PRD Class Genes: Mammals Flashcards
Start with a gene!
Look for duplications/changed in:
- TFs
- signalling molecules
- receptors
PRD :
- some new in humans!
- ARGFX
- LEUTX
- TPRX1 and 2
- DPRX
Research programme
1) how did they originate? (TDS from which “parent”?)
2) when did they originate? (Which species have them)
3) what do they do?
To achieve research programme:
1) compare to other species
2) compare to other homeobox genes
3) look @ chromosome position
Chromosomal position?
- gives us a clue
- 2 genes close to Crx
- 2 more on same chromosome
Crx
Cone rod homeobox
Hypothesis
1) originated from Crx (TD)
2) massive sequence change
3) chromosomal shuffling
- recapitulated across genomes
Only present in Eutheria
- not in: flies, worms, Amphioxus, fish, reptiles, birds, marsupials
- genetic difference in amount of homeobox
- evolutionary effect?
- we need functional annotation!
Still ocular?
- expression
- GOF
- LOF
Expression
- RNA-Seq from IVF embryos
- heatmap
- @ totipotent stage; 8-16 cells
- ARGFX stays on into blastocyst
- shown in mice and cows
32 cells
- compaction
- then cellular differentiation can start
Compaction
- cell contacts change
- stick to each other
- more of a round shape
- positional info by amount of contact
- inside: ICM
- outside: trophectoderm
- affects cellular signalling: triggers first decisions
Until compaction
- All cells are identical; totipotent
- compaction introduces fate
How to analyse RNA-Seq?
1) DEGs (common set of target genes up or down regulated)
2) Enrichment analysis (functional; enrichment of classifications; liable to false +ves / GO)
3) Profile analysis (are gene expression changes relevant to embryo? Classify on temporal expression; profile enrichment)
What is needed for profile analysis?
Every gene in the human genome is categorised into profiles
Profile analysis results
- 0 in oocytes, zygotes, 2&4 cells
- on in 8-16 morula (gene cascade to facilitate differentiation)
- compaction + blastocyst = off
Were these genes recruited for refinement of a new embryonic role: evolution of the set-aside embryo?
- Gain of function KO - difficult w early embryo (they might just not develop)
- need a mammal but not humans
KO GOF
- mouse ESCs taken from ICM genetically engineered to disrupt gene
- blastocyst transfer into host female uterus
- mouse contains mixture of genetically engineering + ICM cells
CRISPR on zygote
- yay
Mice might be a poor choice model for ETCHbox genes
- strange PRD behaviour
- some rodents have lost 3 of them
- others have mass duplicated
- high sequence divergence
Obox6
- KO
- normal early embryonic development
- fertile
You can also KO in a cell
- Not a whole organism
if you KO TPRX1
you can’t reverse development - it is involved in totipotency
Any other examples of “new homeobox genes” in animals?
TALE class
TALE class
- duplicated in Lophotrochozoa (molluscs and annelids esp.)
- 12 SHLE genes
- function in early embryo
- spiral cleavage of mollusc eggs
What’s so special about placental mammals?
What have these genres allowed placental mammals to do?
Wallaby
- non-placental marsupial
- Like chorionic plate and decidua; not as complex
Wallaby blastocyst
- ball of cells in middle of embryo
- disk of cells on surface
- some become membrane
- decision less precise
Better decision =
Better precision?
Why are thee genes so variable between species?
- adaptive?
- neutral reflection of functional overlap?
How could an embryo gene come from an eye gene?
- embryo is of general significance
- studying Crx in marsupials: embryo and eye (extra function!)
Crx evolutionary process
1) gene duplication
2) subfunctionalisation (specialising gene expression refines the gene)
3) specialisation
DDC
Duplication-Degeneration-Complementation
Theory underpinning DDC
- Redundancy is invisible to evolution
- Mutation accumulation and gene loss
- Deleterious mutations more common than beneficial mutations
DDC theory
- equal chance of mutation accumulation enhances chances of retention
- both become essential
- gradual specialisation
Crx and ETCHbox
- TD
- gradual specialisation for novel functions
