High Mutation Rates Have Driven Extensive Structural Polymorphisms

High Mutation Rates Have Driven Extensive Structural Polymorphisms Among Human Y Chromosomes Matthew Byrnes

Outline n n n 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 n Repping et al. (2006) Distal-Yq heterochromatin and IR 3/IR 3 TSPY and AZFc n Conclusions and Summary n n

Evolution of the Y Chromosome n n n X and Y diverged from autosomes of mammalian ancestors ca. 300 MYA 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

n n n 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 n n Only 2 genes, almost identical with Xq 21, a band on the long arm of the X chromosome Caused by an eponymous transposition ca. 3 MYA after divergence with chimpanzees Large inversion within MSY short arm cleaved the region into two non-contiguous segments (total of 3. 4 Mb in length) Do not cross over during male meiosis unlike PARs.

X-degenerate region n n 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 RPS 4 Y 1 and RPS 4 Y 2 are full length homologues of X-linked gene RPS 4 X, which encode two different, full-length isoforms of ribosomal protein S 4. 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 n n By far constitutes more of the MSY than the other two classes(10. 2 Mb) and shows a significantly higher gene density than the other two regions Consists largely of 99. 9% similar sequences which maintain identity over 10 -100 Kb 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 n n 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? n n 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 10 MY(impending demise hypothesis) Contemporaneously, peers proposed integrity of Y chromosome is maintained. 1

Is the Y Chromosome Degenerating Perniciously? n n n Human ampliconic regions consist of 8 v. large palindromic sequences(9 kb-1. 45 Mb) Atleast 6 of these arose before divergence with Pan Paired arms of each palindrome separated by spacer region(2 -170 kb) Proposed that integrity of palindromic sequences is maintained by gene conversion between two arms of the same palindromic region 2 Found to be true, gene conversion confirmed by studies of P 1.

Is the Y Chromosome Degenerating Perniciously? n n n 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? n n n 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 n n n 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 USP 9 Y is vital for spermatogenesis in humans, but in Pan, it only codes for a 675 amino acid chain(cf. 2555) TMSB 4 Y (ubiquitous in humans) is not transcriptionally active at all. Both differ by negligible differences in humans

Homo vs Pan Y Chromosome Studies n n 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 n n 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) n n n 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 n n n n 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 IR 3/IR 3 TSPY AZFc

Regions of Y chromosome and conserved elements in Pan

Distal-Yq heterochromatin n n 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

IR 3/IR 3 n Was inverted in proximal Yp in 16 of the 47 chromosomes n 3. 6 Mb inversion n Attributed to ectopic homologous recombination n 12 independent inversion events n >2. 3 X 10 -4 per father-to-son transmission (same as Yq, why is this so? )

TSPY n Testes-specific protein Y-linked n Often expressed in testicular cancer n n n Showed large scale length variation. Ranged in size from 0. 47 Mb-1. 3 Mb Highly similar 20. 4 Kb repeat units of gene and transcription factor Result of multiple mutations

TSPY n n >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 n n Highest mutation rates(20 rearrangements and mutation rate of 3. 8 X 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 b 2/b 4 deletion removes entire region most common cause of spermatogenic failure

AZFc n n n gr/gr mutation removes 1. 6 Mb, 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 b 2/b 3 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 n n n 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.

n n n 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. 6 Mb deletion of human Y chromosome through balance between recurrent mutation and haploid selection. Nature genetics. vol 35 3