high mutation rates have driven extensive structural polymorphisms among human y chromosomes

High Mutation Rates Have Driven High Mutation Rates Have Driven Extensive Structural Extensive Structural

Polymorphisms Among Human Y Polymorphisms Among Human Y ChromosomesChromosomes

Matthew ByrnesMatthew Byrnes

OutlineOutline The Y Chromosome and its Apparent The Y Chromosome and its Apparent

ProblemsProblems Origins of the Y chromosomeOrigins of the Y chromosome Is the Human Y chromosome degenerating perniciously?Is the Human Y chromosome degenerating perniciously? Homo vs. PanHomo vs. Pan Y chromosome studies Y chromosome studies High Mutation Rates in Human Y High Mutation Rates in Human Y

ChromosomeChromosome Repping Repping et al.et al.(2006)(2006) Distal-Yq heterochromatin aDistal-Yq heterochromatin annd d IR3IR3//IR3IR3 TSPY and AZFcTSPY and AZFc Conclusions and SummaryConclusions and Summary

Evolution of the Y ChromosomeEvolution of the Y Chromosome X and Y diverged from autosomes of mammalian X and Y diverged from autosomes of mammalian

ancestors ancestors ca. ca. 300MYA300MYA Differentiation of X and Y only occurred after Differentiation of X and Y only occurred after

recombination suppressionrecombination suppression There are 19 homologous genes on both the X There are 19 homologous genes on both the X

and Y chromosomesand Y chromosomes Located on tip of short arm in X and in 4 Located on tip of short arm in X and in 4

contiguous blocks. But are fragmented across contiguous blocks. But are fragmented across length of Y.length of Y.

Attributed to four major inversions on the Y Attributed to four major inversions on the Y chromosome. Prevented recombination of X-Ychromosome. Prevented recombination of X-Y

ca.ca. 5% of Y is capable of recombining with X. These 5% of Y is capable of recombining with X. These areas are known as pseudoautosomal regions(PAR) areas are known as pseudoautosomal regions(PAR) located at telomeres.The other 95% is known as the located at telomeres.The other 95% is known as the male-specific region(MSY).male-specific region(MSY).

MSY contains 78 genes which code for 27 distinct MSY contains 78 genes which code for 27 distinct proteins.proteins.

MSY split into three euchromatic classes;MSY split into three euchromatic classes;11

X-transposed regionX-transposed region X-degenerate regionX-degenerate region Ampliconic regionAmpliconic region

X-transposed regionX-transposed region Only 2 genes, almost identical with Xq21, a band Only 2 genes, almost identical with Xq21, a band

on the long arm of the X chromosomeon the long arm of the X chromosome

Caused by an eponymous transposition Caused by an eponymous transposition ca. ca. 3MYA 3MYA after divergence with chimpanzeesafter divergence with chimpanzees

Large inversion within MSY short arm cleaved the Large inversion within MSY short arm cleaved the region into two non-contiguous segments (total of region into two non-contiguous segments (total of 3.4Mb in length)3.4Mb in length)

Do not cross over during male meiosis unlike Do not cross over during male meiosis unlike PARs.PARs.

X-degenerate regionX-degenerate region Replete with single-copy genes or pseudogene Replete with single-copy genes or pseudogene

homologues of 27 X-linked geneshomologues of 27 X-linked genes

Possible remnants of an ancient Possible remnants of an ancient autosome,homology indicative of coevolution of autosome,homology indicative of coevolution of both X and Y from autosome.both X and Y from autosome.

e.g Y-linked genes 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 Summary of X-transposed and X-degenerate protein familiesfamilies

Ampliconic regionAmpliconic region

By far constitutes more of the MSY than the other By far constitutes more of the MSY than the other two classes(10.2Mb) and shows a significantly two classes(10.2Mb) and shows a significantly higher gene density than the other two regionshigher gene density than the other two regions

Consists largely of 99.9% similar sequences which Consists largely of 99.9% similar sequences which maintain identity over 10-100Kbmaintain identity over 10-100Kb

Originated from amplification of X-degenerate Originated from amplification of X-degenerate genes (RBMY, VCY)genes (RBMY, VCY)

transposition and amplification of autosomal transposition and amplification of autosomal genes (DAZ from chromosome 3)genes (DAZ from chromosome 3)

And retroposition and amplification of autosomal And retroposition and amplification of autosomal genes (CDY). genes (CDY).

