Which anatomical features are shared in vertebrates?
pharyngeal arches dorsally located nervous system segmented trunk muscles vertebrae complex head with sensory organs
What is the relationship between:
a) human arm, seal limb, bird wing and bat wing?
b) bird wing and bat wing?
a) all developed from a common tetrapod andestor = are homologous
b) evolved independently from each other = are analogous
What is a developmental hourglass model?
predicts an hourglass-like divergence during animal embryogenesis:
- embryos more divergent at the earliest and latest stages
- conserved during a mid-embryonic (phylotypic) period
= source of the basic body plan for animals within a phylum
Why is there the biggest diversity in the eary embryogenesis and in the pharyngula stage (talking about hourglass model)?
beginning: signal gradients induce activity throughout the gastrula
- Hox genes
- environmental and developmental constraints
- developmental burden
- random chance
end (pharyngula stage): a lot of local inductive interactions that are confined to their own modules and allow possible modifications
Gene regulatory networks can be of different hierarchies. In which 4 boxes do we divide them?
Box I: establish broad domains that regionaize the organism with respect to major body axes
Box II: define progenitor fields within the body parts
Box III: define identity and spatial boundaries of body parts
Box IV: terminal cell fate specification
–> differentiation gene batteries
What is a developmental genetic toolkit?
a set of a few 100 genes that are involved in 3 key processes:
- cell differentiation (Hox)
- cell-cell communication (Wnt)
- cell adhesion
conserved ones can be exchanged from one animal group to another
e.g. Pax6 -> eyes in mice and Drosophila even tho not homologous structures and even ectopically
Which properties allow for generation of morphological diversity?
- evolvability (size vs number of vertebrae)
- modularity
- cis-regulatory mutations (in enhancers)
- duplications and sub-functionalizations
- structural mutations (in coding regions, following duplications)
What are
a) enhancers?
b) cis-regulatory elements?
a) sequence modules that contain binding motifs for transcription factors
b) genomic regions containing the enhancers
Around mammalian developmental genes, regulatory landscapes can be very big (up tu 1Mb or more). Which event in mamm. evolution allowed de novo evolution of enhancers and diversification of their use?
2 rounds of genome replication
What is
a) heterotopy?
b) heterochrony?
a) evolutionary change in the spatial arrangement of an animal’s embryonic development
b) a change to the rate or timing of a development process
How can cis-regulatory networks be identified and compared between species?
- identification of enhancers by searching for conserved sequences
- identification of active enhancers and promoters by ChIP-Seq
What is Chip-Seq?
chromatin immune precipitation and sequencing
- cross-link protein to DNA
- shear DNA strands (sonication)
- immunoprecipitate target protein by bead-attached-antibodies
- unlink protein & purify DNA
- sequence DNA
- map to genome
Which histone marks mark
a) active enhancers?
b) active promoters?
a) H3K27ac
b) H3K4me3
What are possible cis-regulatory mutations?
- loss of TF binding sites in CREs
- insertions/deletions between TF binding sites in CREs
- recruitment of transposable elements as new CREs
- recruitment of new TF to mutations in CREs
Describe an example for a loss of TF binding site in CRE.
Pitx1 = can bind to hindlimb enhancer, if present
- present in marine stickleback
- absent in freshwater stickleback
How do you find sequences that are rapidly evolving or are already lost in the HUMAN lineage, but otherwise phylogenetically conserved (= most likely functional)?
creating catalogs of DNase I hypersensitive sites
DNase I hypersensitive sites demark potentially functional regulatory DNA -> look for those that are conserved in non-human primates, but accelerated in human lineage (haDHS, HARE)
Many exons and regulatory elements of host genes are derived from transposable elements. How is this process called? List examples.
molecular domestication
- ancient endogenous retrovirus (ERV) -> syncytin
- ERV1 insertion -> OCT4 regulated gene
- SINE-B2 (short interspersed nuclear element) insertion generates novel CTCF binding site that stops chromatin spreading
- LTR regulated gene network controls potency of mESC colonies (embryonic or extraembryonic tissue differentiation)
- MalR recruits Prdm9 -> meiotic recombination hotspot
Changes in gene regulatory networks generate morphological diversity. How can a single CRE mutation affect the whole GRN?
CRE mutation could result in co-optive change of the regulatory gene expression
it could:
- lead to loss of function (lose signal expression in subcurciot domain recieving signal or lose stabilitation of state)
- lead to co-option to new domain (e.g. producing structure in another location)
Which three types of changes can modification of enhancers lead to?
heterotopy (change in spatial arrangement)
heterochrony (change in timing)
heterometry (change in amount)
How did loss of eyes happen in cave fish?
Which type of change is that?
increase of Shh signaling by mutation in enhancer
heterometry
How did Darwin’s finches develop and become so diverse?
Which type of change is that?
mutation of enhancers
BMP4 (heterochronic and heterometric change)
calmodulin (heterometric)
What is heterotypie? Example.
modification in CODING regions, not enhancer
-> changes functional properties of the synthesized protein
OCA2 loss-of-function in some cave fish
2 genome duplications occured at the root of the vertebrate taxon and gave rise to paralogues. What are the pros of that?
- diversification of the proteins
- new expression patterns
- subfunctionalization
- might initiate new GRNs (TFs can increase and exchange their functionalities)
- retention of both copies relaxes developmental constraint and allows the paralogs to diverge through acquisition of mutations
How can DNA binding evolve in modular ways?
TF-blue can bind blue DNA binding site
TF-red can bind red DNA binding site
TF-purple can bind red and blue DNA binding site
specificity of the purple for the red binding site could change without altering function governed by the blue site
