Objectives
By the end of this lesson you should be able to:
- Explain the effect of chromatin and DNA chemical modification on gene expression
- Explain your understanding of epigenetics
- Describe methods utilized by the eukaryotic cell in the regulation of transcription initiation
- Describe methods utilized by the eukaryotic cell in the regulation of gene expression after transcription
- Explain the role of non-protein-coding RNA in gene regulation
- Explain briefly, the basis of cell differentiation
- Explain the genetic basis of cancer
The eukaryotic gene can control DNA expression at many stages. In this lesson we will look at gene regulation of chromatin structure, regulation of transcription and post-transcriptional initiation, and the role of non-coding RNAs in controlling gene expression.
Regulation of Chromatin Structure
Remember that DNA is tightly wound around protein structures called nucleosomes, and that the nucleosome consists of units of proteins called histones. Each histone has a tail that protrude outwards of the nucleosome. These tails are accessible to enzymes that can add or remove chemicals from them e.g., methyl, acetyl, and phosphate groups.
Histone methylation increases DNA condensation, making it bind more tightly to the histone and hence reducing accessibility to RNA polymerase for transcription. The addition of a phosphate group to an amino acid located next to a methylated amino acid can reduce condensation. DNA acetylation reduce condensation, promoting transcription.
In addition to the modification of histones, DNA can also be directly modified. The cytosine base is typically the site of modification. Methylation of cytosine for example, is associated with inactivation of DNA transcription.
Although these chemical modifications do not affect the DNA sequence, they are transferred from one generation to another. Nevertheless, they are not permanent, but can be reversed.
The inheritance of traits that are not associated with changes in the DNA is referred to as epigenetic inheritance. Epigenetic changes can occur during the lifetime based on diet, stress, exercise and smoking. The term used to characterize all the chemical modifications to the genome is epigenome.
Regulation of Transcription Initiation
The DNA consists of non-coding sequences called control elements. They are transcription factor binding-sites also known as enhancers which turn genes on or off. Some transcription factors may be general (used for all protein coding) or specific (used for only certain types of proteins. Transcription factors may act as activators or repressors. Activators bind to enhancers to enable assembly of the transcription mechanism needed to make mRNA. Repressors may inhibit gene expression by binding to enhancers, blocking the binding of activators, or blocking the binding of activators to other proteins in the transcription mechanism.
Transcription factors may cause epigenetic changes by recruiting enzymes to methylate or acetylate histones.
Transcription initiation in different cells is also controlled by the combination of activators present. For example, a liver cell and a lens cell may share one of a number of their activators. That does not mean that they will both express the same proteins. For that to happen, they must have the same combination of activators.
Finally, transcription initiation may be controlled as a result of signals from outside the cell. For example, hormones produced outside of the cell may enter the cell and form complexes with proteins to act as activators. In some cases, the molecule does not enter the cell but sticks onto the cell surface and indirectly trigger signal transduction pathways that leads to activation of activators or repressors.
Post Transcriptional Regulation
The expression of a protein-coding gene is ultimately measured by the amount of functional protein a cell makes. The amount of functional protein is determined by processes after transcription. For example, alternate RNA spicing, mRNA degradation, and protein processing and degradation.
Alternate RNA Splicing
Different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as introns and which as exons.
mRNA Degradation
Nucleotide sequences in the untranslated region (UTR) at the 3’end of the mRNA regulates protein production by determining how long the mRNA remains intact before it degrades.
Initiation of Translation
Regulatory proteins may bind to the UTR at the 3’ or 5’ of the mRNA, preventing attachment of ribosomes. Ribosome attachment may also be inhibited when the polyA tail lacks sufficient length. Some organisms initially store mRNAs with short poly A tails but extend them at the appropriate time during embryonic development. Global regulation of mRNAs in a cell may be regulated simultaneously by activating the synthesis of protein factors required for translation.