Ampliconic regionAmpliconic region Each of these genes has been amplified, one of them Each of these genes has been amplified, one of them

(TSPY) has multiplied itself 35 times.(TSPY) has multiplied itself 35 times. 9 of the distinct protein families are expressed exclusively 9 of the distinct protein families are expressed exclusively

in testesin testes

Summary of Ampliconic protein familiesSummary of Ampliconic protein families

Is the Y Chromosome Is the Y Chromosome Degenerating Perniciously?Degenerating Perniciously?

Clonal transmission paternally poses a problem Clonal transmission paternally poses a problem for Y chromosomefor Y chromosome

Chromosome is greatly emaciated, Chromosome is greatly emaciated, ca. ca. 30% and 30% and less than 10% length and gene content of X less than 10% length and gene content of X chromosomeschromosomes

On this notion,it has been proposed that the Y On this notion,it has been proposed that the Y chromosome will be bereft of functional genes in chromosome will be bereft of functional genes in 10MY(impending demise hypothesis)10MY(impending demise hypothesis)

Contemporaneously, peers proposed integrity of Y Contemporaneously, peers proposed integrity of Y chromosome is maintained.chromosome is maintained.11


Human ampliconic regions consist of 8 v.large Human ampliconic regions consist of 8 v.large palindromic sequences(9kb-1.45Mb)palindromic sequences(9kb-1.45Mb)

Atleast 6 of these arose before divergence with Atleast 6 of these arose before divergence with PanPan

Paired arms of each palindrome separated by spacer Paired arms of each palindrome separated by spacer region(2-170kb)region(2-170kb)

Proposed that integrity of palindromic sequences is Proposed that integrity of palindromic sequences is maintained by gene conversion between two arms of maintained by gene conversion between two arms of the same palindromic regionthe same palindromic region22

Found to be true,gene conversion confirmed by studies Found to be true,gene conversion confirmed by studies of P1. of P1.


Gene conversion acts at a slow rate. Balanced Gene conversion acts at a slow rate. Balanced between rates of mutations that cause differences between rates of mutations that cause differences between arms.between arms.

Indicates that process may not be driven by Indicates that process may not be driven by selective constraints, but rather a weak direction selective constraints, but rather a weak direction bias which favours preservation of original bias which favours preservation of original sequences.(at least in humans)sequences.(at least in humans)

But what about X-degenerate genes?But what about X-degenerate genes?


No gene conversion takes place in X-degenerate No gene conversion takes place in X-degenerate regions. So extensive gene decay is expectedregions. So extensive gene decay is expected

16 X-degenerate and 11 pseudogenes both 16 X-degenerate and 11 pseudogenes both present in chimpanzees and humans present in chimpanzees and humans

Therefore, none or little gene decay has occurred Therefore, none or little gene decay has occurred in human lineage since divergence with in human lineage since divergence with PanPan..

Functional proteins exhibit less interspecies Functional proteins exhibit less interspecies divergence(divergence(Homo vs pan)Homo vs pan) than intronic DNA than intronic DNA sequencessequences

Suggests stabilizing selection is imperative to Suggests stabilizing selection is imperative to maintaining functionality of human X-degenerate maintaining functionality of human X-degenerate regionsregions

Homo vs Pan Y Chromosome StudiesHomo vs Pan Y Chromosome Studies In significant contrast, pernicious X-degenerate In significant contrast, pernicious X-degenerate

gene decay was prevalent in chimpanzeegene decay was prevalent in chimpanzee Of the 8 genes found to have >1.0% divergence, 5 Of the 8 genes found to have >1.0% divergence, 5

had undergone truncations, which was either had undergone truncations, which was either caused by splice-site disruption, or expression of caused by splice-site disruption, or expression of stop codons.stop codons.

e.ge.g USP9Y is vital for spermatogenesis in USP9Y is vital for spermatogenesis in humans,but in humans,but in PanPan, it only codes for a , it only codes for a 675 amino acid chain(675 amino acid chain(cf.cf.2555)2555)

TMSB4Y (ubiquitous in humans) is not transcriptionally active at all.

