Gene regulatory codes are usually read by certain types of proteins. In fact, it is the transcription factor that is usually assimilated and read by such proteins. Most of these proteins have been discovered. Nonetheless, the sequence followed by the transcription factors has not been vividly understood.
The main purpose of the experiment was to analyze and determine how human transcription factors are specifically bound by DNA. The researchers sought to examine how human TFs undergo the DNA binding process. While there are numerous techniques that may be used in this assessment, the researchers opted to apply both Chip sequencing and SELEX.
In most experimental studies of this nature, each transcription factor has a target gene. The genes should be cataloged in order to comprehend transcriptional networks that regulate the growth and development of animals. In addition, pathological and physiological aspects should be well understood before undertaking such an experiment.
After attaining the stability of an environment, a simple model may be used to determine central transcription factors. For instance, early embryonic development is a typical example of a stable environment. Chromatin immunoprecipitation and classical genetics are well known and effective methods for examining human transcriptional networks.
Genome is the central point of attachment for transcriptional factors. It might be a complex exercise trying to understand the binding system and patterns of transcriptional factors. However, a principled biochemical model that depends on mass action and affinity might be instrumental in comprehending the whole process.
Moreover, the position of binding cannot offer an accurate explanation of why transcriptional factors choose to bond in specific locations. All the likely DNA sequences influence the affinity of a binding specificity model.
Development and disease are directly affected by transcriptional regulation. In spite of this importance, minimal and less conclusive experimental studies have been done in this area. Most human transcriptional factors have been systematically analyzed in the methodology and result sections of this work. In the methodology section, DBDs and the full-length transcriptional factors demonstrated that the basic DNA-binding specificity is defined by DBD in most cases. Besides, individual DNA and transcriptional factors interact on their own without necessarily relying on each other. When it comes to A or T residues, a strong base interdependence is observed.
After carrying out an experiment on the binding nature of mammalian transcription factors, crucial outcomes, or results were obtained. To begin with, an assay of TF-DNA binding specificity in a Genome scale indicated that a total of 303 human DBDs were sufficiently enriched. Similar enrichment results were obtained from the human full-length and mouse experiments. On the other hand, the low success rate was recorded in two of the large transcriptional factors family. For most HMG proteins that were not being bound systematically, consistent results were obtained.
Both the ratio method and SELEX generated similar matrix results. From past studies, homodimers and monomers are bound in a similar way, and eventually, a strong orientation between the two structures is visible. A sum of 830 binding profiles was obtained by the researchers.
Results also indicate that similar sequences are bound by isolated BDBs and full-length transcriptional factors. This implies that TF-binding specificities can be precisely determined by analyzing DBDs. Moreover, 15.6 bits of data were contained in PWMs after assessing the coverage and width of the model.
In conclusion, it is vital to reiterate that binding specifications have unique coverage and outstanding similarities. High confidence human transcriptional factors can be retrieved and used to evaluate the coverage while KL distance analyzes PWMs that contain proteins.