After decades of research aiming to understand how DNA is usually organized in human cells, scientists at the Gladstone Institutes have shed brand new light on This specific mysterious field by discovering how a key protein helps control gene organization.
Humans have nearly 30,000 genes of which determine traits via eye coloration to risk for hereditary diseases. Those genes sit along six feet of DNA, which are carefully organized into chromosomes as well as stuffed into each as well as every microscopic human cell.
“The extreme compacting of DNA into chromosomes is usually like taking a telephone cord of which stretches via San Francisco to brand new York, as well as stuffing of which into a backpack,” described Benoit Bruneau, PhD, a senior investigator at Gladstone as well as lead author of a brand new study. “The organization of chromosomes is usually not random, yet rather very complex, as well as of which is usually critical for normal development. When This specific process goes wrong, of which can contribute to various diseases.”
How is usually our DNA organized?
Chromosomes are coiled into loops as well as then organized into many large domains called topologically associating domains, or TADs. Within each TAD, several genes as well as the elements of which regulate them are packaged together, as well as they are insulated via those in neighboring TADs.
“Imagine TADs are like adjoining rooms: like the genes in each TAD, people in each room can talk to one another, yet not to people within the next room,” explained Elphège Nora, PhD, postdoctoral scholar in Bruneau’s laboratory as well as first author of the study. “In previous work, we showed of which TADs package genes together as well as insulate them via neighboring genes. The burning question then became: what controls This specific TAD organization?”
within the brand new study, published within the renowned scientific journal Cell, the scientists discovered of which the key to organizing these TADs is usually a protein called CTCF.
“CTCF is usually a fascinating protein,” said Bruneau, who is usually also a professor at the University of California, San Francisco. “of which can be found at the boundaries of TAD domains, as well as was previously thought to be involved in many aspects of chromosome organization. We wanted to see what might happen to the structure of chromosomes if we removed all the CTCF via cells.”
CTCF: observing a protein of which is usually impossible to study
Researchers have struggled with studying the role of CTCF within the past, because of which is usually absolutely essential to cells’ survival. Therefore, completely removing CTCF might cause cells to die, producing them impossible to study.
“We used a brand new genetic method to completely eliminate CTCF in mammalian cells,” said Nora. “Using This specific technique, we destroyed the protein very quickly to ensure of which we could study the cells before they died. This specific allowed us to look at the entire genome within the absence of CTCF as well as observe the effects.”
In collaboration that has a team of computational biologists led by Leonid A. Mirny at the Massachusetts Institute of Technology, as well as a team of biochemists led by Job Dekker at the University of Massachusetts Medical School, the Gladstone scientists demonstrated the importance of CTCF for the insulation of TADs.
“We noticed of which, within the absence of the CTCF protein, the insulating boundaries of TAD domains had almost fully disappeared, to ensure of which genes as well as regulatory elements could right now interact with those in adjacent TADs,” added Nora. “This specific might be like removing the wall between adjoining rooms, to ensure of which people could right now freely interact with others within the neighboring room.”
However, the absence of CTCF had little effect on how genes connect within 1 TAD. This specific indicates of which CTCF is usually required for insulating TADs via one another, yet not for packaging genes within these domains. This specific represents the first conclusive study to show of which the two mechanisms are separate as well as controlled by different proteins.
Redefining our understanding of CTCF
right now of which the scientists finally had a way of removing CTCF via cells, as well as disrupting the organization of TADs, they could start studying its impact on various aspects of the genome. They leveraged This specific brand new ability to examine additional levels of chromosome organization.
“We looked at a level of organization called compartmentalization, which separates active as well as inactive genes within a cell nucleus,” said Nora. “This specific helps the cell identify which genes to use. For example, skins cells don’t need eye-related genes, so these genes might be tightly packaged in a compartment as well as put away, because the cell will never use them. We used to think of which boundaries of TAD domains were a prerequisite for the organization of these compartments.”
“To our surprise, we found of which is usually not the case,” said Bruneau. “When we deleted the CTCF protein, which caused TAD boundaries to disappear, we saw no effect on the organization of the larger compartments. This specific interesting finding revealed of which CTCF as well as TAD structure are not required for compartmentalization yet, rather, of which an independent mechanism is usually responsible just for This specific chromosome organization.”
“Our findings redefine the role of CTCF in gene regulation as well as provide brand new insights about the fundamental processes of which govern genome organization” added Bruneau. “With This specific knowledge, we can right now start reevaluating the cause of several diseases, as chromosome organization-including TADs-is usually often disrupted in many cancers as well as involved in significant developmental defects, such as congenital heart disease.”
Prior to its publication within the peer-reviewed journal Cell, a preliminary edition of the study was posted on bioRxiv, an open-access distribution service for unpublished preprints within the life sciences, as well as downloaded nearly 5,000 times over the past few months.
“Websites like these offer brand new, exciting, as well as more direct ways to share research results,” said Bruneau. “of which also provided us with valuable input of which helped shape our final manuscript as well as future research.”
Protein factors tie the genome up in a bow for gene expression