SMiLE sequencing technique was developed by Alina Iskova along with Bart Deplancke at EPFL’s Institute of Biotechnology. It basically resolves the binding motifs of single and dimeric TFs over a wide affinity range, without any restrictions of DNA bait length.
Selective Microfluidics based ligand enrichment followed by sequencing, commonly simplified as SMiLE sequencing is a novel technique to characterize protein-DNA interactions.
Transcription factors (TF) are proteins involved in converting or transcribing DNA into RNA, in the process of transcription. Therefore, they are responsible for the regulation of transcription as well as gene expression and their mutations may cause disorders.
All TFs contain at least one DNA-binding domain which attaches to a specific DNA sequence adjacent to the genes they regulate. TFs may be monomeric or dimeric, in which case they may be homodimers or heterodimers.
Furthermore, dimers may be obligate (where the TF must be present as a dimer with a specific partner in order to bind DNA) or facultative (TFs may or may not be dimers) and naturally, they behave differently as dimers than they did as monomers.
SMiLE seq technique was developed by Alina Isakova along with Bart Deplancke at EPFL’s Institute of Biotechnology. It basically resolves the binding motifs of single and dimeric TFs over a wide affinity range, without any restrictions of DNA bait length.
The results of SMiLE seq were validated by analyzing 58 full-length human, mouse, and Drosophila TFs from distinct structural classes. The core or principle of this technique is microfluidics (liquid manipulation).
Firstly, the passive loading of samples is achieved through the action of capillary pumps (integral components of passive microfluidic devices). Synthetic polymer poly-dIdC represses nonspecific interactions and is added along with DNA sequence and in vitro transcribed and translated TF.
Next, the target TF-DNA complex is isolated on a chip though immunocapturing, which is actually an antigen-antibody reaction. This is followed by selection of DNA that is specifically bound to TFs, elution (extracting one material from another by washing with a solvent) and then amplification in a PCR.
This is coupled with screening by high-throughput sequencing (screening for activity against biological targets) and Hidden Markov Model (HMM) (a statistical model) based TF motif discovery pipeline.
This technique has been applied to not only characterize already known TFs but also de novo ones like C2H2 zinc finger protein motifs. It is a very rapid and cost-effective process.
Theoretically, we can even study RNA-protein interactions. It is a new and emerging technology and has a lot of potential. As we explore new dimensions within this technique, we will be able to discover new horizons as to the feasibility and application of SMiLE seq.
This article is jointly written by Hafsa Tayyab, Summaya Lucman and Tehreem Fatima