Explaining the Y chromosome: Definition, Structure and Function – Genetic Education

Explaining the Y chromosome: Definition, Structure and Function

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“Y chromosome is the shortest acrocentric human chromosome present only in males and has only some  important genes for maleness.” 

To understand the Y chromosome and its function precisely we need to first understand what chromosomes are and how DNA is arranged on it. 

Chromosomes are the structure made up of DNA and protein. In other words, we can say chromosomes are the structure where DNA is located, it helps total cell DNA to fit inside the cell nucleus. 

Functionally, chromosomes not only help to package DNA but also to inherited traits and other variations to offsprings. 

Related article: What is a chromosome?- definition, structure and Function.

Different species have different numbers of chromosomes, The number of chromosomes in humans’ are 46, arranged in 23 pairs. The 22 pairs are known as the autosome while a single pair of chromosome X and Y is known as the sex chromosomes or allosomes. 

Allosomes help to decide the gender of the fetus and for the development of other secondary sex characters and organs. 

Females have two X chromosomes while males have one X and one Y chromosome present as a pair of sex chromosomes. We already have discussed the autosomes in our previous article. 

The Y chromosome decides the sex of the fetus, however, it isn’t similar in some other organisms, the mechanism of sex determination is totally different and insane. In some, it’s defined by the environmental factors, while in others, by the female herself. Some are hermaphrodites having both types of sexes while in some (like us) the gender is decided by genetic factors. 

In the present article, we are going to talk about the Y chromosome. Actually, we will unfold it, know it’s structure, genes’ location and other related information. We will also learn its importance in males. 

Disclaimer: repeated use of some inappropriate words can penalize our blog, therefore we will use maleness, male gonadal development like words in the present article. 

What is the Y chromosome? 

In 1905, Nettie Stevens in collaboration with Bryn Mawr discovered sex chromosomes- X and Y in mammals. 

The Y chromosome is the smallest chromosome only present in male individuals of mammals. It’s a kind of hemizygous- single chromosome. It is inherited from fathers to their male children but not to girls or female children. 

It has very few genes present on its single-arm, in comparison with other chromosomes. 

Some information: 

  • The Y chromosome evolved before 300,000 years ago from autosomes. 
  • The Y chromosome is the smallest acrocentric chromosome 
  • The size of it is 57,227,415bp. 
  • Genes on Y chromosome: around 200 in which the structure and function of only 50 to 60 genes are known to us.
  • The centromere is located at the position of 10.4Mb. 
  • Only a single Y chromosome is present in the male individuals of the mammalian population. 
  • The Y chromosome is not present in females, usually. 


The Y chromosome is the smallest mammalian sex-determining chromosome that is responsible for maleness and decides the sex of the fetus. 

Inheritance pattern of Y chromosome: 

Genes and chromosomes follow a distinct pattern of inheritance. Interestingly, the Y chromosome follows a unique pattern of inheritance that is known as the Y-linked inheritance in which the genes on the Y chromosome only transmit from father to their male child only. 

See the image below, 

The inheritance pattern of the Y chromosome and related genes.
The inheritance pattern of the Y chromosome and related genes.

As the Y chromosome is only present in males, during the process of embryo formation it favors maleness and hence it is only present in the male individuals. 

The inheritance pattern of the Y chromosome is widely useful for tracing the lineage of only the paternal side of the whole family. 

Genes located on Y chromosomes only inherited to male individuals only that is the reason, diseases or traits associated with the Y chromosome only inherited in the male individual of the family. 

List of Y linked genes: 

Gene  Name 
SRY  Sex determining region on Y 
ZFY Zinc finger protein 
PRKY Protein kinase, Y linked 
TDF Testing determining region 
AMGL Amelogenin 
AZF1 Azoospermia factor 1
AZF2 Azoospermia factor 2
DAZ Deleted in azoospermia 
UTY Ubiquitously transcribed TPR gene on the Y chromosome 
RBM The RNA-binding motif on Y 


Structurally, the Y chromosome is a smaller- acrocentric chromosome having a short p arm and a long q arm. The p arm mostly contains genes and DNA sequences that are necessary for maleness, for example, the TDF and SRY. We will talk about it later. 