Both differ by negligible differences in humans

Homo vs Pan Y Chromosome Homo vs Pan Y Chromosome StudiesStudies

Why have chimpanzees suffered gene decay Why have chimpanzees suffered gene decay severely, and humans negligibly?severely, and humans negligibly?

Strong positive selection at another locality on Y? Strong positive selection at another locality on Y? (genetic hitchhiking)(genetic hitchhiking)

Natural selection acts on Y as a unit,as it has Natural selection acts on Y as a unit,as it has nothing else with which to recombine.nothing else with which to recombine.

Deleterious mutations can be selected until Deleterious mutations can be selected until fixation has occurred by fixation has occurred by linkage to beneficial linkage to beneficial mutations on other Y-mutations on other Y-linked geneslinked genes

Homo vs Pan Y Chromosome Homo vs Pan Y Chromosome StudiesStudies

Ampliconic regions bear many testes-restricted genesAmpliconic regions bear many testes-restricted genes These play a vital role in spermatogenesis and These play a vital role in spermatogenesis and

spermatogenic failure, therefore these regions may be spermatogenic failure, therefore these regions may be under intense selection pressureunder intense selection pressure

Especially in taxa such as Especially in taxa such as Pan Pan which exhibit a complex which exhibit a complex mating system,mainly promiscuity. This gives rise to mating system,mainly promiscuity. This gives rise to intense sperm competitionintense sperm competition

Monogamy, the prevailing strategy in humans, may Monogamy, the prevailing strategy in humans, may allow for higher preservation of testes-restricted genesallow for higher preservation of testes-restricted genes

High Mutation Rates in Human Y High Mutation Rates in Human Y ChromosomeChromosome

Repping et al.(2006)Repping et al.(2006) Use of ampliconic DNA sequences to determine Use of ampliconic DNA sequences to determine

causes of frequently recurring polymorphisms in causes of frequently recurring polymorphisms in Human male genealogy.Human male genealogy.

Are these polymorphisms recurrent independent Are these polymorphisms recurrent independent mutations are do they originate from a single mutations are do they originate from a single ancestor?ancestor?

How are these polymorphisms governed? And How are these polymorphisms governed? And what effect does natural selection have on these what effect does natural selection have on these areas?areas?

High Mutation Rates in Human Y High Mutation Rates in Human Y ChromosomeChromosome

47 chromosomes were collected, each representing a 47 chromosomes were collected, each representing a major branch of global diversity and major genealogical major branch of global diversity and major genealogical lineageslineages

9 categories of potential structural variation were 9 categories of potential structural variation were investigated. And four of these showed sufficient investigated. And four of these showed sufficient variation to be further consideredvariation to be further considered

Minimum-mutation histories and lower bound mutation Minimum-mutation histories and lower bound mutation rates over 52,000 generations were calculatedrates over 52,000 generations were calculated

Distal-Yq heterochromatin Distal-Yq heterochromatin IR3/IR3 IR3/IR3 TSPY TSPY AZFcAZFc

Regions of Y chromosome and Regions of Y chromosome and conserved elements in conserved elements in PanPan

Distal-Yq heterochromatinDistal-Yq heterochromatin

Showed large-scale length variation (29%-54% of Showed large-scale length variation (29%-54% of the length of metaphase Y)the length of metaphase Y)

Consists of low-complexity sequences in tandem Consists of low-complexity sequences in tandem arraysarrays

Distinct lengths must be due to multiple Distinct lengths must be due to multiple mutationsmutations

