapping to each gene =expression level

Interpreting gene expression data

• Data is displayed in a grid where each row represents a gene and each column represents a sample taken from a different tissue, stage, species or environmental condition

• Red represents up-regulated genes and green represents down-regulated genes. Black represents unchanged expression.

• The heatmap may also be combined with clustering methods which group genes together based on the similarity of their gene expression pattern.

Highly conserved gene regulation

specific sequences + regulatory mechanisms involved in controlling gene expression remain relatively unchanged across different species/ within a single organism over evolutionary time

What can gene regulation allow organisms to do?

• Respond to changing environments

• Links to phenotypic plasticity

Example: Killifish gene expression responds to ecological variation

Gene regulation and adaptive evolution

• Beak size in Darwin’s Finches varies among species and is key to ecological niches.

• Crushing beaks → wider/ larger than probing beaks

• Whitehead et al. 2011 PNAS

• Experiment looked at differences in expression in stages of beak development + compared crushing + probing beak

• How can beak shape vary so much in species with very little genetic difference?

• Bmp4 expressed in crushing beak early

Is all gene expression adaptive?

• No

• Across 5,636 genes divergence from human is roughly clock-like (testis genes are an exception) →Suggests most change in gene expression due to drift

• Genes not under selection → change at same rate

• Brawand et al. 2011

Signatures of lineage-specific adaptive change

• Romero et al. 2012 Nature Reviews Genetics

• Studies use RNAseq to compare the expression of orthologous genes in different groups of mammals RNA can be extracted from various tissues  (e.g prefrontal cortex  cerebellum, heart liver and testes) and relative expression levels measured.

Human-specific adaptive expression shifts

• Modules with specific expression states in human brain (prefrontal cortex; 259 genes) and primate cerebellum (189 genes) are shown.

• Bars represent the weighted average expression of all genes in a module, for each sample (horizontal grey line indicates average bar height).

• Samples above the red line are considered to have a distinct expression state.

• The large number of gene ontology categories related to neural ensheathment etc probably reflects the larger proportion of myelinated axons (white matter) in the human prefrontal cortex than in that of other primates

• Pre-Frontal cortex important for primates

• Brawand et al. 2011 Nature

• graph = number of gene pathways/ modules with lineage-specific adaptive shifts

Human-specific adaptive expression shifts at cellular resolution (more recent study)

Caglayan et al. (2023) Nature

• Comparative studies of whole brain region expression have identified genes/pathways that affect synaptogneisis and myelination

• Brodmann area 23 is part of the posterior cingulate cortex, involved in higher-order cognitive processes such as theory of mind. Single cell RNAseq analysis comparing cells from this region in Humans, Chimpanzees and Macaques carried out

• Results suggest that an evolutionary modification in human brain may have been achieved through loss-of-expression mutations of genes (e.g. SH3RF3) expressed in oligodendrocyte progenitors that delay their maturation and prolong brain plasticity

Most supported theory of sex chromosome evolution

1. Many genes under “sex-antagonistic selection.” Different alleles are favoured in females and males.

2. Genetic factors controlling the male coloration traits in guppies are concentrated on the male-determining factor carrying chromosome

   e.g males → colourful → conspicuous to predators but more conspicuous to mates → outweighs negative

   females → does not outweigh

3. Selection favours decreased recombination between genes under sex-antagonistic selection and the locus that determines sex where this keeps male-favouring alleles in cis with the male-determining factor (and vice versa for females)

   Inversion mutation → suppress recombination

   ^ long term deleterious side effects

   Invert region around sex determining factor → colouring genes can’t recombine onto female chromosome

What leads to Y chromosome decay?

Reduced recombination between proto-X and Y

Muller’s Ratchet

Genetic Hitchhiking

Sex chromosome evolution

Major and minor sex chromosome pairs start as homologous autosomes

1. Origin of new sex determining gene on one chromosome

2. When near a sexually antagonistic locus selection for inversions which prevents recombination

3. Without recombination, minor orthologs loses non-essential genes

4. New regions of the Y brought in proximity to sex determining gene

5. Repeat across length of chromosomes

   

Exceptions to the classical model of sex chromosome evolution

• Reduction of Y chromosome true in mammals → species of shrew → lost Y chromosome but produces males through different form of sex determination

• In many non-model organisms new methods for detecting sex-linked sequences indicate that ancestral sex chromosomes have reverted to autosomes, and been replaced by a new set of sex-determining chromosomes (sex-chromosome turnover)

• Clades where recurrent non-homologous sex-chromosome turnover has been detected

  • African cichlids

  • True frogs

  • Flies

  • Medaka fishes

  • African clawed frogs

Modelling sex-chromosome turnover and conservation

Why is male: female X chromosome dosage compensation needed?

• Sex chromosome divergence means X chromosome copy number is different in males and females

• Copy number correlates to transcription and translation rate

• Loss of Y genes leaves males with just one functional X chromosome = ½ original gene dose

• Level of gene expression = function of the number of copies of genes

  Y chromosome shrinking → males have 1 copy → half the dose

• Potentially large phenotypic consequences to the heterogametic sex

How are sex chromosomes regulated?