The short Yp regions are more euchromatin in nature, which is transcriptionally active. Around 95% portion of the Y chromosomes is dedicatedly present for maleness while the rest of the 5% region is known as PAR- pseudoautosomal regions. Usually, the PAR sequences are transcriptionally inactive. 

The centromere between the p and q arm helps in correct chromosomal segregation during the cell division. The centromere is also heterochromatin, a transcriptionally inactive region. 

The approximate size of the Y chromosome is 59 million base pairs with 100 to 200 known genes. However, only 40 to 75 genes’ functions are known to us. 

Usually, the Y chromosome is almost the same in all other mammals as well. 

For instance, the Y chromosome of our closest relative chimpanzee is only 30% different in terms of sequences, not size. 

Related article: Where are Genes Located? 

MSY- Male-specific region of Y: 

The major portion of the Y chromosome is made up of the euchromatin and heterochromatin regions, collectively known as male-specific regions of Y. This region possesses sequences and genes for male gonadal development, spermatogenesis, and testis development. 

The euchromatin region has SRY, TDF and AZF like genes while the heterochromatin region contains tandemly repeated SINEs sequences throughout the MSY region. 

Around 5000 copies of repetitive sequences are present in this region. 

SRY gene: 

In the MSY, on the p arm, the SRY gene is located, which is very very important for the development of maleness. 

The SRY gene is the sex-determining region on Y, located just near the pseudoautosomal region on the p arm. It has a single function exon, encodes a protein having approximately 204 amino acids. 

Structurally, the SRY gene is located within the specific region on the Y chromosome known as Testis determining region on Y- TDF having C terminus and N- terminus domain. In between the CTD and NTD domains the special type of high mobility group DNA sequence region is present, known as the SOX.

Scientists believe that the SRY gene might have evolved from the SOX gene of the X chromosome. 

The SRY gene is one of the most important genes in the pathway of male sex determination and differentiation, thus it is known as the ‘candidate gene’ in the gonadal development. 

Other DNA sequences of the male-specific regions are the TDF region, the AZF region and the heterochromatin portion of the rest of the Y chromosome. Though the heterochromatin region is noncoding DNA sequences, it regulates gene expressions. 

Now let us look at another important region excluding the MSY.  

The structure of Y chromosome.
The structure of the Y chromosome.


The PAR is known as a pseudoautosomal region located on extreme ends of Y chromosomes. The PAR on p arm is around 2.5Mb in size while the PAR on q arm is around 1Mb in size. 

The PAR region, a pseudoautosomal region, has genes homologous to the X chromosomes that take part in the recombination during meiosis cell division. During the male meiosis PAR regions of X and Y combine and exchange genetic material. 

However, the rest of the regions of Y remain conserved. 

Interesting information: 

The Y chromosome contains only 50 to 55 known genes while the X chromosome contains 900 known genes, the size of the Y chromosome is one-third of the X chromosome. 

Why Y? 

Why is it known as the Y chromosome? students wonder that this is because of its shape, but that is not true, previously, scientists had discovered a chromosome of this class and named it as ‘X’ and hence another chromosome of this class is denoted as ‘Y’. 

A ‘gene-poor’ chromosome Y only possesses 2 to 3% of the total human genome. 

Read further: DNA: Definition, Structure, Function, Evidence and Types.

Function of Y chromosome: 

Not the X but the Y chromosome is an important player, decides the sex of the fetus. The reason is, if it is present, the fetus becomes male, if not, the fetus becomes not male! 

Note that the XX chromosome is required for normal female and female gonadal development. A single X without another X or Y is known as the monosomy condition. 

Simply put, the main function of the Y chromosome, or we can say genes on the Y chromosome cause male development. The Y chromosome is responsible for primary and secondary sexual phenotypes in males. 

The SRY gene- an active region on the Y has a very fascinating function. It determines the male sex plus it favors the testis development. Another region known as the TDF- testis determining factor has a significant role in normal testicular development. 

Mutation or change in gene expression of SRY or TDF leads to abnormal genital and testis development. 

Noteworthy, the SRY is not the only gene that decides the fate of the fetus. Other autosomal and X-linked genes like SOX9,  RSPO1, WNT, WT3 and SF1 have significant effects on the development of male gonads. 

