Human genetic makeup consists of 23 pairs of chromosomes with nearly 30,000 genes that codes proteins which determine traits from eye colour to risk for hereditary diseases. Genes are embedded into six feet DNA which are looped inside chromosomes into each and every chromosome.
Chromosomes are twisted into loops and then structured into many large domains called Topologically Associating Domains (TADs). Inside each TAD, numerous genes and the elements that control them are packaged together, and they are insulated from those in neighbouring TADs.
Dr. Elphège Nora, a postdoctoral researcher at the Gladstone Institute of Cardiovascular Disease, said that TADs were like adjacent rooms like the genes in each TAD and people in each room could talk to one another but not to people next door.
Dr. Nora expressed that in previous work they showed that TADs packaged genes together and insulated them from neighbouring genes. What controlled this TAD organization was the next hot topic of researchers.
Dr. Nora and co-authors revealed in their new study that the key to organizing these TADs is a protein named CTCF (also known as 11-zinc finger protein or CCCTC-binding factor).
Senior author Dr. Benoit Bruneau, professor and senior investigator at the University
of California, San Francisco, at the Gladstone Institute of Cardiovascular Disease said that CTCF was an interesting protein and it could be found at the boundaries of TAD domains which were previously thought to be involved in many phases of chromosome organisation. He was also curious to see what would happen to the structure of chromosomes if all the CTCF were removed from the cells.Many studies were undertaken on the role of CTCF, by the scientists, in the past since it was very much essential for the survival of the cell. Thus, completely removing CTCF would cause cells to die, making them impossible to study.
Dr. Nora explained that they used a new genetic method to completely eliminate CTCF in mammalian cells and using that technique they destroyed the protein quickly so that they could study cells before they die which allowed them to look at the entire genome in the absence of CTCF and noted the effects.
The importance of CTCF for the insulation of TADs was demonstrated by the team.
Dr. Nora said that in the absence of CTCF protein they observed that the insulating edges of TAD domains had almost completely disappeared so that the genes and regulatory elements could now interact with those in adjacent TADs, which would be like removing the walls between adjacent rooms and allowing people to freely interact with their neighbours. It was indicated that CTCF is required for insulating TADs from one another, but not for wrapping genes within these domains, since the absence of CTCF had little or no effect on how genes connects within a single TAD. This has become the first conclusive study to show that the two mechanisms are separate and controlled by different proteins.
Now that the authors have a way of removing CTCF from cells, and disrupting the organization of TADs, they can initiate studying its effect on various characteristics of the genome.
They explored this new capacity to examine other levels of chromosome organization.
Dr. Nora said they looked at a level of organisation called compartmentalisation which separated active and inactive genes within the nucleus. This helped the cell which genes could be used. For example, skins cells don’t need eye-related genes, so these genes would be tightly packaged in a compartment and put away, because the cell will never use them.
Dr. Bruneau said that they had thought that boundaries of TAD domains were a prerequisite for the organisation of those compartments but for their surprise they found that was not the case. When they deleted the CTCF protein which caused TAD boundaries to disappear they saw no effect on the compartmentalisation.
Dr. Bruneau said that the finding revealed that CTCF and TAD structure were not required for compartmentalisation but rather it was an independent mechanism which was responsible for chromosome organisation.
With this background, the conclusion stated was that the root cause of several diseases could be evaluated, as chromosome association — including TADs — was often disrupted in many cancers and involved in significant developmental defects, such as congenital heart disease.
