Y Chromosome
Specialised chromosomes determine birth sex in humans and other mammals.
Females have a pair of X chromosomes, whereas males have a single X and a much smaller Y chromosome.
The Y chromosome is male-determining because it bears a gene called SRY, which directs the development of a ridge of cells into a testis in the embryo.
The embryonic testis make male hormones, and these hormones direct the development of male features in a baby boy.
Without a Y chromosome and a SRY gene, the same ridge of cells develops into an ovary in XX embryos.
Female hormones then direct the development of female features in the baby girl.
The Y chromosome is very different from X and the 22 other chromosomes of the human genome.
Y chromosome is smaller and bears few genes (only 27 compared to about 1,000 on the X).
These genes include SRY, a few genes required to make sperm, and several genes that seem to be critical for life – many of which have partners on the X.
Many Y genes (including the sperm genes RBMY and DAZ) are present in multiple copies.
Some Y genes occur in weird loops in which the sequence is inverted and genetic accidents that duplicate or delete genes are common.
The Y also has a lot of DNA sequences that don’t seem to contribute to traits.
This “junk DNA” is comprised of highly repetitive sequences that derive from bits and pieces of old viruses, dead genes and very simple runs of a few bases repeated over and over.
This last DNA class occupies big chunks of the Y that literally glow in the dark; you can see it down the microscope because it preferentially binds fluorescent dyes.
Sequencing of Y Chromosome
It’s only recently that new technology has allowed sequencing of bases along individual long DNA molecules, producing long-reads of thousands of bases.
These longer reads are easier to distinguish and can therefore be assembled more easily, handling the confusing repetitions and loops of the Y chromosome.
The Y is the last human chromosome to have been sequenced end-to-end, or T2T (telomere-to-telomere).
Even with long-read technology, assembling the DNA bits was often ambiguous, and researchers had to make several attempts at difficult regions – particularly the highly repetitive region.
Implications from the sequencing
A few new genes have been discovered, but these are extra copies of genes that were already known to exist in multiple copies.
The border of the pseudoautosomal region (which is shared with the X) has been pushed a bit further toward the tip of the Y chromosome.
We now know the structure of the centromere (a region of the chromosome that pulls copies apart when the cell divides), and have a complete readout of the complex mixture of repetitive sequences in the fluorescent end of the Y.
Some groups will now examine the details of Y genes.
They will look for sequences that might control how SRY and the sperm genes are expressed, and to see whether genes that have X partners have retained the same functions or evolved new ones.
Others will closely examine the repeated sequences to determine where and how they originated, and why they were amplified.
Many groups will also analyse the Y chromosomes of men from different corners of the world to detect signs of degeneration, or recent evolution of function.
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