unusual structure of y

chromosome

PRESENTED BY: SOMASHREE DAS

STREAM: M.Sc BIOTECHNOLOGY

(4TH SEMESTER)

Ms ramaiah college of arts, science and commerce

Department of biotechnology

1/

UNUSUAL STRUCTURE OF Y CHROMOSOME

INTRODUCTION

The Y chromosome is one of two sex chromosomes (allosomes) in mammals, including humans, and many other animals.

The Y chromosome was identified as a sex-determining chromosome by Nettie Stevens at Bryn MawrCollege in 1905 during a study of the mealworm Tenebrio molitor.

Y is the sex-determining chromosome in many species, since it is the presence or absence of Y that determines the male or female sex of offspring produced in sexual reproduction.

In mammals, the Y chromosome contains the gene SRY, which triggers testis development.

The DNA in the human Y chromosome is composed of about 59 million base pairs.

The Y chromosome is passed only from father to son.

With a 30% difference between humans and chimpanzees, the Y chromosome is one of the fastest-evolving parts of the human genome.

To date, over 200 Y-linked genes have been identified.

MSRCASC (Dept. of Biotechnology) 2/22

Y CHROMOSOME IN HUMAN MALE KARYOTYPE

SOURCE: WIKIPEDIA

MSRCASC (DEPT. OF BIOTECHNOLOGY) 3/22

UNUSUAL STRUCTURE OF Y CHROMOSOME

ORIGIN

The X and Y chromosomes are thought to have evolved from a pair of identical chromosomes,

termed autosomes, when an ancestral mammal developed an allelic variation, a so-called "sex

locus“ – simply possessing this allele caused the organism to be male.

The chromosome with this allele became the Y chromosome, while the other member of the pair

became the X chromosome.

MSRCASC (Dept. of Biotechnology) 4/22

UNUSUAL STRUCTURE OF Y CHROMOSOME

THE Y CHROMOSOMEIn Humans:-

In human beings, two homologous regions exist, one at either end of the X and Y chromosomes,

allowing the chromosomes to pair during meiosis. These regions are termed as

“pseudoautosomal”.

In humans, the Y chromosome spans about 58 million base pairs and represents approximately

1% of the total DNA in a male cell.

The human Y chromosome contains over 200 genes, at least 72 of which code for proteins.

Traits that are inherited via the Y chromosome are called holandric traits.

Some cells, especially in older men and smokers, lack a Y chromosome. It has been found that

men with a higher percentage of hematopoietic stem cells in blood lacking the Y chromosome

have a higher risk of certain cancers and have a shorter life expectancy.

Men with "loss of Y" have been found to die 5.5 years earlier on average than others. Thus Y

chromosome plays a role going beyond sex determination and reproduction.

MSRCASC (Dept. of Biotechnology) 5/22

unusual structure of y chromosome

In Drosophila:-

The Drosophila Y chromosome is known to carry genes for atleast 6 fertility factors, 2 on the

short arm (ks-1 and ks-2) and 4 on the long arm (kl-1, kl-2, kl-3 and kl-5).

The Y chromosome carries two other known genes: bobbed, which is a locus of ribosomal

RNA genes (the nucleolar organizer) and Suppressor of Stellate or Su (Ste), a gene required

for RNA splicing.

The fertility factors code for proteins needed during spermatogenesis.

E.g:- kl-5 codes for part of the dynein motor needed for sperm flagellar movement.

MSRCASC (Dept. of Biotechnology) 6/22

UNUSUAL STRUCTURE OF Y CHROMOSOME

NON COMBINING REGION OF Y

The human Y chromosome is normally unable to recombine with the X chromosome, except for small pieces of pseudoautosomal regions at the telomeres (which comprise about 5% of the chromosome's length).

These regions are relics of ancient homology between the X and Y chromosomes.

The bulk of the Y chromosome, which does not recombine, is called the "NRY", or non-recombining region of the Y chromosome.

The single-nucleotide polymorphisms (SNPs) in this region are used to trace direct paternal ancestral lines.