>12 large-scale changes equate to a rate >12 large-scale changes equate to a rate of >2.3 X 10of >2.3 X 10-4-4 per father-to-son transmission per father-to-son transmission

IR3/IR3IR3/IR3 Was inverted in proximal Yp in 16 of the 47 Was inverted in proximal Yp in 16 of the 47

chromosomeschromosomes

3.6Mb inversion3.6Mb inversion

Attributed to ectopic homologous recombinationAttributed to ectopic homologous recombination

12 independent inversion events12 independent inversion events

>2.3 X 10>2.3 X 10-4-4 per father-to-son transmission (same per father-to-son transmission (same as Yq, why is this so?)as Yq, why is this so?)

TSPYTSPY Testes-specific protein Y-linkedTestes-specific protein Y-linked

Often expressed in testicular cancerOften expressed in testicular cancer

Showed large scale length variation. Ranged in Showed large scale length variation. Ranged in size from 0.47Mb-1.3Mbsize from 0.47Mb-1.3Mb

Highly similar 20.4Kb repeat units of gene and Highly similar 20.4Kb repeat units of gene and transcription factortranscription factor

Result of multiple mutationsResult of multiple mutations

TSPYTSPY >23 changes in length >4.4 X 10>23 changes in length >4.4 X 10-4-4 per father-to- per father-to-

son transmission son transmission Specimens who displayed frequent changes also Specimens who displayed frequent changes also

showed limited copy number variation.showed limited copy number variation.

AZFAZFcc Highest mutation rates(20 rearrangements and Highest mutation rates(20 rearrangements and

mutation rate of 3.8X 10mutation rate of 3.8X 10-4)-4) . Higher variation of . Higher variation of copy number (does this correspond with copy number (does this correspond with significant mutations in this region?)significant mutations in this region?)

Very important as it bears many testes-specific Very important as it bears many testes-specific genesgenes

Many common deletions result in large sections of Many common deletions result in large sections of AZFAZFc being removedc being removed

b2/b4 deletion removes entire region most b2/b4 deletion removes entire region most common cause of spermatogenic failurecommon cause of spermatogenic failure

AZFAZFcc gr/gr mutation removes 1.6Mb, it has arose 14 times gr/gr mutation removes 1.6Mb, it has arose 14 times

independently in human genealogy.independently in human genealogy. And as deleterious mutations are usually not able to become And as deleterious mutations are usually not able to become

polymorphic this is an indicator of haploid selection being in polymorphic this is an indicator of haploid selection being in balance with homologous recombination balance with homologous recombination

b2/b3 similar to gr/gr, does not delete full copies on genes, b2/b3 similar to gr/gr, does not delete full copies on genes, and retains some copies.and retains some copies.4,54,5

Are ampliconic regions so duplicated to withstand intense Are ampliconic regions so duplicated to withstand intense natural selection?natural selection?

Are these deleterious mutations selected in conjunction with Are these deleterious mutations selected in conjunction with other Y-linked genes with positive effects on fitness?other Y-linked genes with positive effects on fitness?

Conclusions Conclusions Natural selection acts on Y in a v.different way to Natural selection acts on Y in a v.different way to

autosomes,and selects it as one unit. This allows for autosomes,and selects it as one unit. This allows for different kinetics which must be further elucidated.different kinetics which must be further elucidated.

High duplication in the MSY allows many functional genes to High duplication in the MSY allows many functional genes to be retained by homologous recombinationbe retained by homologous recombination

Direct and indirect natural selection on certain genetic units Direct and indirect natural selection on certain genetic units play in integral roleplay in integral role

Natural selection may help preserving vital spermatogenic Natural selection may help preserving vital spermatogenic genes by exerting a stabilizing selection on gene copy genes by exerting a stabilizing selection on gene copy variancevariance

Contemporary evidence points away from impending Contemporary evidence points away from impending demise hypothesis for humans.demise hypothesis for humans.

ReferencesReferences 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

http://www.nature.com/nature

high mutation rates have driven extensive structural polymorphisms among human y chromosomes

Documents