Protein Processing and Degradation
The final opportunity for controlling gene expression occurs after translation. Often eukaryote polypeptides must be processed to produced functional proteins. Processing mechanisms may include cleavage of proteins, and chemical modification, e.g. addition of sugars and functional groups to amino acids. The length of time proteins remain active is determined be selective degradation. Generally, proteins are tagged by ubiquitin for degradation by proteasomes.
Role of Non-Coding RNAs in Controlling Gene Expression
A significant amount of the genome can be transcribed into non-protein-coding RNAs (ncRNAs). These include micro RNAs (mRNAs) and small interfering RNAs (siRNAs). They both silence gene expression by binding to mRNA and causing them to be either degraded or blocked from translation.
Fundamentals of Differential Gene Expression in Multicellular Organisms
During development, cells organize themselves into tissues, tissues organize into organs, and organs organize into organ systems. How do we get from a single cell to a complex multicellular organism with moving parts that looks and behave so differently? Consider the difference in appearance and function or your eye versus your tongue. The answer lies in gene expression. While all of our cells have the same genome, the genes they express vary depending on the location of the cell.
The process by which immature, unspecialized cells take on very specific characteristics is called cell differentiation. Cell differentiation is brought about by (1) cytoplasmic determinants and (2) external environment of the cell. These determinants include RNA, proteins and other substances in the egg. During cell division, they are unevenly distributed. This makes the cytoplasmic environment of genetically identical daughter cells different from each other. This difference will determine their pathways and ultimate fate e.g., becoming part of the brain or the kidney. Factors outside of the cell also determines its fate. For example, cell surface molecules and growth factors secreted by neighboring cells.
Genetic Basis for Cancer
Cancer is the uncontrolled division of abnormal cells in the body. It can be caused by random spontaneous mutation that alter genes that regulate the cell cycle or due to mutagens such as chemical carcinogens, X-rays, high-energy radiation, and viruses. Cancer genes are referred to as oncogenes while those that promote normal growth are called proto-oncogenes. Proto-oncogenes can be turned into oncogenes due to:
- Movement of DNA within the genome
- Amplification of proto-oncogenes
- Point-mutations in a control element or in a proto-oncogene
Cancer cells are frequently found to contain chromosomes that have broken off and rejoined in the wrong place (translocation). If a translocated proto-oncogene ends up near a promotor, its transcription will increase, making it an oncogene. Amplification increases the number of copies of proto-oncogenes. A point-mutation in the coding sequence could produce a protein product that is more resistant to mutation. If the role of that protein is to stimulate cell growth, its persistence will cause excessive cell division.
Apart from genes that promote cell growth, some genes inhibit growth. These are called tumor-suppressant genes. When these are mutated, they are unable to make tumor suppressant proteins. The cell may therefore be put on a path towards malignancy.
The proteins encoded by many proto-oncogenes and tumor-suppressing genes are components of various cell-signaling pathways. Disruption of these pathways leads to cancer. Mutations in the ras proto-oncogene and the p53 tumor suppressor genes amount to 30% and 50% of all human cancer respectively.
The ras gene is stimulated by a protein factor and produces the ras protein. The ras protein in turn participates in a metabolic cascade essential in stimulating a protein that is needed in cell division. A mutation of the ras gene causes hyperproduction of ras protein without the need of a growth factor. Proliferation of ras protein leads to excessive cell division, and hence cancer.
The p53 gene produces a transcription factor that is necessary in inhibiting the cell cycle. Mutation of p53 prevents the production of this protein. Hence, while ras gene mutation causes cancer by increasing the rate of cell division, p53 mutation causes cancer by failing to inhibit cellular division.
Viruses play a significant role in cancer development. They can donate an oncogene to the cell, disrupt a tumor suppressor gene, convert a proto-oncogene to an oncogene, and produce proteins that inactivate p53 and other tumor-suppressing genes. We will focus on viruses in our next study.
Reference: Reece, J. B., & Campbell, N. A. (2011). Campbell biology. Boston: Benjamin Cummings / Pearson.