MSRCASC (Dept. of Biotechnology) 7/22

UNUSUAL STRUCTURE OF Y CHROMOSOME

THE HUMAN Y CHROMOSOME

Genes encoded on the human Y chromosome include:

NRY, with corresponding gene on X chromosome

AMELY/AMELX (amelogenin)

RPS4Y1/RPS4Y2/RPS4X (Ribosomal protein S4)

NRY, other

AZF1 (azoospermia factor 1)

BPY2 (basic protein on the Y chromosome)

DAZ1 (deleted in azoospermia)

DAZ2

PRKY (protein kinase, Y-linked)

RBMY1A1

SRY (sex-determining region)

TSPY (testis-specific protein)

USP9Y

UTY (ubiquitously transcribed TPR gene on Y chromosome)

ZFY (zinc finger protein)

MSRCASC (Dept. of Biotechnology) 8/22

Unusual structure of y chromosome

Y chromosome

SOURCE: Principles of Genetics-Tamarin

MSRCASC (Dept. of Biotechnology) 9/22

UNUSUAL STRUCTURE OF Y CHROMOSOME

THE BIZZARE PART OF THE HUMAN

GENOME The Y chromosome is probably the most bizarre part of the human genome, reflecting its

unique status as a huge block of largely non-recombining DNA, maintained in a permanently

heterozygous state, and transmitted solely through males.

HJ Muller inferred that the X and Y were originally homologous chromosomes, and that the Y

had lost most of the genes that it once contained, in response to its lack of recombinational

exchange with the X and its permanent heterozygosity.

It is also now known that Y chromosomes have evolved independently in many different

groups of animals and plants that have sex chromosomes; the Y chromosomes of mammals

share a common origin with each other, but have nothing in common with their counterparts in

birds or Drosophila.

In addition, Y chromosomes tend to be unusually rich in repetitive DNA, which is contributed

both by transposable elements and by tandem arrays of satellite DNA sequences.

Much of the human Y chromosome consists of heterochromatin, made up entirely of such

repeats.

MSRCASC (Dept. of Biotechnology) 10/22

SOURCE: genomebiology.biomedcentral.com

The structure of the human Y chromosome . The black regions at each end of the Y chromosome

are the pseudoautosomal regions, which cross over with homologous sequences on the X

chromosome. The gray regions are heterochromatin. The white region contains the 23 megabase

portion of the Y chromosome sequenced by Skaletsky et al.

MSRCASC (Dept. of Biotechnology) 11/22

UNUSUAL STRUCTURE OF Y CHROMOSOME

THE HUMAN Y CHROMOSOME HAS AN UNUSUAL

STRUCTURE….

The Y and the X chromosome have originated a few hundred millions years ago from the same ancestral autosome.

The two then diverged in sequence such that today only relatively short sequences at either end of the Y chromosome are homologous to the corresponding regions of the X chromosome.

The remaining 95% of the modern-day Y chromosome is male specific and is designated as MSY (male specific region of Y).

The MSY region is a mosaic of heterochromatic sequences and three classes of euchromaticsequences.

1. X-transposed

2. X-degenerate

3. Ampliconic

MSRCASC (Dept. of Biotechnology) 12/22

Unusual structure of y chromosome

1. X-transposed: The X-transposed sequences are 99% identical to DNA sequences in Xq21,a band in the midst of the long arm of the human X chromosome. The X-transposed sequences exhibit the lowest density of genes. The rest of this region are populated with repeat elements including Alu (transposons -jumping genes, each consisting of 300 bases), retroviral (deposited by virus via reverse transcription), and LINE1 (long interspersed nuclear element 1).

2. X-degenerate:They display between 60% and 96% sequence identity to their X-linked homologues, and seem to be surviving relics of ancient autosomes (non-sex chromosomes) from which the X and Y chromosome co-evolved. The sex-determining gene SRY was introduced into this region 300 million years ago.

3. The ampliconic region - The ampliconic sequences exhibit by far the highest density of genes.

Ampliconic genes were derived through three converging processes:

amplification of X-degenerate genes (RBMY, VCY)

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

retroposition and amplification of autosomal genes (CDY).