• Dosage Compensation

  • Hyper-transcription of male X

  • Hypo-transcription of both X’s in females

  • X chromosome inactivation in females

Dosage compensation in Drosophila

Lucches and Kuroda (2015) CSH Perspect. Biol.

Hyper-transcription of male X

• Xmale= Xfemale

• Xmale=Automale

• MSL complex binds to regions containing transcriptionally active promoter and chromatin modifications (marks) mediate increased transcription at those promoters

• How is MSL binding/activity targeted to a single chromosome? Involves roX non-coding RNAs and in-cis spreading from specific initiation sites

Sex determination in Drosophila

• different mechanism for sex determination

• females = XX

• males = X + tiny Y with hardly any genes

Dosage Compensation in C. elegans

Lau & Csankovszki (2015). Curr. Opin. Genet. Dev

2,801 genes on X

20,176 genes total

= 14% of functional genome

no Y chromosome

Hyper-transcription of X in males & hermaphrodites by unknown mechanism

• Xmale=Automale

• Xmale= ½ Xherm

• Xherm=2Autoherm

DCC mediated hypo-transcription  of X  in hermaphrodites

• Xfemale=Autoherm

• Xmale=Xherm

Upregulates males + hermaphrodites

Down regulate females

Ohno’s Hypothesis (1967)

X or Z linked genes will be expressed at twice the level of autosomes per active domain in the heterogametic sex

Wright and Mank PNAS 2012

How are mammalian sex chromosomes regulated?

• Therian (non-egg laying) mammals

• X chromosome inactivation in females

  • X_male=X_female

  • X_male= ? Auto_male

  • X_female= ? Auto_female

When did X-inactivation evolve?

Reviewed in Graves 2016

Incomplete/gene by gene dosage compensation

• Studies across a broader range of taxa suggest that complete dosage compensation is the exception rather than the rule (monotreme mammals, birds, snakes, frogs, fish and plants).

• Not all sex-linked genes are similarly sensitive to dose. Lowly expressed genes less sensitive, retained orthologues more sensitive

• Complete dosage compensation more common in XY systems.

Telomeres

• Repetitive nucleotide sequence at ends of chromosomes

• A and T rich

• Shorten at each cell division

• Length inversely correlated with ageing

• Protect genes near the ends of chromosomes from deterioration

What are germline cells protected from?

shortening by enzyme telomerase

Centromeres

• No defined sequence

• Role is to link sister chromatids (chromosome arms) in cell division

• Attach to spindle fibres during meiosis

• Role in enabling disjunction - chromosome segregation - when cell divides to generate normal chromosomal complement

General rule of gene action + chromosome location

• In multicellular organisms, evolution + gene action are independent of chromosome location

Exception to general rule of gene action + chromosome location: Position Effects in Hox Genes

• HOX genes in plants and animals affect patterning of early embryos.

• Mutations in HOX genes cause   transformation of one body part   into another.

• HOX genes are clustered together.

• Remarkably, their sequence along the chromosome corresponds to the order of segments in the body that they control.

• Given the complexity of the interdependent developmental processes that they control, their co-location enables efficient regulation.

Exception to general rule of gene action + chromosome location: Tight Linkage

• Selective forces acting on one gene can affect neighbours.

• Consider nucleotide diversity within a region of sequence.

• Plotted against distance to important site known to be under strong selective pressure. 

• At that site, diversity drops because one favoured variant is selected. Also, the

• “well of diversity” effect extends to closely linked loci.

Chromosomes as units of evolution

• Can act as genetic elements

• Selection on a chromosome acts on 100s - 1000s of genes at a time

• •The evolutionary effect on whole chromosomes depends on chromosome size – larger chromosomes typically (though not always) carry more genes.

Example of larger chromosomes carrying more genes

Drosophila melanogaster

Karyotype

• Chromosomal genotypes

• Karyotype also means the numbers of chromosomes in a haploid (1n) or diploid (2n) cell

• Karyotype + chromosome number vary across species

Chromosome Mutations

Polyploidy – multiplication of the entire karyotype (e.g from 2n to 4n)

• Autopolyploidy

• Allopolyploidy

Chromosomal rearrangements

• Translocation

• Fusions

• Fission

• Inversions

Polyploidy

• doubling of chromosome number

• known as Paleopolyploidy in eukaryotes

• Common in plants, less so in animals, some cases in fish + amphibians + also in fungi

What is polyploidy caused by?

• nondisjunction during meiosis

  • a pair of homologous chromosomes has failed to separate or segregate at anaphase so that both chromosomes of the pair pass to the same daughter cell

• autopolyploidy = both sets of chromosomes from a single specie s

Why are autopolyploids selected for in domesticated plants?

• produce more protein per cell due to doubled dose of genes

• Examples of domesticated autopolyploids

  • potato

  • banana

  • coffee

  • peanut

Why are polyploids reproductively isolated from parental diploid species?

