Fruit fly: novel method to study nuclear matrix
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The nuclear matrix is a scaffolding that helps package the genome differently in different types of cells

August 27, 2022 07:30 pm | Updated 07:30 pm IST

A Drosophila cell showing oozing out of genomic DNA (in blue and green) upon extraction with high salt. After treatment, what stays is the meshwork of nuclear architecture.

A Drosophila cell showing oozing out of genomic DNA (in blue and green) upon extraction with high salt. After treatment, what stays is the meshwork of nuclear architecture.

Every cell that makes up an organism contains a copy of its genome. This genome is packaged in special ways with the help of a structure known as the nuclear matrix. The nuclear matrix gives an organisation and architecture to the nucleus. A familiar figure, the nuclear matrix of fruit flies, for instance, has been studied for many years, mainly by isolating it in nuclei that have been taken out from fruit fly embryos.

Now, using a novel method, a group of researchers from CSIR-Centre for Cellular and Molecular Biology, Hyderabad (CCMB) and Tata Institute for Genetics and Society, Bengaluru (TIGS), have established a way of studying the nuclear matrix of the fruit fly ( Drosophila melanogaster) without removing the nucleus from the embryo.

This allows comparative study of nuclear matrix in different cells within the embryo, giving a boost for fruit fly genetics.

Two of the most recent papers on this work have been published in the journals Nucleus and Molecular and Cell Proteomics.

Nuclear matrix

The nuclear matrix is like a scaffolding. Using biochemical means, if the nucleus is taken out and treated with an enzyme that digests all the DNA, then washed with a solution of high salt concentration so that viable DNA proteins or protein-protein interactions are removed, what is then left is a fibrous meshwork of proteins called the nuclear matrix. This is like a building from which all movables have been sucked out, leaving only the beams, ceiling, walls, plug points, etc.

Analogous to the building, the nuclear matrix creates the architecture in which the genome is packaged.

“The genome is in the nucleus, embedded and protected by the jelly-like nuclear matrix. This is a dynamic material providing access for the regulation of different genes in different cells. Studying the nuclear matrix is, therefore, very important to get a better picture of how precisely development progresses every time a new individual is born,” says Prof. Shashidhara, an India developmental biologist working at IISER, Pune, who was not involved in this study.

Packaged differently

“We have 220 different types of cells in the body, but all contain identical genomes,” says Dr. Rakesh Mishra, Director of TIGS, who led the research. “The same genome sequence is present in neurons, where it works for thinking; in the liver, the same sequence enacts metabolism; and in the intestine, it works to digest. So, this information is packaged differently in different cell types,” he explains.

To give an example that justifies the different way in which the genome is folded and packaged in different types of cell, consider proteases. These are enzymes that digest proteins and are active in the intestine. The intestine contains a lining that prevents these enzymes from digesting the proteins present there, thereby protecting the intestine. The same are found in the brain cells also. If they were allowed to be active, they would digest the brain cells which do not have the protective epithelium, and that would be disastrous. So, the genome, despite carrying all the genetic material, is packaged such that some genetic material is hidden in such a way that it is never seen by transcription machinery.

“This can happen only by packaging in such a way that something becomes so dense and interior that it is not seen,” says Dr. Mishra. “Our body has about 220 different kinds of cells. So, that means the same genome can be packaged in 220 different ways.”

NuMat preparation

The researchers collect embryos which are between zero and 16 hours old. They make, for the first time, the in situ nuclear matrix preparation using this entire collection of embryos. Then, they image them. Some are in very early developmental stages, where they are made up of nuclei only, or just making a mono layer of nuclei across the embryos or have gone through differentiation. The array is made available in one preparation.

“Depending upon your interest, you can look at mitotic waves and different stages of cell cycle; you can choose the early embryos, when they are dividing; or if you want to look at more specialised kind of cells, then you can see them in late embryogenesis,” says Dr. Mishra.

New avenues

“So far, much of the work in this area was by tracking single molecules such as DNA-binding regulatory proteins, typically, studying one at a time. This new method will open new avenues for studying complex regulatory processes,” says Prof. Shashidhara.

This method opens the whole field of Drosophila genetics to study nuclear organisation or nuclear architecture using genetic and cell biology approaches, which was limited earlier only to biochemical approaches.

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