Scientifically, it is proven that mutation in any of the genres listed above, can adversely affect normal gonadal development in male. 

The region present on the q arm which is majorly the heterochromatin region also has a dedicated role in spermatogenesis. 

Spermatogenesis is a process of sperm cell formation from an immature cell. A path of spermatid to sperm formation is governed by a locus known as AZF- azoospermia factor. 

The AZF locus is comparatively larger in size than the SRY gene and thus divided into three regions; AZFa, AZFb and AZFc. mutation in the regions of AZF leads to failure in spermatogenesis, the condition is commonly known as azoospermia. 

Depending upon which region is deleted, the amount of region deleted and alteration in its gene expression is proportional to the severity of azoospermia. 

For instance, if AZFa and AZFb both regions are deleted, the condition of azoospermia is more serious for a person. Physical mapping indicated that the AZF region is located on Yq11.

Conclusively, the main function of the Y chromosome and genes located on the Y chromosome are, 

  • Development of maleness 
  • Male gonadal differentiation and development 
  • Male sex determination 
  • Sperm cell development 
  • Testis development 
  • Development of other secondary male reproductive phenotypes 

Recent studies are evidence that the Y chromosome is also involved in brain development. By expressing directly into the neural and brain tissues or via forming hormones, the SRY gene helps in the development and strengthening of the brain. 

The mystery!

It is believed that the X and Y chromosomes were not independently present in mammals in the past (i am talking about the evolution process!). The X and Y chromosomes were evolved later during the course of evolution to reserve reproductive phenotypes.

The inheritance of the Y chromosome in the male lineages of the family.
The inheritance of the Y chromosome in the male lineages of the family.

Recombination and translocation between X and Y: 

Much like autosomes, genes on the X and Y can neither perform recombination nor translocation, normally. It is harmful to the organism. The Y chromosome diverged from X just before 300 million years ago!

As we said, genes, gene expressions, and other regions on the Y chromosomes are dedicatedly working for maleness, if it translocates on the X, it causes big problems for a female. 

Suppose if some of the sequences from the SRY or the whole SRY gene is translocated on X chromosome through recombination, it adversely affects the female primary and secondary gonadal development. 

This is also true for males as well thus it is very important to protect some of the important sequences of the Y chromosomes to recombine with the X or to translocate on the X. 

However, recombination is an autonomous and natural process so it may occur. At a safe side, some of the regions as we said above, known as the PAR, are present on both ends of the Y chromosome that undergo recombination with X and protect the Y specific regions. 

Translocation of genes and chromosomal recombination is not good for normal gonadal development. 

Detection, testing and diagnosis of Y chromosomes: 

Mutations associated with the Y chromosomes or genes on it majorly cause infertility, lack of maleness and underdevelopment of secondary sex characters. 

Using several testing techniques, we can detect anomalies associated with it or diagnose the conditions. 

Detection of Y chromosome: 

There are two methods the presence or absence of Y chromosomes can be encountered viz karyotyping and Polymerase chain reaction

In the karyotyping by cell culture, incubation, harvesting and microscopic examination, the presence or absence of the Y chromosome can be determined. The karyotyping is a traditional cytogenetic method based on cell culture. 

In the polymerase chain reaction, a primer set specific to the Y chromosomes is anneal to amplify the DNA sample. 

Here SRY or any other Y DNA sequence-specific primer is designed and used for amplification. By denaturation, annealing and extension, the DNA sequence is denatured, primer annealed and new DNA synthesized. 

By agarose gel electrophoresis, the presence of amplification or Y chromosome is conformed. 

Comparatively, the PCR method is more reliable, accurate and faster than the conventional karyotyping method

Y chromosome microdeletion: 

Azoospermia can be encountered by testing the AZF regions on the q arms. A special modification in the conventional PCR technique known as the microdeletion STS PCR is used to detect Y chromosome microdeletion. 

There are many STS- sequence tag site regions or markers on the q arm of the Y chromosomes used to screen which region is deleted. 

Usually, 3 STS markers from each region (AZFa, AZFb, AZFc) are selected to cover the whole portion of the azoospermic region. 