• due to the formation of triploids

• unable to produce balanced gametes = sterile

• speciation

Example: triploid sterile rainbow trout

• Many fishery-raised fish populations are triploid (easy to generate: apply pressure  to eggs, induces non-disjunction & bigger).

• Allows for stocking for sport fishing, but prevents released fish from breeding with local populations and introducing non-native genetic diversity.

Allopolyploidy

• two sets of chromosomes

• each from a different parent species

• result of hybridisation + nondisjunction

• can make viable gametes

Allopolyploidy formation in Wheat, Triticum aestivum

• Wheat = allohexaploid (2N chromosomes from each of 3 species) produced from two separate hybridisation events.

• Each hybridisation was followed by chromosome doubling in the new hybrid; this enabled normal bivalent formation at meiosis and thus the production of fertile plants.

• Genetic evidence suggests spontaneous hybridisation between T. urartu, einkorn wheat (A genome donor) and T. speltoides/searsii  (B genome donor) created tetraploid species T. turgidum (emmer wheat).

• Hexaploid wheat arose from second hybridisation between new tetraploid and another diploid, T. tauschii (D genome donor).

Chromosomal rearrangements

• translocation

• fusion

• fission

• inversion

• segmental duplication

Reconstructing phylogenies using chromosomal movements

1. Take a species + isolate individual chromosomes on a basis of size/ weight

2. Search for areas of hybridisation to identify chromosomal movements during evolutionary time

3. Reconstruct phylogeny to common ancestor

Translocation

• rearrangement between 2 non-homologous chromosomes

• often result of incorrect chromosome pairing and recombination

• no phenotypic consequence → still 2 copies of every gene

Example of translocation

• “Philadelphia” karyotype

• chronic myeloid leukaemia

• translocation causes uncontrolled cell division

Chromosomal Fusions

• When two chromosomes combine

• More common in telocentric or acrocentric chromosomes due to centromere

• Fusion of two telocentric chromosomes results in a metacentric chromosome with one functional centromere

• Fusion of two metacentric chromosomes results in a dicentric chromosome (two functional centromeres). Can lead to chromosome breakage and sterility during meiosis.

• Can be of evolutionary significance.

Example of chromosomal fusion

Human chromosome 2 is a result of the fusion of 2 acrocentric chromosomes after the last common ancestor with chimpanzees

Chromosomal Fissions

• When a chromosome breaks in two

• Technically possible, but far less common than fusion due to the need for a centromere

• Without a centromere, a chromosome is not transmitted through meiosis, unable to attach to the spindle.

• Other product has lost a chunk of material.

• Usually deleterious and selected against.

Chromosomal inversions

• Rearrangement where segment of chromosome rotated through 180 degrees

• Homologous chromosomes can’t pair normally→ need to form a loop

• Recombination between normal and inverted forms generate many gametes with incomplete complements, missing some vital genes

Consequences of crossing over within inversions

In this example:

• 2 out of 4 gamete types are fine

• 1 has lost 1 of the 5 gene regions

• 1 has lost most of its genes

Within a population, there will be selection against recombination within inversion

Adaptive inversions

• Different inversions can arise in each population. Could allow local adaptation.

• Due to suppressed recombination, an inversion might capture 2 or more alleles that are adapted to local environmental conditions and spread due to its selective advantage

• Inversions might be adaptive sometimes because the suppression of recombination can link co-adapted alleles at nearby genes.

• Genes that function in a related way can become strongly linked→ a “supergene”

Fire ant social forms: Monogyne

• Workers tolerate only one queen → execute any others

• New colony founded by new queen immediately following mating fight

• extensive dispersal

• Queen phenotype: larger, higher fecundity

2 copies of non-inverted SB/SB

Fire ant social forms: Polygyne

• workers tolerate multiple queens

• new colonies of queens and workers bud from existing colonies

• dispersal not far

• queen phenotype: smaller, lower fecundity

1 non-inverted + 1 inverted SB/Sb

No recombination.

Sb/Sb non-viable.

Adaptive inversions in Fire Ants -Wang et al. Nature 2013

• Suppression of recombination between inversions can link co-adapted alleles at nearby genes

• Monogyne & polygyne phenotypes are composed of multiple genes.

• Phenotypes underpinned by 2 divergent forms of a chromosome (SB and Sb).

• Region of chromosome with complete suppression of recombination between SB and Sb.

• Study showed that different phenotypes map to a large inversion.

• Evidence that genomic rearrangements maintain divergent phenotypes via local limits on recombination.

Segmental Duplications

• Result from incorrect pairing and recombination

• Half of resulting gametes have 2 copies of region (deleterious if any

  genes are dosage sensitive)

• Half of resulting gametes lack region (often lethal)

• Bias towards smaller segmental duplications → less likely to have deleterious consequences

Example of Segmental Duplication: COWS

Normal beef breed = Aberdeen Angus

Belgian blue (double dose of myosin gene)

• huge extra musculature

• segmental duplication spans myosin gene

• increased copy number of myosin gene I

• increased production of myosin protein

• into muscle formation