Please answer #2. Short paper #1 Describe the basics of how transcriptional regu

Question

Please answer #2.

Short paper #1 Describe the basics of how transcriptional regulation of gene expression occurs and can lead to differential gene expression during development. Include how a gene regulatory network is established and is involved in specification of cell fate and differentiation. What is modular control of transcription? If you have isolated a gene expressed in two tissues, say the thyroid and tongue, how would you use reporter constructs to identify the sequences important in regulating expression in the two tissues? What would you expect to find? If you have identified a gene encoding a protein you think might be important in heart development, how would you determine if the protein functions in the heart? Describe three types of evidence. 1. 2. 3.

Explanation / Answer

Answer 2) Transcription is a process in which information from a DNA strand is copied to a Ribonucleic acid (RNA) transcript, important for the gene expression. The eukaryotic transcription process is regulated by several factors. Modular control of transcription is due to these transcription factors which bind to the specific Deoxyribonucleic acid (DNA) sequences and switch on/off the transcription accordingly. The transcription factors adhere to the DNA with the help of the most common DNA-binding protein domain known as the zinc finger motifs. For controlling gene expression, these array of zinc finger motifs bind to the specific DNA sequences that can be introduced to a synthetic promoter. This transcriptional control is dependent on RNA polymerase binding onto the promoter controlled by several well studied protein domains. Enhancers and insulators affect the transcription process by recruiting and blocking the binding of RNA polymerase respectively.

Assays of reporter genes have been effectively proven to study the level of gene expression. A reporter gene acts as a 'tag' for another gene or DNA sequence of interest. The target sequence to be tracked can be easily known by monitoring the reporter gene expression. It eases in locating the genes in the body which have been tagged by the reporter. It also helps in accessing the varying and differential expression of the tagged gene in different tissues of the body. For instance, beta-galactosidase gene (lacZ) is one such reporter gene, whose activity can be monitored and detected by a color change in the indicator plates. This process is done by inserting a promoter 'upstream' of the reporter gene in a vector, then the vector is transfected into an organism. By analyzing the expression of the reporter, one can decide the tissues in which the tagged promoter is functional. Another common reporter gene used encodes a green fluorescent protein (GFP). The tissues which show the gene expression emit a distinguishable green fluorescent light. Hence, in the given question, for identifying the location of the genes expressed in the tongue and thyroid regions, one can construct a vector by adding a reporter gene to it as discussed above. Examination and analysis of the gene expression can also be done by northern blot analysis. As a result, we can find differential gene expression in both the tissues.

The transcriptional control function—recruiting or blocking RNA polymerase binding—is performed by protein domains already known to exhibit the function (in this case the VP16 activator domain). Interaction between TFs is fostered by incorporating protein-protein interaction domains. Since they were working in yeast, the authors of this particular paper used animal protein domains that interact in pairs. This allowed for cooperative binding, where the binding of one TF encourages binding of others to nearby sites, increasing efficiency.

TFs will be an integral part of the devices that can result from integrating synthetic biology with systems biology2. Mimicking existing cells, large regulatory networks with many TFs could be made possible by a modular toolkit.

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