Download High Mutation Rates Have Driven Extensive Structural

High Mutation Rates Have Driven
Extensive Structural
Polymorphisms Among Human Y
Chromosomes
Matthew Byrnes
Outline





The Y Chromosome and its Apparent
Problems
Origins of the Y chromosome
Is the Human Y chromosome degenerating perniciously?
Homo vs. Pan Y chromosome studies
High Mutation Rates in Human Y
Chromosome

Repping et al.(2006)
Distal-Yq heterochromatin and IR3/IR3
TSPY and AZFc

Conclusions and Summary


Evolution of the Y Chromosome





X and Y diverged from autosomes of mammalian
ancestors ca. 300MYA
Differentiation of X and Y only occurred after
recombination suppression
There are 19 homologous genes on both the X
and Y chromosomes
Located on tip of short arm in X and in 4
contiguous blocks. But are fragmented across
length of Y.
Attributed to four major inversions on the Y
chromosome. Prevented recombination of X-Y






ca. 5% of Y is capable of recombining with X.
These areas are known as pseudoautosomal
regions(PAR) located at telomeres.The other 95%
is known as the male-specific region(MSY).
MSY contains 78 genes which code for 27 distinct
proteins.
MSY split into three euchromatic classes;1
X-transposed region
X-degenerate region
Ampliconic region
X-transposed region




Only 2 genes, almost identical with Xq21, a band
on the long arm of the X chromosome
Caused by an eponymous transposition ca. 3MYA
after divergence with chimpanzees
Large inversion within MSY short arm cleaved the
region into two non-contiguous segments (total
of 3.4Mb in length)
Do not cross over during male meiosis unlike
PARs.
X-degenerate region




Replete with single-copy genes or pseudogene
homologues of 27 X-linked genes
Possible remnants of an ancient
autosome,homology indicative of coevolution of
both X and Y from autosome.
e.g Y-linked genes RPS4Y1 and RPS4Y2 are full
length homologues of X-linked gene RPS4X,
which encode two different, full-length isoforms
of ribosomal protein S4.
Contains 16 of 27 protein families in
MSY;including the sex-determining gene SRY and
all 12 of the ubiquitously expressed genes
Summary of X-transposed and X-degenerate protein
families
Ampliconic region





By far constitutes more of the MSY than the other
two classes(10.2Mb) and shows a significantly
higher gene density than the other two regions
Consists largely of 99.9% similar sequences
which maintain identity over 10-100Kb
Originated from amplification of X-degenerate
genes (RBMY, VCY)
transposition and amplification of autosomal
genes (DAZ from chromosome 3)
And retroposition and amplification of autosomal
genes (CDY).
Ampliconic region


Each of these genes has been amplified, one of them
(TSPY) has multiplied itself 35 times.
9 of the distinct protein families are expressed exclusively
in testes
Summary of Ampliconic protein families
Is the Y Chromosome
Degenerating Perniciously?




Clonal transmission paternally poses a problem
for Y chromosome
Chromosome is greatly emaciated, ca. 30% and
less than 10% length and gene content of X
chromosomes
On this notion,it has been proposed that the Y
chromosome will be bereft of functional genes in
10MY(impending demise hypothesis)
Contemporaneously, peers proposed integrity of Y
chromosome is maintained.1
Is the Y Chromosome
Degenerating Perniciously?





Human ampliconic regions consist of 8 v.large
palindromic sequences(9kb-1.45Mb)
Atleast 6 of these arose before divergence with Pan
Paired arms of each palindrome separated by spacer
region(2-170kb)
Proposed that integrity of palindromic sequences is
maintained by gene conversion between two arms of
the same palindromic region2
Found to be true,gene conversion confirmed by studies
of P1.
Is the Y Chromosome
Degenerating Perniciously?



Gene conversion acts at a slow rate. Balanced
between rates of mutations that cause differences
between arms.
Indicates that process may not be driven by
selective constraints, but rather a weak direction
bias which favours preservation of original
sequences.(at least in humans)
But what about X-degenerate genes?
Is the Y Chromosome
Degenerating Perniciously?





No gene conversion takes place in X-degenerate
regions. So extensive gene decay is expected
16 X-degenerate and 11 pseudogenes both
present in chimpanzees and humans
Therefore, none or little gene decay has occurred
in human lineage since divergence with Pan.
Functional proteins exhibit less interspecies
divergence(Homo vs pan) than intronic DNA
sequences
Suggests stabilizing selection is imperative to
maintaining functionality of human X-degenerate
regions
Homo vs Pan Y Chromosome Studies





In significant contrast, pernicious X-degenerate
gene decay was prevalent in chimpanzee
Of the 8 genes found to have >1.0% divergence, 5
had undergone truncations, which was either
caused by splice-site disruption, or expression of
stop codons.
e.g USP9Y is vital for spermatogenesis
in humans,but in Pan, it only codes for
a 675 amino acid chain(cf.2555)
TMSB4Y (ubiquitous in humans) is not
transcriptionally active at all.
Both differ by negligible differences in
humans
Homo vs Pan Y Chromosome
Studies




