Tag Archives: 3D-SIM

High res imaging of DNA double strand breaks: Clearing the nucleus or marking the spot

DNA can be damaged in many ways. Consequently, there are numerous mechanisms to repair it. It is a fascinating field full of innovative concepts (“DNA repair” was my favorite course during my undergrad studies).  Double strand breaks (DSBs) are considered the most genotoxic, which is why many DNA damaging drugs and treatments intended to treat cancer are intended to create DSBs. On the other hand, DSBs can lead to chromosome translocations which can promote cancer, and can actually be viewed as a hallmark of cancer cells. DSBs also occur naturally during recombination events at Meiosis, and are important intermediates in immune system development.

DSBs are recognized by repair complexes that act to mark and repair the damage. Though the sequence of event has been studied biochemically, knowledge on the in vivo temporal and spatial arrangement has been limited due to lack of good high-res methods to visualize DSBs and repair proteins at DBS sites.

Two papers recently published take two different approaches to get  high-resolution images of events at DSBs.

The first paper, from Stephen Jackson’s lab, implemented a simple method to reduce the background fluorescence in the nucleus, thus increasing the signal/noise ratio. They study the non-homologous end joining (NHEJ) process which initiates with the Ku complex recognizing the DSB, followed by recruitment of the DNA dependent protein kinase (DNA-PK) and ending with ligation by XRCC4. DNA-PK phosphorylates the histone H2AX near DSB (gamma-H2AX). This is a known marker for DSB.

They used laser illumination to create a streak of DSB, and immunofluorescence (IF) against gamma-H2AX and Ku. They used a buffer called CSK that is known to release soluble proteins, thus removing background. Though the gamma-H2AX appears as a clear streak, Ku is all over the nucleus. Ku is also an RNA binding protein. So they added an RNase to the CSK wash. Miraculously, only DNA-bound Ku was now visible.

Look at the image – it looks amazing!

Hi-res image of Ku at DSB

Addition of RNase to the CSK buffer during IF allows for high-resolution imaging of DNA repair proteins. Source: Britton et al (2013) JCB vol 202(3):579-595.

Using this simple upgrade to the protocol, which removed most of the background, and combined with 3D structured illumination (3D-SIM) super resolution microscopy*, they were able to study co-localization (here’s a video), measure distances and study composition of different components of the repair complex. They also used Ku foci count to asses the effect of different drugs on DSBs repair efficiency.

I found this paper important mostly because  this simple improvement in their protocol yielded a vast improvement in imaging. This technique could be useful for studying many other nuclear processes which involve proteins that associate with both DNA and RNA (e.g. transcription complexes).

The second paper, from Tom Misteli’s lab, took a very different approach. They wanted to see sites of chromosomal translocations  following DSBs. First, instead of getting random, or multiple DSBs using drugs, radiation or laser (as in Jackson’s paper), they introduced restriction sites for the rare-cutting IsceI restriction enzyme. One site, on chromosome 7, was surrounded by multiple repeats (256) of the LacO sequence. Other sites, on chromosomes 1 & 10, were surrounded by 96 TetO repeats. The LacO and TetO arrays can be viewed by fusion of GFP to the Lac repressor (which binds LacO) and mCherry to the Tet repressor which binds TetO. Thus, each potential DSB site is marked by a fluorescent array in distinct colors. Expression of ISceI enzyme from a plasmid induces DSB. They then followed the temporal position of the green and red spots, until they get co-localization of the colors – meaning chromosomal translocation has occurred.

Time-Lapse microscopy of cells after transfection with ISceI enzyme, showing the translocation of two distinct sites (marked by GFP and mCherry) into a co-localized spot. Source: Roukus et al. (2013) Science vol 341:660-664.

Time-Lapse microscopy of cells after transfection with ISceI enzyme, showing the translocation of two distinct sites (marked by GFP and mCherry) into a co-localized spot. Source: Roukus et al. (2013) Science vol 341:660-664.

Like in Jackson’s paper, they used this system to look at temporal and spatial events, including recruitment of proteins (tagged with a third color: BFP), and to study the effect of different mechanisms that perturb the DSB repair machinery.

In conclusion: both approaches yielded beautiful and informative images about DSBs behavior and repair. Jackson’s method has a more global and immediate application, since it can be used to study other nuclear processes. Misteli’s system requires a lot of “genetic engineering” but can provide a more precise temporal resolution (since it enables live-cell imaging, unlike Jackson’s modified IF which only uses fixed cells). Misteli’s method can also provide insight into specificity (studying DSBs at specific genomic locations). These arrays can also be used to study chromosome dynamics (i.e. movements within the nucleus, during cell division, or transport of specific genomic regions during transcription induction e.g. to the nuclear pore complex). I am actually using such an array myself, to mark the location of my gene of interest.

* 3D-SIM uses laser light that passes through an optical grating. A series of images created by these striped patterns, generated at high spatial frequency, can then be processed by a computer algorithm into a high resolution imaging. See ref. below for more details.

ResearchBlogging.orgBritton S, Coates J, & Jackson SP (2013). A new method for high-resolution imaging of Ku foci to decipher mechanisms of DNA double-strand break repair. The Journal of cell biology, 202 (3), 579-95 PMID: 23897892
Roukos V, Voss TC, Schmidt CK, Lee S, Wangsa D, & Misteli T (2013). Spatial dynamics of chromosome translocations in living cells. Science (New York, N.Y.), 341 (6146), 660-4 PMID: 23929981
Schermelleh L, Heintzmann R, & Leonhardt H (2010). A guide to super-resolution fluorescence microscopy. The Journal of cell biology, 190 (2), 165-75 PMID: 20643879