To better learn transcription factors through SMiLE-seq

EPFL scientists have developed a technique through recombinant rat proteins to make DNA-binding proteins faster, more accurate and more efficient. The results were published in the Jan. 16 issue of Nature-Methods.

The gene contains the DNA code used to produce all the proteins in the cell. To begin the process, the gene must first be transcribed from DNA into RNA. This requires a huge family of DNA-binding proteins called transcription factors, which are of great interest to biologists because of their importance in gene expression. However, due to their pure numbers, their ability to combine into pairs and the difficulty of studying their DNA binding properties in the lab, scientists have known little about transcription factors despite of much effort.

The Bart Deplancke lab at the EPLL Institute of Biotechnology has now invented a new technology called SMiLE-seq, which can greatly accelerate the process with a small amount of transcription factors. The technology uses microfluidics: the science of controlling minute liquids in the same tiny space. Microfluidics is fast becoming an outstanding area of ??EPFL, bringing together many different fields and disciplines.

SMiLE-seq works by adding a small amount of transcription factors (or factors when detecting heterodimers) in microfluidic devices that have microchannel-sized chips that allow liquid to flow therethrough. Once the transcription factor is attached to the surface of the chip, large libraries of random DNA are gently pumped into the chip and flow through them. This allows the transcription factor to recognize its corresponding DNA sequence. Thereafter, the transcription factor-DNA complex is physically captured by dropping the microfluidic control button, and the unbound DNA is simply washed off.

Next, the bound DNA is removed from the device and ready for sequencing to identify which portion is captured by the transcription factor. This information is input into specialized software that allows the researcher to determine the DNA binding properties of transcription factors or heterodimers. This, in turn, helps to better predict the in vivo DNA binding profile.

The use of microfluidics in SMiLE-seq offers three major advantages: First, it reduces the amount of transcription factor required for this type of experiment because it only requires their picogram. Second, it greatly accelerated the experimental process, from a few days to less than an hour. Finally, SMiLE-seq is not limited by the length of the DNA target sequence, nor is it biased towards a stronger affinity protein-DNA interaction. Flarebio provides you with high-quality recombinant proteins like recombinant NPP1 at competitive prices.