Hox Clusters: Changes To Gene Function And Regulation Flashcards
Homeosis
changing a structure to a different position
Homeotic gene (Hox)
- gene for position
- 8 in drosophila (Hox)
- homeotic mutants (e.g. bithorax)
Hox genes
- A-> P axis
- cluster: near each other in chromosomes
Homeobox
Recognisable c180bp DNA region
Homeodomain
- c60aa protein region coded by Homeobox
- helix 3 facilitates TF
Spatial colinearity
- Hox genes are expressed along the body in the same order they are found in the embryo
Mus
39 Hox genes in 4 clusters
Somites
Form into vertebrae in the vertebral column
Hox similarities
- sequence between sp
- expression pattern between sp
Broken cluster?
- Drosophila -> 5 and 3 separated by 100s of other gens
- ancestrally once cluster, secondarily split
- relaxed selection pressure
Other clades
Also have broken clusters, suggesting that these mutations are tolerated and not v important
Mosquitoe
- complete, unbroken cluster
- can they tolerate cluster breakage?
C. elegans clusters
Broken into chunks
Ciona
- sea squirt
- broken + chromosome migration
- you can still tell “which is which” from aa sequnece
Is there anything in common between animals where Hox clusters have broken?
- yes! Fast developing (model sp.)
- e.g. Drosophila lays eggs in rotting fruit
Slow development
Temporal colinearity
Fast development
- no temporal colinearity
- allows the cluster to break?
Spatial colinearity
- arthropods, annelids, molluscs, tunicates, amphioxus, vertebrates; pretty much all bilaterians
- probably dates to the base
- debated in Echinoderms
- not the case for other genes
Temporal colinearity
- need a biochemical mechanism for turning them on one at a time, from A-> P during gastrulation
Epigenetic temporal colinearity
- remove complete heterochromatin over a series of days
- transcriptional activation
- highly descriptive evidence
Removing heterochromatin
- H3K27me3: transcriptional repression
- gradually removed A->P
- measured using chromatin immunoprecipitation in an ESC (mimics early development)
Observing H3K27me3
- 8.5 days =3 active
- 9.5 days =more
- time sequence
- studying mouse hard pre8.5
Transcriptional activation
- H3K9Ac
- gradually moves A->P (close developmental time points)
Development
- Posterior elaboration
- progressive activation of sequence
Temporal colinearity causes
Spatial colinearity
Was temporal colinearty ancestral for Metazoa?
Non-conserved genes evolved for Hox activation in annelids and Crustacea
Extra clusters?
Most - 1
Mice - 4 (tetrapods, sharks)
Teleosts - 7/8 (some lost); paralogy groups 13. 1 cluster went thru WGD, genes lost.
Salmonids - 16
Identifying gene loss
- Look at 39 Hox gene protein sequences to divine relations
- number them
- gaps; gene loss
- 14 in vertebrates; 1 lost in mammals
Cluster colinearity
- in each cluster
- overlap
- some cluster on different chromosomes: 2, 7, 12, 17
Is WGD selectively advantageous?
- subfunctionalisation (tissue specificity)
- spiders and horseshoe crab
- mouse; gene KO = homeotic transformations tolerable; subtle tissue-specific expr swoon
Drosophila
- other homeoboxes not involved in segment identity
- functional differentiation? Neofunctionalisation?
- expressed in stripes in embryo
- segment cascade (earlier than Hox)
- e.g. maternally deposited bcd
z2 and zen
- roles in EEMs
- evolved from Hox3
- less developmental significance
- changed functions and duplicated
Butterflies, moths and hover flies
- dozens of extra zen-like genes expressed in membranes around egg
In insects, some hox genes have
Completely changed function
How is changing role achieved without lethality?
- hox mutant = homeosis
- expression domain sliding, functional redundancy, Neofunctionalisation
Hox TD
Might be just as bad as KO due to regulatory interference
Are all 39 genes actually Hox?
- KO expts
- if you KO B4, slight changes to vertebral column; modifies axis segment; homeotic transformation
- look for G/LOF
LOF Hox mutation
Found for all
GOF Hox mutations
Done for some eg a7
B13 KO
- does not change segment type (expected under homeosis)
- makes tail longer; segment counting gene
- spatially segregated (Mouse genome browser view)
- broken cluster + escape
Hoxbl3
- in domestic sheep w/ long tails
- nearby regulatory region insertion mutations; changed regulation
Extra roles?
- w/o tandem duplication
- genital bud
- limb bud (posterior genes of Hoxa, Hoxd)
- blood cells (mainly Hoxb)
Hoxb in blood cells
- establish using haematopoesis in situ hybridisation
- functional in haematopoetic stem cells
- KO; loses multipotency
- necessary
Extra Hox in mollusc shells
- ventral: nerve cord -> normal colinear expression
- dorsal: no colinearity ; expressed in rings of shell formation
Hypothesis: decoupled D/V regulation; shell development recruitment
