Lecture 11

Question 1

Human Y chromosome

Answer 1

Is a sex limiting Y chromosome - deteriorated and diverged from the Y chromosome

Question 2

How are the mammalian X and Y differentiated

Answer 2

Human X contains 1000 genes but Y only encodes 45

Question 3

What does recombination suppression do

Answer 3

Its the critical catalyst in sex chromosome evolution

Leads to lots of neutral and adaptive processes that cause identical chromosomes to dramatically diverge from each other- happened with the human Y and other mammalian XY chromosomes

Question 4

What happens with recombination is suppressed

Answer 4

you get this reduction in the efficacy in selection - means you get linkage between the different alleles and you can’t break down. You get things like hitchhiking (where you’ll get selection for this beneficial mutation that will drag along a deleterious mutation

Question 5

Whats the Hill-Robertson affect

Answer 5

You cannot shuffle the combinations of beneficial alleles - smooths out the efficacy of selection which has led to widespread assumption

Question 6

What’s the function of the Y chromosome

Answer 6

One of the main functions for the mammalian Y chromosome - is that its this single gene (male determining region on the Y)- its a transcription factor that controls the expression of lots of different genes in a sex specific manner

Question 7

Whats the SRY gene

Answer 7

is a transcription factor meaning that it regulated and controls the expression of lots of genes. It encodes for a protein that contains around 200 amino acids and contains this conserved DNA binding domain - makes sense because its a transcription factor.

It activates this other transcription factor called SOX9- important for triggering male development

Question 8

What does SOX9 gene do

Answer 8

represses lots of genes that are important in ovary development and it activates lots of the testicular genes - continuing the formation and maintenance of the male gonad

This leads to the development of the testes, when you have developed testes, this leads to testosterone production and these sex chromosomes act on different tissues across the entire body to produce secondary sexual differences in other tissues (not those associated with reproduction).

Question 9

In humans and animals what is sex chromosome determination

Answer 9

This set process where the sex chromosome is the intitial trigger that determines the date of this bipotential gonadal ridge to develop either into a testes or an ovary. Once that has happened, the second process is the production of hormones to influence secondary sexual development

Question 10

What does sexual development hinge on

Answer 10

whether you have SRY or not- but there are also lots of different genes that are important in this network that are important in determining how the Gonad develops

Question 11

What can changes in different regulatory networks lead to

Answer 11

the development of a male phenotype or a female phenotype- sex chromosomes aren’t necessarily the marker for male/ female development

Question 12

What are the two main regions on the Y chromosome (heterochromatic)

Answer 12

the heterochromatic region (very big)- assumed to be genetically inert and it varies in length hugely in male populations and its comprised of two repeptitive families called DYZ1 and DYZ2 and each of those are present in thousands of copies, so therefore that copy can vary a lot in males and across different Y chromosomes in different populations

These repetitive elements are transcribed but theyre not coding - regulating the expression of other genes.

Question 13

What are the two main regions on the Y chromosome (euchromatic)

Answer 13

regions (45 protein coding genes)- comprised of 3 regions, X-transposed, X-degenerate and ampliconic

Question 14

What are X-transposed regions

Answer 14

3-4 million years ago (not present in other mammalian Y chromosomes). Most of these sequences are repetitive elements - some genes in that region and they tend to have ubiquitious tissue expression

Question 15

What are X-degenerate regions

Answer 15

region thats homologous to the X chromosome (present on the ancestral autosomes that started to not recombine and then gradually decay)- reminants of the ancestral autosomes

Question 16

What are ampliconic regions

Answer 16

harbour these protein coding multi copy gene families and they’re expressed primarily in the testes

9 protein coding ampliconic gene families on Y (present in multiple copies)

Expressed in testes and undergo gene conversion to have this sneaky recombination. There’s some evidence that they’re important in male fertility

Question 17

Whats the DAZ gene

Answer 17

one of the first that was originally identified in playing this role - copies of this gene are frequently deleted in the Y chromosome of males that are infertile

Those copies are expressed in spermatagonia (present in sperm- encodes an RNA binding protein thats important for spermatogenesis and deletion of this gene family accounts for 10% of males - that have defects with this sperm (important role in male fertility)

Question 18

Whats the BPY2 gene family

Answer 18

expressed in the testes and it produces this protein thats important in male germ cell development - basic spermatogenesis

Question 19

What are the two primary hypotheses to why these genes are present in such copy number

Answer 19

1. its just a product of genetic drift (if you do get gene duplication, just because you have lots of copies, if there’s genetic drift it means that you can sometimes have crossover events (where they pair and cross over that creates additional copies- if there’s not a huge amount of selection on these gene families, when they’re pairing up in those palindromes and crossing over, that simple process of crossing over can result in chunks being moved between and creating new copies- random
2. the number you have is really important and there’s selection influencing the number - sperm competition. If you have more genes you might produce more sperm

Question 20

Why so many copies?

Answer 20

More copies, more crossing over when they form those loops (exchanging genetic materal), more crossing over means you have a greater chance for errors to produce other copies- gene duplication through this crossing over process. Having more doesn’t help you, its just a copy of having more copies - more produced (runaway process driven by how recombination is working)

Question 21

Sex with reduced sex chromosomes die earlier- why?

Answer 21

Pattern that the sex that has the heteromorphic sex chromosomes (XY chromosomes) tend to die earlier than individuals that have homomorphic sex chromosomes (XX)

Question 22

Whats the toxic Y effect?

Answer 22

When you have lots of repetitive elements within a genome- those repetitive elements can hop around the genome. They can cause mutations - land in a gene and disrupt its function

The way a gene responds to that is that it produces heterochromatin - covering that goes over the chromosome that silences these transposons - they silence them so they can’t jump about

The heterochromatin is present in these repetitive regions - it silences these transposable elements that jump about

The Y chromosome is degenergated in humans and also in this species and we know that it contains loads of repeptiive elements - these need to be masked otherwise they’d cause lots of mutations

Theres only a finite amount of heterochromatin that you can produce- costly - can be much harder to suppress those elements on the Y chromosome in males because they have this huge Y chromosome in males and its much harder to mask it in males than it is in females that don’t have the Y

Masking of these repetiive elements is less efficient in males and so therefore theyre causing more damage and die earlier