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B3.0 > PRD Class Genes: Mammals > Flashcards

PRD Class Genes: Mammals Flashcards

1
Q

Start with a gene!

A

Look for duplications/changed in:
- TFs
- signalling molecules
- receptors

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2
Q

PRD :

A
  • some new in humans!
  • ARGFX
  • LEUTX
  • TPRX1 and 2
  • DPRX
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3
Q

PRD:

A
  • some new in humans!
  • ARGFX
  • LEUTX
  • TPRX1 and 2
  • DPRX
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4
Q

PRD:

A
  • some new in humans!
  • ARGFX
  • LEUTX
  • TPRX1 and 2
  • DPRX
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5
Q

Research programme

A

1) how did they originate? (TDS from which “parent”?)
2) when did they originate? (Which species have them)
3) what do they do?

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6
Q

To achieve research programme:

A

1) compare to other species
2) compare to other homeobox genes
3) look @ chromosome position

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7
Q

Chromosomal position?

A
  • gives us a clue
  • 2 genes close to Crx
  • 2 more on same chromosome
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8
Q

Crx

A

Cone rod homeobox

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9
Q

Hypothesis

A

1) originated from Crx (TD)
2) massive sequence change
3) chromosomal shuffling
- recapitulated across genomes

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10
Q

Only present in Eutheria

A
  • not in: flies, worms, Amphioxus, fish, reptiles, birds, marsupials
  • genetic difference in amount of homeobox
  • evolutionary effect?
  • we need functional annotation!
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11
Q

Still ocular?

A
  • expression
  • GOF
  • LOF
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12
Q

Expression

A
  • RNA-Seq from IVF embryos
  • heatmap
  • @ totipotent stage; 8-16 cells
  • ARGFX stays on into blastocyst
  • shown in mice and cows
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13
Q

32 cells

A
  • compaction
  • then cellular differentiation can start
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14
Q

Compaction

A
  • 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
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15
Q

Until compaction

A
  • All cells are identical; totipotent
  • compaction introduces fate
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16
Q

How to analyse RNA-Seq?

A

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)

17
Q

What is needed for profile analysis?

A

Every gene in the human genome is categorised into profiles

18
Q

Profile analysis results

A
  • 0 in oocytes, zygotes, 2&4 cells
  • on in 8-16 morula (gene cascade to facilitate differentiation)
  • compaction + blastocyst = off
19
Q

Were these genes recruited for refinement of a new embryonic role: evolution of the set-aside embryo?

A
  • Gain of function KO - difficult w early embryo (they might just not develop)
  • need a mammal but not humans
20
Q

KO GOF

A
  • mouse ESCs taken from ICM genetically engineered to disrupt gene
  • blastocyst transfer into host female uterus
  • mouse contains mixture of genetically engineering + ICM cells
21
Q

CRISPR on zygote

A
  • yay
22
Q

Mice might be a poor choice model for ETCHbox genes

A
  • strange PRD behaviour
  • some rodents have lost 3 of them
  • others have mass duplicated
  • high sequence divergence
23
Q

Obox6

A
  • KO
  • normal early embryonic development
  • fertile
24
Q

You can also KO in a cell

A
  • Not a whole organism
25
Q

if you KO TPRX1

A

you can’t reverse development - it is involved in totipotency

26
Q

Any other examples of “new homeobox genes” in animals?

A

TALE class

27
Q

TALE class

A
  • duplicated in Lophotrochozoa (molluscs and annelids esp.)
  • 12 SHLE genes
  • function in early embryo
  • spiral cleavage of mollusc eggs
28
Q

What’s so special about placental mammals?

A

What have these genres allowed placental mammals to do?

29
Q

Wallaby

A
  • non-placental marsupial
  • Like chorionic plate and decidua; not as complex
30
Q

Wallaby blastocyst

A
  • ball of cells in middle of embryo
  • disk of cells on surface
  • some become membrane
  • decision less precise
31
Q

Better decision =

A

Better precision?

32
Q

Why are thee genes so variable between species?

A
  • adaptive?
  • neutral reflection of functional overlap?
33
Q

How could an embryo gene come from an eye gene?

A
  • embryo is of general significance
  • studying Crx in marsupials: embryo and eye (extra function!)
34
Q

Crx evolutionary process

A

1) gene duplication
2) subfunctionalisation (specialising gene expression refines the gene)
3) specialisation

35
Q

DDC

A

Duplication-Degeneration-Complementation

36
Q

Theory underpinning DDC

A
  1. Redundancy is invisible to evolution
  2. Mutation accumulation and gene loss
  3. Deleterious mutations more common than beneficial mutations
37
Q

DDC theory

A
  • equal chance of mutation accumulation enhances chances of retention
  • both become essential
  • gradual specialisation
38
Q

Crx and ETCHbox

A
  • TD
  • gradual specialisation for novel functions

B3.0 (23 decks)

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