Hox Clusters: Changes To Gene Function And Regulation

Question 1

Homeosis

Answer 1

changing a structure to a different position

Question 2

Homeotic gene (Hox)

Answer 2

• gene for position
• 8 in drosophila (Hox)
• homeotic mutants (e.g. bithorax)

Question 3

Hox genes

Answer 3

• A-> P axis
• cluster: near each other in chromosomes

Question 4

Homeobox

Answer 4

Recognisable c180bp DNA region

Question 5

Homeodomain

Answer 5

• c60aa protein region coded by Homeobox
• helix 3 facilitates TF

Question 6

Spatial colinearity

Answer 6

• Hox genes are expressed along the body in the same order they are found in the embryo

Question 7

Mus

Answer 7

39 Hox genes in 4 clusters

Question 8

Somites

Answer 8

Form into vertebrae in the vertebral column

Question 9

Hox similarities

Answer 9

• sequence between sp
• expression pattern between sp

Question 10

Broken cluster?

Answer 10

• Drosophila -> 5 and 3 separated by 100s of other gens
• ancestrally once cluster, secondarily split
• relaxed selection pressure

Question 11

Other clades

Answer 11

Also have broken clusters, suggesting that these mutations are tolerated and not v important

Question 12

Mosquitoe

Answer 12

• complete, unbroken cluster
• can they tolerate cluster breakage?

Question 13

C. elegans clusters

Answer 13

Broken into chunks

Question 14

Ciona

Answer 14

• sea squirt
• broken + chromosome migration
• you can still tell “which is which” from aa sequnece

Question 15

Is there anything in common between animals where Hox clusters have broken?

Answer 15

• yes! Fast developing (model sp.)
• e.g. Drosophila lays eggs in rotting fruit

Question 16

Slow development

Answer 16

Temporal colinearity

Question 17

Fast development

Answer 17

• no temporal colinearity
• allows the cluster to break?

Question 18

Spatial colinearity

Answer 18

• arthropods, annelids, molluscs, tunicates, amphioxus, vertebrates; pretty much all bilaterians
• probably dates to the base
• debated in Echinoderms
• not the case for other genes

Question 19

Temporal colinearity

Answer 19

• need a biochemical mechanism for turning them on one at a time, from A-> P during gastrulation

Question 20

Epigenetic temporal colinearity

Answer 20

• remove complete heterochromatin over a series of days
• transcriptional activation
• highly descriptive evidence

Question 21

Removing heterochromatin

Answer 21

• H3K27me3: transcriptional repression
• gradually removed A->P
• measured using chromatin immunoprecipitation in an ESC (mimics early development)

Question 22

Observing H3K27me3

Answer 22

1. 8.5 days =3 active
2. 9.5 days =more
   - time sequence
   - studying mouse hard pre8.5

Question 23

Transcriptional activation

Answer 23

• H3K9Ac
• gradually moves A->P (close developmental time points)

Question 24

Development

Answer 24

• Posterior elaboration
• progressive activation of sequence

Question 25

Temporal colinearity causes

Answer 25

Spatial colinearity

Question 26

Was temporal colinearty ancestral for Metazoa?

Answer 26

Non-conserved genes evolved for Hox activation in annelids and Crustacea

Question 27

Extra clusters?

Answer 27

Most - 1 Mice - 4 (tetrapods, sharks) Teleosts - 7/8 (some lost); paralogy groups 13. 1 cluster went thru WGD, genes lost. Salmonids - 16

Question 28

Identifying gene loss

Answer 28

- Look at 39 Hox gene protein sequences to divine relations - number them - gaps; gene loss - 14 in vertebrates; 1 lost in mammals

Question 29

Cluster colinearity

Answer 29

- in each cluster - overlap - some cluster on different chromosomes: 2, 7, 12, 17

Question 30

Is WGD selectively advantageous?

Answer 30

- subfunctionalisation (tissue specificity) - spiders and horseshoe crab - mouse; gene KO = homeotic transformations tolerable; subtle tissue-specific expr swoon

Question 31

Drosophila

Answer 31

- 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

Question 32

z2 and zen

Answer 32

- roles in EEMs - evolved from Hox3 - less developmental significance - changed functions and duplicated

Question 33

Butterflies, moths and hover flies

Answer 33

- dozens of extra zen-like genes expressed in membranes around egg

Question 34

In insects, some hox genes have

Answer 34

Completely changed function

Question 35

How is changing role achieved without lethality?

Answer 35

- hox mutant = homeosis - expression domain sliding, functional redundancy, Neofunctionalisation

Question 36

Hox TD

Answer 36

Might be just as bad as KO due to regulatory interference

Question 37

Are all 39 genes actually Hox?

Answer 37

- KO expts - if you KO B4, slight changes to vertebral column; modifies axis segment; homeotic transformation - look for G/LOF

Question 38

LOF Hox mutation

Answer 38

Found for all

Question 39

GOF Hox mutations

Answer 39

Done for some eg a7

Question 40

B13 KO

Answer 40

- does not change segment type (expected under homeosis) - makes tail longer; segment counting gene - spatially segregated (Mouse genome browser view) - broken cluster + escape

Question 41

Hoxbl3

Answer 41

- in domestic sheep w/ long tails - nearby regulatory region insertion mutations; changed regulation

Question 42

Extra roles?

Answer 42

- w/o tandem duplication - genital bud - limb bud (posterior genes of Hoxa, Hoxd) - blood cells (mainly Hoxb)

Question 43

Hoxb in blood cells

Answer 43

- establish using haematopoesis in situ hybridisation - functional in haematopoetic stem cells - KO; loses multipotency - necessary

Question 44

Extra Hox in mollusc shells

Answer 44

- ventral: nerve cord -> normal colinear expression - dorsal: no colinearity ; expressed in rings of shell formation Hypothesis: decoupled D/V regulation; shell development recruitment

Question 45

Structure:

Answer 45

1. Definitions 2. Are they always in clusters? 3. Breaking the cluster: colinearity 4. Extra clusters 5. Is WGD selectively advantageous 6. Changing roles 7. Are they all actually Hox? 8. Extra roles