“Rethinking the Rotting Y ”

Sex Chromosome Evolution: Y as Rotting X

SRY SRY SRY

A pair of X Y X Y X Y autosomes

1 Nature 415, 963 (2002) The future of sex R. John Aitken and Jennifer A. Marshal Graves

“The is particularly vulnerable … because it is not a matching partner for the X chromosome, so it cannot retrieve lost genetic information by recombination….

The original Y chromosome contained around 1,500 , but during the ensuing 300 million years all but about 50 were inactivated or lost….

At the present rate of decay, the Y chromosome will self-destruct in around 10 million years.”

2 The Human Y Chromosome: An early map

Testis Determining Factor (TDF) Three Stooges Appreciation (Curly Stimulation Factor, CSF) Channel Flipping (FLP) p Catching And Throwing (BLZ1) CEN Self-confidence (BLZ2) (unlinked to ability) Ability to remember and tell jokes (GOT1) q Sports Page (BUD-E) Addiction to death & destruction movies (T-2) Air Guitar (RIF) Ability to Identify Aircraft (DC-10) Preadolescent fascination with Arachnida/Reptilia (MOM-4U) Spitting (P2E) Sitting on toilet reading (linked to Sports Page) Inability to express affection over the phone (ME-2) Selective hearing loss (HUH) heterochromatin Total lack of recall for dates (OOPS)

The MSY, the Male-Specific Region of the Human Y Chromosome

Euchromatin 23 Mb  1% of Heterochromatin p q

The MSY differs from other nuclear : - specific to one sex - no crossing over

3 Spermatogenic Specialization of MSY Revealed by Genomics Analyses

• DNA sequence of chromosome

• Catalog of genes

• Y deletions  spermatogenic failure

Tomoko Helen Kuroda- Skaletsky Kawaguchi

David Page

4 MSY Euchromatin: Three Sequence Classes

X-transposed (99% X-Y identity) X-degenerate Ampliconic p q

Y-specific repeated blocks (amplicons) comprise one third of MSY’s euchromatic DNA

Considerations in Sequencing the Euchromatic MSY 1. Y-specific repeats ("amplicons") of unknown number, structure, and unit length may account for 1/3 of euchromatic MSY Vollrath et al., Science 258: 52 (1992) Foote et al., Science 258: 60 (1992)

2. Amplicon-rich regions of MSY contain genes; should not be ignored Reijo et al., Nature Genet. 10: 383 (1995) Lahn & Page, Science 278: 675 (1997)

3. Case of DAZ genes suggested that MSY amplicons might be >99% (even 99.9%) identical in DNA sequence Saxena et al., Nature Genet. 14: 292 (1996) Saxena et al., Genomics 67: 256 (2000) 4. Polymorphic differences between Y chromosomes in two men (0.1%) might approximate sequence divergence among amplicons within one Y chromosome

5 Disentangling Amplicon Copies Differing by as Little as 1 per 10,000 bp

one chromosome  no polymorphism

BAC mapping BAC sequencing (BACs comparable to amplicons in length)

big overlaps between sequenced BACs  detect map assembly errors

no tolerance for sequence discrepancies between overlapping BACs

accurate final assembly (~1 error / Mb)

Ampliconic Sequences Defined by High Similarity to Other MSY Sequences

100 100

75 75

Intrachromosomal 50 50 similarity (% identity) 1 Mb

6 18 Single-Copy MSY Genes with X Homologs

PCDH11Y RPS4Y2 SRY RPS4Y ZFY TGIF2LY AMELY TBL1Y PRKY USP9Y DBY UTY TMSB4Y NLGN4Y CYorf15A CYorf15B SMCY EIF1AY

Most of these X-Y genes are ubiquitously expressed. All are located outside the ampliconic regions.

