The field of genetics is all set to receive a massive boost thanks to a new technology that will help speed up the characterization of DNA-binding proteins while also increasing the accuracy and efficiency of the process.
Transcription factors play a major role when it comes to production of proteins from the code embedded into our DNA. For the production of proteins, genes must first be transcribed from DNA into RNA and this is where the transcription factors are required.
Mammals — including humans — have between 1300-2000 transcription factors, many of which combine with others into “heterodimers” in order to bind genes and induce their transcription into RNA. Since one transcription factor can pair up with different ones depending on the cell type in which they are active, the number of possible combinations can be very high.
Because of their sheer number, their ability to combine into different pairs, and the technical difficulty to study their DNA-binding properties in the lab, we still know very little about many transcription factors despite extensive efforts.
This is where the latest work by Ecole Polytechnique Fédérale De Lausanne scientists comes in as they have developed microfluidics-based technique that can greatly speed up the process with a minimum of materials needed, and that can be extended to other molecules and research e.g. analyzing protein-RNA interactions.
The new study has been published in Nature Methods wherein they have shown how they have used the technique to determine the DNA binding properties of over 60 transcription factors including nine new ones. The lab of Bart Deplancke at EPFL’s Institute of Biotechnology has invented a new technique called SMiLE-seq, which can greatly speed up the process with only tiny amounts of transcription factors needed. The technique makes use of microfluidics, which is the science of controlling tiny amounts of liquids in equally tiny spaces. Microfluidics is fast-becoming an area of excellence at EPFL, bringing together a number of different fields and disciplines.
SMiLE-seq works by attaching small amounts of the transcription factor (or factors when probing heterodimers) in a microfluidic device — this is a chip with micrometer-size channels that allow liquid to flow through. Once the transcription factors are attached to the chip’s surface, a large library of random DNA is gently pumped into the chip and flows over them. This allows the transcription factors to recognize their corresponding DNA sequences. Thereafter, the transcription factor-DNA complex is physically trapped by dropping down a microfluidically steered button, while the DNA that is not bound is simply washed away.
Next, the bound DNA is taken off the device and prepared for sequencing to identify which part of it got caught by the transcription factors. This information is fed into specialized software that allows researchers to work out the DNA-binding properties of the transcription factors or heterodimers. In turn, this helps to better predict their in vivo DNA-binding profiles.
The use of microfluidics in SMiLE-seq offers three main advantages: First, it cuts down on the amount of transcription factors needed for this type of experiment, as it only needs picograms of them. Second, it speeds up the process considerably, from days to less than an hour. And finally, SMiLE-seq is not limited by neither the length of the DNA target sequence, nor is it biased toward stronger affinity protein-DNA interactions as current methods can be.
Deplancke’s team used SMiLE-seq on 67 full-length human, mouse, and Drosophila transcription factors, successfully analyzing several that were never studied before. In the future, he intends to exploit the technique’s versatility into other molecules, such as RNA. His team has filed a patent, and a startup is in the works to take the technological concept of SMiLE-seq into the commercial world.