Gene Expression

1. Gene Expression Biology for Majors

2. Regulating Gene Expression All cells control or regulate the synthesis of proteins from information encoded in their DNA. The process of turning on a gene to produce RNA and protein is called gene expression.  The regulation of gene expression conserves energy and space.  Gene regulation is how a cell controls which genes, out of the many genes in its genome, are “turned on” (expressed). Thanks to gene regulation, each cell type in your body has a different set of active genes—despite the fact that almost all the cells of your body contain the exact same DNA.

3. Gene Regulation Different cells have different genes “turned on.”

4. Factors that Affect Gene Expression A cell’s gene expression pattern is determined by information from both inside and outside the cell. • Examples of information from inside the cell: the proteins it inherited from its mother cell, whether its DNA is damaged, and how much ATP it has. • Examples of information from outside the cell: chemical signals from other cells, mechanical signals from the extracellular matrix, and nutrient levels.

5. How Cells Respond Cells have molecular pathways that convert information —such as the binding of a chemical signal to its receptor—into a change in gene expression, as in the growth factor at right.

6. How Cells Respond Diagram Explained • The cell detects the growth factor through physical binding of the growth factor to a receptor protein on the cell surface. • Binding of the growth factor causes the receptor to change shape, triggering a series of chemical events in the cell that activate proteins called transcription factors. • The transcription factors bind to certain sequences of DNA in the nucleus and cause transcription of cell division-related genes. • The products of these genes are various types of proteins that make the cell divide (drive cell growth and/or push the cell forward in the cell cycle).

7. Gene Regulation in Prokaryotes Prokaryotic transcription and translation occur simultaneously in the cytoplasm, and regulation occurs at the transcriptional level.

8. Gene Regulation in Eukaryotes Eukaryotic gene expression is regulated during transcription and RNA processing, which take place in the nucleus, and during protein translation, which takes place in the cytoplasm. Further regulation may occur through post-translational modifications of proteins.

9. Differences in the Regulation of Gene Expression of Prokaryotic and Eukaryotic Organisms

10. Regulatory Molecules in Prokaryotes The DNA of prokaryotes is organized into a circular chromosome supercoiled in the nucleoid region of the cell cytoplasm. Proteins that are needed for a specific function are encoded together in blocks called operons. In prokaryotic cells, there are three types of regulatory molecules that can affect the expression of operons: • Repressors - proteins that suppress transcription of a gene in response to an external stimulus • Activators - proteins that increase the transcription of a gene in response to an external stimulus • Inducers - small molecules that either activate or repress transcription depending on the needs of the cell and the availability of substrate

11. Operons in Prokaryotes In prokaryotes, structural genes of related function are often organized together on the genome and transcribed together under the control of a single promoter. The operon’s regulatory region includes both the promoter and the operator. If a repressor binds to the operator, then the structural genes will not be transcribed. Alternatively, activators may bind to the regulatory region, enhancing transcription.

12. The trp Operon: A Repressor Operon

13. CAP: An Activator Regulator When glucose levels fall, E. coli may use other sugars for fuel but must transcribe new genes to do so. As glucose supplies become limited, cAMP levels increase. 

14. The lac Operon: An Inducer Operon

15. Eukaryotic Epigenetic Gene Regulation Epigenetic mechanisms control access to the chromosomal region to allow genes to be turned on or off. These mechanisms control how DNA is packed into the nucleus by regulating how tightly the DNA is wound around histone proteins. The addition or removal of chemical modifications (or flags) to histone proteins or DNA signals to the cell to open or close a chromosomal region. Therefore, eukaryotic cells can control whether a gene is expressed by controlling accessibility to transcription factors and the binding of RNA polymerase to initiate transcription.

16. Histones and Nucleosomes DNA is folded around histone proteins to create (a) nucleosome complexes. These nucleosomes control the access of proteins to the underlying DNA. When viewed through an electron microscope (b), the nucleosomes look like beads on a string.

17. Histonesand Gene Expression When nucleosomes are spaced closely together (top), transcription factors cannot bind and gene expression is turned off. When the nucleosomes are spaced far apart (bottom), transcription factors can bind. Changes to the histones and DNA affect nucleosome spacing.

18. Epigenetics Histone proteins and DNA nucleotides can be modified chemically. Changes affect nucleosome spacing and gene expression.

19. Are these changes permanent? The changes that occur to the histone proteins and DNA do not alter the nucleotide sequence and are not permanent. Instead, these changes are temporary (although they often persist through multiple rounds of cell division) and alter the chromosomal structure (open or closed) as needed. 

20. Eukaryotic Transcription Gene Regulation To start transcription, general transcription factors, such as TFIID, TFIIH, and others, must first bind to the TATA box and recruit RNA polymerase to that location. The binding of additional regulatory transcription factors to cis-acting elements will either increase or prevent transcription. In addition to promoter sequences, enhancer regions help augment transcription. Enhancers can be upstream, downstream, within a gene itself, or on other chromosomes. Transcription factors bind to enhancer regions to increase or prevent transcription.

21. Enhancer An enhancer is a DNA sequence that promotes transcription. Each enhancer is made up of short DNA sequences called distal control elements. Activators bound to the distal control elements interact with mediator proteins and transcription factors. Two different genes may have the same promoter but different distal control elements, enabling differential gene expression.

22. Post-transcriptional Control Post-transcriptional control can occur at any stage after transcription, including RNA splicing, nuclear shuttling, and RNA stability. Once RNA is transcribed, it must be processed to create a mature RNA that is ready to be translated. This involves the removal of introns that do not code for protein. Spliceosomes bind to the signals that mark the exon/intron border to remove the introns and ligate the exons together. Once this occurs, the RNA is mature and can be translated. RNA is created and spliced in the nucleus, but needs to be transported to the cytoplasm to be translated. RNA is transported to the cytoplasm through the nuclear pore complex.

23. Splicing Pre-mRNA can be alternatively spliced to create different proteins.

24. Modes of Gene Splicing

25. Control of RNA Stability The protein-coding region of mRNA is flanked by 5′ and 3′ untranslated regions (UTRs). The presence of RNA-binding proteins at the 5′ or 3′ UTR influences the stability of the RNA molecule.

26. RNA Stability Once the RNA is in the cytoplasm, the length of time it resides there before being degraded, called RNA stability, can also be altered to control the overall amount of protein that is synthesized. T he RNA stability can be increased, leading to longer residency time in the cytoplasm, or decreased, leading to shortened time and less protein synthesis. RNA stability is controlled by RNA-binding proteins (RPBs) and microRNAs (miRNAs). These RPBs and miRNAs bind to the 5′ UTR or the 3′ UTR of the RNA to increase or decrease RNA stability. Depending on the RBP, the stability can be increased or decreased significantly; however, miRNAs always decrease stability and promote decay.

27. Practice Question Why did cells evolve gene regulation?

28. Quick Review • Why doesn’t every cell express all of its genes? • How are prokaryotic and eukaryotic gene regulation similar and different? • What are the steps in gene regulation in prokaryotic cells? • What is the role of repressors in negative gene regulation? What is the role of activators and inducers in positive gene regulation • How does epigenetic regulation work? • What is the role of transcription factors in gene regulation? • What is RNA splicing and how does it regulate gene expression? • How is RNA stability important in gene regulation?