Why do calico cats look so funky? Geneticists explain.

Ever wondered why calico cats have that unique speckled pattern on their fur?

It appears that inactivation or "silencing" of one of the X chromosomes (cells of female mammals contain two X chromosomes) gives their fur that orange and black patchwork or "tortoiseshell" pattern, according to a team of researchers from the University of California, San Francisco (UCSF). The researchers will present their results at the 58th Annual Biophysical Society Meeting, between Feb. 15 and Feb. 19, in San Francisco.

Out of the two X chromosomes females have, one X chromosome is "turned off." In the case of calicos, one X chromosome carries an orange fur color gene and another one carries a black fur color gene. The random inactivation of one of the X's in each cell results in the cat's patchwork pattern. But researchers still do not know how "silencing" of one of the X chromosomes occurs.

"Silencing" can also help researchers better understand epigenetic inheritance, in which the DNA sequences remain unchanged but heritable changes are brought about by other mechanisms. 

Such "gene activity can be inherited without changing the DNA code," said Elizabeth Smith, a member of the team carrying out the study and a postdoctoral fellow working in Carolyn Larabell's lab in the anatomy department at UCSF. "It can help answer other questions such as if and how traits like obesity can be passed down through generations."

To further understand the process of inactivation in X chromosomes – the effect of which is so pronounced among calico cats – the team had to first image the chromosomes in their natural position within an intact cell.

"A cell's nucleus contains the genetic code, its DNA. But while the structure of the DNA was determined more than 50 years ago, and we're rapidly determining the position of specific genes on chromosomes, no one had visualized the DNA within an intact nucleus – an unfixed, hydrated whole cell," explained Dr. Smith. "We decided to try."

Smith and her team examined immortalized mouse cell lines (immortalized cell lines are types of cells that can be made to grow for long periods for experimental purposes and are used in many biological experiments).  Using the process of vitrification (a superfast freezing process that prevents cell damage) Smith ensured that the nucleus of the cell was kept intact. After the cell was preserved, it was first imaged with a fluorescence microscope, followed by an X-ray microscope, Smith told the Monitor.

Using this "correlated imaging" technique, scientists could obtain a high-resolution, three-dimensional view of the intact nucleus. "We were able to identify one specific chromosome, the inactive X chromosome of female cells," Smith said.

The researchers also observed variations in the biomolecular density and topography of the nucleus, Smith said.

The high biomolecular density of this inactive X chromosome could explain why this X chromosome is inactive in the first place, Smith added.

The research is still in a ascent stage, and preliminary studies have been done on mouse cell lines. If developed, Smith said, this research could be replicated in other organisms, too. "With new fluorescent probes, we can start identifying the position of specific genes in context – inside the tangled network of DNA within the intact nucleus," she said.