DNA break, a multi-scale dance

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02/21/2019
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Inspiration from Judith Miné-Hattab's research at the Columbia University Medical Center, New York, USA, and at the Ecole Normale Supérieure in Paris (iBens).
Increased chromatin mobility in response to DNA damage

The genetic information that defines living organisms is stored in one of the most amazing molecule: the DNA. The information contained in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). These chemical bases are aligned in the form of a long fiber. The order of these bases determines the information necessary for building and maintaining aliving organism, similar to the way in which letters of the alphabet appear in a certain order to form words and sentences.Human DNA consists of about 3 billion bases stored in each of our cells nucleus; unfolded, this DNA measures 2 meters andhas to fit inside a 10mm diameter nucleus. How a 2 meters fiber can fit inside a sphere 200 000 times smaller in diameter remains unclear.

Inside cell’s nucleus, DNA is highly packed into large-scale structures that occupy distinct domains of the nucleus.The3-dimenstionnal DNA organization is a key contributor to genome functions: in particular, it allows the sequences of active genes to be more accessible while inactive genes are less accessible. Importantly, DNA organization is profoundly altered in cells from diseased tissue, thus it is crucial to understand how this organization is regulated.

During the life of a cell, our genome is constantly damaged by a variety of agents such as UV light or chemical agents. Among the most genotoxic injuries, double-strand breaks have dramatic outcomes for the cell. Failure torepair a single double-strand break leads to either cell death or genomic instability and cancer. Eukaryoticorganisms use two major mechanisms to repair double strand breaks, among them, homologous recombination. Homologous recombination uses an intact DNA carrying the same sequence (called homologous sequence) to repair the damaged DNA molecules. For this process to succeed, the damaged sequence has to find an intact homologous DNA and uses it as a template to restore the damaged genetic information. The search for a homologous DNA across the genome is amazingly efficient considering how densely DNA is packed inside nucleus. Taken the large size of our genome, searching a homologous DNA sequence across the whole genome would be equivalent to searching a specific sentence into 10 volumes of “Les Miserables”.Once homology is found, the damaged DNA invades the intact DNA homologous sequence, ultimately restoring genetic information disrupted at the damaged site.

Using baker’s yeast as a model system, we have recently investigated the mobility of DNA inside living cells by microscopy. To explore chromosome mobility in the context of DNA repair in vivo, we marked fluorescently two homologous sites in baker’s yeast cells and measured their dynamics before and after induction of a double-strand break.We found that DNA “giggles” much more in the presence of double strand breaks in the genome (Miné-Hattab et al, 2012). The most affect sequence in the genome is the damaged site, which can explore a nuclear volume 10 times larger. However, surprisingly, we found that even undamaged DNA is also more mobile: in other words, DNA damage provokes a global change in DNA dynamics affecting the entire genome. Such increased DNA mobility facilitates the pairing between initially distant homologous DNA sequences.

More recently, using fast microscopy, we investigated DNA mobility at several time scales, up to 1000 times faster than previously observed (Miné-Hattab et al., MBoC 2017). These experiments revealed that DNA motion is more complex than what we have previously described. Indeed, we show that damaged DNA moves differently at different time scales. Our results indicate that DNA become globally stiffer following DNA damage, this effect being stronger at the damaged site. We proposed that upon DNA damage, DNA end acts like a “needle in a globally stiffer ball of yarn”, enabling it to escape adjacent obstacles more efficiently.

 

References:

Increased chromosome mobility facilitates homology search during recombination.Miné-Hattab et al., Nat Cell Biol. 2012.

Multi-scale tracking reveals scale-dependent chromatin dynamics after DNA damage. Miné-Hattab et al., Mol Biol Cell. 2017.

Multi-scale tracking reveals scale-dependent chromatin dynamics after DNA damage.

Miné-Hattab et al., Mol Biol Cell. 2017.