It is suggested that since these genes never received maintenance through "crossover" ("recombination"), the integrity is maintained via swapping between these copies in a process called "gene conversion".

MSRCASC (Dept. of Biotechnology) 13/22

Unusual structure of y chromosome

Structure of the Y chromosome with each sub-structure represented by different colour.

Source: universe-review.ca/R11-14-Ychromosome.htm

MSRCASC (Dept. of Biotechnology) 14/22

Unusual structure of y chromosome

About 15% of the MSY consists of X-transposed sequences and they are still 99% identical to their X chromosome counterparts.

These sequences are dominated by a high proportion of dispersed repetitive sequences and contain only two genes.

A further 20% of the MSY consists of X-degenerate sequences that are most distantly related to the X chromosome and has higher gene content than X-transposed sequences.

The remainder of MSY consists of a web of Y-specific repetitive sequences (amplicons) that make up a series of palindromes.

The ampliconic DNA has the highest gene content and a very high pseudogene content compared with the rest of the MSY.

Three regions in MSY called AZFa, b, and c, are recognized to be vital for sperm development. Deletions of any of these regions will cause spermatogenic failure.

MSRCASC (Dept. of Biotechnology) 15/22

UNUSUAL STRUCTURE OF Y CHROMOSOME

Y Chromosome Evolution

Source: universe-review.ca/R11-14-Ychromosome.htm

MSRCASC (Dept. of Biotechnology) 16/22

UNUSUAL STRUCTURE OF Y CHROMOSOME

PALINDROMES ON Y CHROMOSOME Palindromes - It is a segment of DNA in which the nucleotide sequence in one strand read from

one end is the same as the sequence in the complementary strand read from the opposite end.

E.g: the sequence GGTACC is a palindrome when the complementary strand is CCATGG.

These palindromes come in a range of sizes, upto 3Mb in length, with the two arms of the

palindrome having 99.9% identity.

Source: universe-review.ca/R11-14-Ychromosome.htm

MSRCASC (Dept. of Biotechnology) 17/22

UNUSUAL STRUCTURE OF Y CHROMOSOME

The Y chromosome repeats are organized as palindromes, with two very similar long sequences

pointing in opposite directions, connected by a 'spacer‘.

There is very little sequence divergence between the arms of the palindromes, compared to the

divergence between human and chimpanzee sequences. This strongly suggests that there is

ongoing gene conversion between the arms, maintaining their sequence similarity.

A consequence of the existence of the palindromes is that ongoing gene conversion will inhibit

the spread by genetic drift of a deleterious mutation through just one of the two arms, allowing

selection to preserve the functionality of both copies.

MSRCASC (Dept. of Biotechnology) 18/22

Unusual structure of y chromosome

Source: genomebiology.biomedcentral.com

MSRCASC (Dept. of Biotechnology) 19/22

UNUSUAL STRUCTURE OF Y CHROMOSOME

CONCLUSION

The organization of the human Y chromosome thus reflects a combination of several evolutionary processes: the degeneration of the bulk of the genes, which were originally common to the primeval X/Y chromosome pair; the accumulation of genes with male-specific functions by sporadic transpositions from the X chromosome and autosomes; and a unique recent transposition of a large piece of X chromosomal material.

Some species have indeed lost all trace of the Y chromosome, so that males are XO, not XY. But this can happen only if the male-determining function of the Y chromosome is abolished and is replaced by an X/autosome-balance sex-determination system of the kind found in Drosophila .

In the terminal stages of the degeneration of the Y chromosome, other chromosomes increasingly take over genes and functions formerly associated with it. Finally, the Y chromosome disappears entirely, and a new sex-determining system arises.

MSRCASC (Dept. of Biotechnology) 20/22

UNUSUAL STRUCTURE OF Y CHROMOSOME

REFERENCES

Principles of Genetics- Tamarin

The organization and evolution of the human Y chromosome, Genome Biology, BioMed Central

Ltd 2003

Wikipedia-Y chromosome

https://universe-review.ca/R11-14-Ychromosome.htm

MSRCASC (Dept. of Biotechnology) 21/22

THANK YOU…..