9 Testis-Specific MSY Families: 60 Members, All Located in Amplicons

TSPY

RBMY

VCY

XKRY

CDY

HSFY

PRY

BPY2

DAZ

7 And most of the testis genes are in palindromes...

Structure of an MSY Palindrome

99.9% - 99.99% identity

1 or more testis genes

1 or more testis genes testis more or 1 up to 1.5 million bp

8 8 Palindromes and 1 Inverted Repeat Comprise 25% of MSY Euchromatin

VCY XKRY HSFY RBMY PRY CDY BPY2 DAZ

Yp Yq 867 54IR2 32 1

DNA Sequence Dot Plot: An Ampliconic Region vs. Itself

window: 500 bp stringency: 500 bp P1

P3 P2 cen qter 1 Mb

9 Uniform AZFc Deletions Detected in Azoospermic Males

cen qter t2 g1 r4 t1 r1 r2 r3 u1 b1 b3 y1 y2 b4 u2 b2 u3 g2 g3 1 Mb

3.5 Mb AZFc Deletions Caused by Homologous Recombination Between 229 kb Direct Repeats

window: 500 bp stringency: 500 bp 99.9%

P1 1 Mb

P3 P 2 cen qter recombination targets

10 In silico Fractionation of MSY Euchromatic DNA

0.20 0.20

0.15 0.15

0.10 0.10 sequence 0.05 0.05

Fraction of euchromatic 0.00 0.00 90 95 98 70 80 99 99.9 100.0 Intrachromosomal similarity (% identity) 30% of euchromatin displays > 99.9% identity to other MSY sequences

Intact Testis Genes Located in  99.9% Fraction of MSY; Pseudogenes Located Throughout # of intact genes with # of pseudogenes with  99.9% identity to other MSY < 99.9%  99.9% < 99.9% sequences DAZ 4 0 0 0 CDY 4 0 17 4 PRY 2 0 4 0 BPY2 3 0 many many RBMY 6 0 6 17 HSFY 2 0 0 0 VCY 2 0 0 0 XKRY 2 0 6 0 Total 25 0 >33 >21

11 > 99.9% arm-to-arm identity in MSY palindromes implies either: 1) very recent origin (~100,000 yrs ago) or 2) ongoing homogenization via nonreciprocal recombination

Do the “same” (orthologous) palindromes exist on chimp Y chromosome?

Gene Conversion

- a result of homologous recombination; initiated by double strand breaks

- nonreciprocal transfer of info from one DNA duplex to another (as opposed to crossing over, which is reciprocal)

- between homologs, sister chromatids, or repeats on a single chromosome

- can occur in meiosis or mitosis

12 Concerted Evolution of MSY Palindrome Arms

0.021 % 0.028 %

1.44 %

Human Chimpanzee

Arm-to-Arm Gene Conversion in our Species

T T C T C C

M34 M117

M58 M123 M78 M81 M9M922 M134 M50 pSRY373 USP9Y+3636 SRY10831

DYS271 M35 M67M6 7 M1M122 M82 M122 M119 M95 M76 M124 M3 M173

M118 M75 YAPPN2 M172 M52 M175 USP9Y+3178 M20 M4 M45

M13 M51 M9 M170 p12f M69 M9

M144 M109 M112 YAP RPS4Y711 M89

M32 M14 M60 M168 M91 SRY10831 C T

13 MSY Gene Conversion

- 30% of euchromatic DNA

- maintains > 99.9 % DNA identity

- approx. 600 bp per generation

- molecular mechanism unknown

- recombination partners in inverted orientation (e.g., palindromes)

- 8 of 9 testis-specific gene families (2, 4, 6 … rule)

- speculation: preserves gene function in absence of sex (ual recombination)

Two Forms of Productive Recombination in Human Y Chromosome

Male-specific region Yp Yq

1. X-Y crossing-over in pseudoautosomal regions

2. Y-Y gene conversion in portions of MSY that exhibit >99.9% intrachromosomal identity

14 Old and New Understandings of the MSY ~76 protein-coding genes  genetic wasteland 27 distinct proteins; spermatogenic specialization

many genes imported (from merely a rotting copy of autosomes and X) during primate an ancient autosome evolution; gene amplification

gene-rich palindromes of full of junky repeats unprecedented scale + precision no productive recombination gene conversion  method of  all genes disintegrating preserving gene integrity? (Muller’s Ratchet)

Primates Carnivores H. sapiens

Marsupials Rodents Monotremes

Birds

Amphibians Reptiles

Fishes Vertebrate genomes: Chordata Completed, in progress or pending

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