Why have chimpanzees suffered gene decay
severely, and humans negligibly?
Strong positive selection at another locality on Y?
(genetic hitchhiking)
Natural selection acts on Y as a unit,as it has
nothing else with which to recombine.
Deleterious mutations can be selected until
fixation has occurred
by linkage to beneficial
mutations on other
Y-linked genes
Homo vs Pan Y Chromosome
Studies




Ampliconic regions bear many testes-restricted genes
These play a vital role in spermatogenesis and
spermatogenic failure, therefore these regions may be
under intense selection pressure
Especially in taxa such as Pan which exhibit a complex
mating system,mainly promiscuity. This gives rise to
intense sperm competition
Monogamy, the prevailing strategy in humans, may
allow for higher preservation of testes-restricted genes
High Mutation Rates in Human Y
Chromosome
Repping et al.(2006)



Use of ampliconic DNA sequences to determine
causes of frequently recurring polymorphisms in
Human male genealogy.
Are these polymorphisms recurrent independent
mutations are do they originate from a single
ancestor?
How are these polymorphisms governed? And
what effect does natural selection have on these
areas?
High Mutation Rates in Human Y
Chromosome







47 chromosomes were collected, each representing a
major branch of global diversity and major genealogical
lineages
9 categories of potential structural variation were
investigated. And four of these showed sufficient
variation to be further considered
Minimum-mutation histories and lower bound mutation
rates over 52,000 generations were calculated
Distal-Yq heterochromatin
IR3/IR3
TSPY
AZFc
Regions of Y chromosome and
conserved elements in Pan
Distal-Yq heterochromatin




Showed large-scale length variation (29%-54%
of the length of metaphase Y)
Consists of low-complexity sequences in tandem
arrays
Distinct lengths must be due to
multiple mutations
>12 large-scale changes equate to a
rate of >2.3 X 10-4 per father-to-son transmission
IR3/IR3

Was inverted in proximal Yp in 16 of the 47
chromosomes

3.6Mb inversion

Attributed to ectopic homologous recombination

12 independent inversion events

>2.3 X 10-4 per father-to-son transmission
(same as Yq, why is this so?)
TSPY

Testes-specific protein Y-linked

Often expressed in testicular cancer



Showed large scale length variation. Ranged in
size from 0.47Mb-1.3Mb
Highly similar 20.4Kb repeat units of gene and
transcription factor
Result of multiple mutations
TSPY


>23 changes in length >4.4 X 10-4 per father-toson transmission
Specimens who displayed frequent changes also
showed limited copy number variation.
AZFc




Highest mutation rates(20 rearrangements and
mutation rate of 3.8X 10-4) . Higher variation of
copy number (does this correspond with
significant mutations in this region?)
Very important as it bears many testes-specific
genes
Many common deletions result in large sections
of AZFc being removed
b2/b4 deletion removes entire region most
common cause of spermatogenic failure
AZFc





gr/gr mutation removes 1.6Mb, it has arose 14 times
independently in human genealogy.
And as deleterious mutations are usually not able to become
polymorphic this is an indicator of haploid selection being in
balance with homologous recombination
b2/b3 similar to gr/gr, does not delete full copies on genes,
and retains some copies.4,5
Are ampliconic regions so duplicated to withstand intense
natural selection?
Are these deleterious mutations selected in conjunction with
other Y-linked genes with positive effects on fitness?
Conclusions





Natural selection acts on Y in a v.different way to
autosomes,and selects it as one unit. This allows for
different kinetics which must be further elucidated.
High duplication in the MSY allows many functional genes to
be retained by homologous recombination
Direct and indirect natural selection on certain genetic units
play in integral role
Natural selection may help preserving vital spermatogenic
genes by exerting a stabilizing selection on gene copy
variance
Contemporary evidence points away from impending
demise hypothesis for humans.





References
1.Helen Skaletsky et al(2003) The male-specific region of the
human Y chromosome is a mosaic of discrete sequence classes.
NATURE VOL 423 www.nature.com/nature
2.Jennifer F. Hughes, Helen Skaletsky et al (2005) Conservation of
Y-linked genes during human evolution revealed by comparative
sequencing in chimpanzee. Nature vol 437
3.Repping et al(2006) High mutation rates have driven
extensive structural polymorphism among human Y
chromosomes.Nature Genetics.Advanced online publication
4. Repping et al.(2004)A family of human Y chromosomes has
dispersed throughout northern Eurasia despite a 1.8-Mb deletion in
the azoospermia factor c region. Genomics vol 83 1046–1052
5.Repping et.al(2003) Polymorphism for a 1.6Mb deletion of human
Y chromosome through balance between recurrent mutation and
haploid selection.Nature genetics.vol 35 3