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Department of Biological and Environmental Sciences

Cell & Molecular Biology
Dr. David A. Johnson
Biol 405    4 Credits   Spring 2017  MWF 11:45-12:50 AM   PH

The Regulation of Gene Expression I: Changes in Gene Copy Number

Gene Expression is Regulated: When a gene is expressed, that means a specific polypeptide (protein) encoded by that gene is being made. Not all possible proteins are made all of the time or in all tissues. For example, the globin genes of human hemoglobin are differentially expressed. Adult hemoglobin is made up of two α globins and two β globins plus 4 iron-containing heme molecules. However, the β globin is replaced by similar β-like globins, the γ globin (α2γ2) in the embryo. So, before birth, the expression of the β gene is turned off, then after birth it is switched on. Conversely, the expression of the γ gene is turned on before birth, then it is switched off. This is temporal regulation of gene expression. That is, the expression of a gene (in a given tissue) is being switched on or off over time. Globin gene regulation also illustrates spatial regulation of gene expression, which is called tissue specific gene expression. For example, the expression of the γ gene in liver is great (the gene is "on") at 12 weeks after conception, but at that same time in a different tissue, like the bone marrow or spleen, the expression of the γ globin gene is nil (the gene is "off"). This illustrates tissue-specific regulation of gene expression. Just how does the regulation of gene expression occur?
  • Transcriptional Regulation: The main mechanism of regulating gene expression is by transcriptional gene regulation. That is, when the gene is "on" it is being transcribed. Its mRNA is being made and therefore the polypeptide encoded by that gene is being made. When the gene is "off" the transcription of that DNA segment is blocked. Since no mRNA is being made, that polypeptide will not be made. Besides "on/off" regulation, transcriptional control may also determine how much of the protein is made by controlling the amount of the mRNA made during transcription. (We will cover this topic next.)
  • Post-Transcriptional Regulation: Even though transcriptional control is the central mechanisms of gene regulation, it is not the only mechanism. Events that occur after translation may be regulated and affect the amount of protein made. This is called post-transcriptional control and includes RNA processing, translational control and post-translational control. (We will cover this topic after we finish transcriptional regulation.)
  • Changes in Gene Copy Number: In some exceptional cases, gene expression is affected by changing the number of copies of a DNA segment. That is, to make more of a gene product, more copies of the gene is made. Or, conversely, a gene is not expressed because it has been lost from the genome. Again, this is NOT the normal mechanism of gene expression, but it does occur.
    • History: In the 1890s, Weismann proposed the germplasm theory, which stated that the cells destined to become gametes were set aside early in development. This basic concept is correct, but Weismann was incorrect in assuming that when development occurs, the germplasm retains all the genetic material but the differentiated cells lose the genetic material they do not need. This model of differentiation is basically incorrect. Early cloning experiments, like that of Steward in 1958, were performed to answer this question of whether or not differentiation involves gene loss. Since  it is possible to clone an entire organism from a single cell, Steward and others demonstrated that the cell must not have lost any genetic material in the course of differentiation.
    • Gene Loss: However, in some rare cases, genes ARE actually lost during the life of an organism, thereby affecting the expression of the genetic material.
      • Chromatin Diminution: In the roundworm Ascaris and its relatives, during early development the somatic cells lose segments of their chromosomes. (This is different from splicing!) The germ line cells, however, retain all of the genetic material. (So Weismann wasn't 100% wrong.) The amount of the genome lost in these worms varies among species from 25% to 85%.
      • Chromosome Elimination: In many sciarid flies, entire chromosomes (not just pieces of chromosomes) are lost in the the somatic cell line.
      • The Strange Case of Paramecium and Tetrahymena: These single-celled ciliates have a very strange life cycle, which includes the formation of two nuclei: a macronucleus and a micronucleus. The macronucleus is the "active" nucleus of the critter (its genes are being expressed: transcription is occurring here). The micronucleus is inactive in the mature ciliate and just for reproductive purposes. The macronucleus is both an example of gene amplification (see below) and gene loss. During the life cycle, the micronucleus (after meiosis, swapping micronuclei, and nuclear fusion) divides and gives rise to both types of nuclei. One event that occurs during the formation of the macronucleus is the loss of specific sequences of the DNA called IESs (internal eliminated sequences). (Again, this is NOT splicing!) Which genes are to be eliminated is an RNA mediated process similar to RNA interference (later). The post-meiotic micronucleus' entire genome is transcribed. Previously, the old macronucleus was entirely transcribed and by a comparison of these two whole-genome transcripts, the determination of which segments to discard is made. In this way, 50,000 or more segments (IESs) are removed in the formation of the macronucleus. (Strange critter!)
      • Cancer Cells: Many chromosomal changes occur in tumors, including chromosome loss. This loss may make the cancer more "viable."
    • Gene "Gain": In some cases, the number of copies of a gene is increased.
      • Repetitive vs. Single-Copy DNA: Some genes are normally present in multiple copies. Therefore, with more copies of the gene, more gene product can be made (rRNA genes). Eukaryotic genomes are typically composed of three types of DNA, as determined by hybridization studies (Cot values).
        • Single-Copy (Unique-Sequence) DNA: In humans, about 50% of the DNA is present only once (one copy) in each genome (two copies per cell). This includes gene coding for proteins. This DNA hybridizes "slowly" (high Cot values).
        • Middle-Repetitive DNA: In humans, about 40% of the DNA is moderately repeated, with copy numbers between 10 and 1,000. This includes the genes for rRNAs and tRNAs.
        • Highly-Repetitive DNA: In humans, about 6% or the DNA is present in very high copy numbers as tandem repeats, with copy numbers of up to 100,000. The repeated segment varies in length from 5 to 300 nucleotides. This DNA is often called satellite DNA (forms a satellite during CsCl centrifugation). It includes transposable elements and repeated segments unique to the centromere and telomere. This DNA is usually heterochromatin (heterochromatin is chromatin that is condensed even during interphase--versus euchromatin that decondenses during interphase and includes active genes)(Dark staining=heterochromatin, lightly staining=euchromatin)
      • Gene Amplification: In some cases, DNA segments (or whole genomes) are replicated without division.
        • Amphibian Oocyte rRNA Genes: rRNA genes in the giant amphibian oocyte are replicated repeatedly, providing more templates to make this ribosome component. This gene amplification can be from 2000 to 1,000,000 fold.
        • Drosophila Polytene Chromosomes: Some dipteran flies, including Drosophila, have giant chromosomes in certain larval tissues. The Drosophila salivary glands have these polytene ("many-stranded") chromosomes. Polytene chromosomes have about 1000 chromatin strands and show somatic pairing. They also have their centromeres together in a structure called the chromocenter.
        • Ciliate Macronucleus: One other event in the development of the macronucleus from the micronucleus is the repeated replication of the DNA (without cell division) producing a giant nucleus with about 800 copies of the remaining segments.
        • Human Liver Cells: For some reason (?), human differentiated liver cells often undergo a round or two of replication without cell division, making a polyploid cell (2-4 times the normal number of chromosomes)(Polyploidy in Liver Cells).
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