DNA Higher-Order Structure Formation

A team of molecular biologists working within the Department of Biological Sciences at The Korea Advanced Institute of Science and Technology (KAIST) has conducted a new study that has revealed how chromatin is formed by using a specific mechanism that uses energy to regulate histone placement onto DNA.

DNA molecule

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The details of their breakthrough were published last November in the journal, Nature Communications. What the team achieved with their innovative study will likely assist in gaining a deeper understanding of how cancers and developmental disorders are established and progress.

Potentially, information attained about the chromatin may eventually help develop new therapies for these illnesses.

The underlying machinery of higher-order DNA structures has eluded scientists

Higher-order structures of DNA are essential to the proper functioning of cells, with abnormalities in the regulation of these structures being linked with developmental disorders and cancer. However, the complexity of the underlying machinery of these higher-order structures has remained elusive. A team of scientists in Korea aimed to uncover an entirely new level of molecular detail of chromatin, the structure that encases DNA.

Chromatin is the higher-order structure that encompasses each cell’s genetic blueprint, its DNA. Within chromatin, the DNA is tightly wrapped around histone proteins, which are capable of efficiently fitting the lengthy DNA strands into a relatively small space.

Also, chromatin plays a key role in regulating the exposure or enclosure or specific genes by allowing the DNA to be locally wound or unwound, thereby governing the genetic expression of a cell, which is vital for normal cell functioning.

Abnormalities of the workings of the chromatin, therefore, are linked with disease. Specifically, cancer and developmental disorders have been associated with chromatin dysregulation. Scientists have recognized that accessing finer-grain detail around the molecular mechanisms of chromatin formation is essential to advancing our understanding of these illnesses, and with increased knowledge comes the potential of developing more effective treatments.

Investigating histone chaperones

The team focused their research on specific proteins known as histone chaperones. During the process of DNA packing, these proteins play an essential role in adding and removing specific histones at exactly the right times, maintaining genome integrity and gene expression states.

Mistakes made here can lead to aberrant DNA replication or defects in gene expression. Because of their key role in DNA packing, histone chaperones are also vital to the assembly and disassembly of the nucleosome, which is the basic repeating unit of chromatin.

Previous research has concluded that histone chaperones prevent histone aggregation and unintended interactions by acting as molecular escorts. What the KAIST team wanted to find out is how histone chaperones use chemical energy when assembling and disassembling nucleosomes.

Currently, only one histone chaperone has been proven to utilize ATP (adenosine triphosphate), a chaperone known as Abo1. Found in abundance in yeast, Abo1 also has an analogous partner known as ATAD2 which is found in humans. Both of these chaperones use ATP as a source of energy.

While ATP is well known to be the power source for cellular activity, it is incredibly rare to find it being used by histone chaperones. All other histone chaperones that have been studied so far do not use ATP at all.

In the study published on Nature Communications, the KAIST team used the DNA curtain assay, a single-molecule fluorescence imaging technique, to visualize the structure of Abo1.

Imaging the histone chaperone with this technique allowed researchers to observe the protein interactions that occur at the level of the single-molecule.

The scientists prepared the molecules of DNA and proteins on a single layer of a microfluidic chamber and viewed their interactions using fluorescence microscopy.

The results

By observing the behavior of Abo1 in real-time using fluorescence microscopy the team was able to determine that this particular histone chaperone is ring-shaped and modifies its structure to facilitate the loading of individual histones onto DNA.

They also saw that ADP (adenosine diphosphate) was the source of power for these structural changes.

Overall, the study successfully uncovered the underlying mechanism by which the Abo1 histone chaperone accommodates specific histones, using ADP as a source of energy to load these histones onto DNA, enabling nucleosome assembly.

Future research

Following the success of their project, researchers at KAIST plan to continue investigating the mechanisms that allow energy-dependent histone chaperones to bind and release histones.

The long-term goal of this research is to facilitate the development of new therapeutics to treat cancer-related abnormalities in Abo1's human counterpart, ATAD2.

Sources:

  • Burgess, R. and Zhang, Z. (2013). Histone chaperones in nucleosome assembly and human disease. Nature Structural & Molecular Biology, 20(1), pp.14-22. https://www.nature.com/articles/nsmb.2461
  • Cho, C., Jang, J., Kang, Y., Watanabe, H., Uchihashi, T., Kim, S., Kato, K., Lee, J. and Song, J. (2019). Structural basis of nucleosome assembly by the Abo1 AAA+ ATPase histone chaperone. Nature Communications, 10(1). https://www.nature.com/articles/s41467-019-13743-9
  • Das, C., Tyler, J. and Churchill, M. (2010). The histone shuffle: histone chaperones in an energetic dance. Trends in Biochemical Sciences, 35(9), pp.476-489. www.cell.com/.../S0968-0004(10)00070-8

Further Reading

Last Updated: Mar 18, 2020

Sarah Moore

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Sarah Moore

After studying Psychology and then Neuroscience, Sarah quickly found her enjoyment for researching and writing research papers; turning to a passion to connect ideas with people through writing.

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