Using the primer 3 software the STS marker specific primer sets are selected and used to amplify the region of the Y chromosome. 

If amplification will not appear, it indicates that a specific region is absent or deleted from the chromosome. 

COMET assay:

COMET assay is yet another technique used to encounter problems related to maleness. Here sperms are allowed to migrate in a gel to know the amount of DNA damaged. If a sheared band appears it indicated DNA damage, a person may face reproductive failure and related problems. 

To know more about the technique of the present essay, you can read this article: COMET assay.

Y chromosome and related disorders: 

The role of the Y chromosome in disease development is also mysterious, as we said it inherited from father to son, but the Y linked diseases may happen not only in males but also in females. Some of them are;

  1. Klinefelter syndrome- XXY 
  2. Double Y chromosome- XYY  
  3. Sex reversal

These are the three common Chromosomal disorders, we are discussing briefly here. 

Double Y chromosome: 

The XYY is not a true chromosomal problem, as there are not more serious problems associated with it. Due to the presence of an extra Y chromosome, a person may appear taller than average. However, infertility and mental and developmental problems are shown less. 

Klinefelter syndrome: 

The Klinefelter syndrome is known as the XXY and commonly observed in males. Here infertility is the main symptom of the condition. 

Due to the random process during cell division known as non-disjunction is the reason, chromosomal distribution does not occur correctly and XXY happens. 

It is reported 1 in 1,000 newly born male babies. 

The symptoms of Klinefelter syndrome included, 

  • Taller, long legs and hands. 
  • Small and firm testicles 
  • Small male genital 
  • Enlarged breast like a woman 
  • Delayed puberty 
  • Less body hair 
  • Note that the Y chromosome is not directly linked with the Klinefelter syndrome. 

Sex reversal: 

Sex reversal though reported less but a major problem directly associated with the Y chromosome. 46, XX or 46, XY sex reversal in male and female are reported 1 in 25,000 to 1 in 50,000 worldwide. It was first reported by De la chappel. 

In the sex reversal, the visible gender of the individual doesn’t match with the genetic sex. For instance, a female has 46, XY chromosomes while a male shows 46, XX chromosomes. 

Abnormal secondary sex characters, problems in sex determination, infertility and gender-related problems are common in sex reversal. 

Although the clear reason for the sex reversal is not yet known, some evidence suggests that recombination between PAR regions may translocate some important genes on wrong chromosomes. 

Related read: The XX chromosome in male: A case of sex reversal.

Y chromosome microdeletion: 

Another chromosomal aberration that is more commonly associated with the Y chromosome is a deletion of AZF region. 

Though the PCR technique is more reliable to detect it, using conventional karyotyping and FISH, microdeletions associated with Y chromosome can be detected. 

Again the symptoms of the condition ar mainly associated with infertility, dysgenesis of testis and secondary sex characters known as gonadal dysgenesis. 

Importance of the Y chromosome: 

The sex chromosome, especially the Y chromosome is more important in maleness. Features like the testosterone level, semen production, development of testis, developing male secondary sex characters, body hair and fertility are associated with the Y chromosome. 

Therefore fore to induce maleness in the womb and normal sex differentiation and determination the Y chromosome is so important. The presence of the absence of the Y chromosome is so crucial for a fetus, as it determines the gender. 

Summary of the article: 

Name  Y chromosome 
Type  Sex chromosome is known as allosomes 
Size  57,227,415bp
Number of genes  50 to 60 (known)
Important genes  SRY, TDF, AZF1, AZF2 and DAZ
Function  Development of maleness, testis, spermatogenesis, male secondary reproductive phenotypes, masculinity and other male-related phenotypes. 
Location of centromere  Acrocentric 
Present in  Male individuals 


Conclusively, we can say though the Y chromosome is the smallerst among all chromosome, its presence is very important for male individuals. However, the sex reversal like conditions are very rare, can be encountered though the microarray like state of the art techniques.


Quintana-Murci L, Fellous M. The Human Y Chromosome: The Biological Role of a “Functional Wasteland”. J Biomed Biotechnol. 2001;1(1):18-24. doi:10.1155/S1110724301000080


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