General Interview Questions - Gene Regulatory Basics

How is the expression of a gene controlled?

What is the difference between a trans and a cis regulatory factor?
How does a cell coordinate the expression of its many genes?
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1. A gene consist of DNA sequences that are transcribed and those that are not. Both transcribed and non-transcribed sequences are used to regulate gene expression. The sequences of DNA that make up a gene need not occupy a single continuous stretch of DNA.
2. The final products of genes can be RNAs or polypeptides. For genes that encode polypeptides a transitional (mRNA) RNA is produced through the processing of the primary transcript RNA.
3. Gene expression refers to the level of the final gene product that a gene produces.
4. The first step in the regulation of gene expression is the control of the number of copies of the gene's transcribed region that are synthesized. This synthesis is catalyzed by RNA polymerases.
5. A gene has at least one, and may have more than one, distinct transcription start site. Each transcription start site is defined by a distinct promoter.
6. A gene's promoter is the region of DNA that, through interactions with regulatory proteins (transaction or transcription factors), determines the binding site, binding affinity and enzymatic activity of RNA polymerase.
7. Promoters can be (semi-arbitrarily) divided into proximal and distal elements. The proximal promoter is located near the transcription start site. Distal elements are located further away from the transcription start site. In humans, promoter elements can occupy many hundreds of kilobases of DNA both 'upstream' and 'downstream' of the transcription start site.
8. It is possible that more than one gene can be present within a specific region of a DNA molecule; in fact more than one gene can use a specific DNA sequence.
9. The ability of transcription factors to recognize and bind to DNA is regulated by the binding of other transcription factors and the packing of the DNA into chromatin.
10. Once transcription begins, the amount of the final transcript that accumulates is a function of transcription, processing and degradation rates. Particularly in eukaryotes, transcript processing can be quite complex and include 5' cap addition, 3' polyadenylation, RNA splicing, RNA editing, RNA modification and RNA transport/localization within the cell.
11. Differential splicing can generate different final RNA transcripts from a single gene. If the RNA is used to direct polypeptide synthesis, different transcripts can produce related by distinct polypeptides. The pattern of splicing can itself be regulated.
12. Some transcripts are rapidly degraded, others are relatively stable. Transcript stability directly impacts gene expression.
13. mRNAs can differ in the efficiency with which they engage the translational machinery. The efficiency of an mRNA's translation can be regulated
14. Once a polypeptide is synthesized, the efficiency with which it folds or assembles into a functional protein through interactions with other polypeptides and co-factors can be regulated. Misfolded proteins are often rapidly degraded.
15.The activity of a protein can be regulated directly, through interactions with allosteric effectors, competitive inhibitors and cooperative interactions. It can be regulated indirectly by controlling the cellular localization and stability.

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