A full-length eukaryotic gene is inserted into a bacterial chromosome. The gene contains a complete promoter sequence and a functional polyadenylation sequence, and it has wild-type nucleotides throughout the transcribed region. However, the gene fails to produce a functional protein. List at least three possible reasons why this eukaryotic gene is not expressed in bacteria.
Table of contents
- 1. Introduction to Genetics51m
- 2. Mendel's Laws of Inheritance3h 37m
- 3. Extensions to Mendelian Inheritance2h 41m
- 4. Genetic Mapping and Linkage2h 28m
- 5. Genetics of Bacteria and Viruses1h 21m
- 6. Chromosomal Variation1h 48m
- 7. DNA and Chromosome Structure56m
- 8. DNA Replication1h 10m
- 9. Mitosis and Meiosis1h 34m
- 10. Transcription1h 0m
- 11. Translation58m
- 12. Gene Regulation in Prokaryotes1h 19m
- 13. Gene Regulation in Eukaryotes44m
- 14. Genetic Control of Development44m
- 15. Genomes and Genomics1h 50m
- 16. Transposable Elements47m
- 17. Mutation, Repair, and Recombination1h 6m
- 18. Molecular Genetic Tools19m
- 19. Cancer Genetics29m
- 20. Quantitative Genetics1h 26m
- 21. Population Genetics50m
- 22. Evolutionary Genetics29m
13. Gene Regulation in Eukaryotes
Epigenetics, Chromatin Modifications, and Regulation
Problem 26
Textbook Question
DNA methylation is commonly associated with a reduction of transcription. The following data come from a study of the impact of the location and extent of DNA methylation on gene activity in eukaryotic cells. A bacterial gene, luciferase, was inserted into plasmids next to eukaryotic promoter fragments. CpG sequences, either within the promoter and coding sequence (transcription unit) or outside of the transcription unit, were methylated to various degrees, in vitro. The chimeric plasmids were then introduced into cultured cells, and luciferase activity was assayed. These data compare the degree of expression of luciferase with differences in the location of DNA methylation [Irvine et al. (2002). Mol. and Cell. Biol. 22:6689–6696]. What general conclusions can be drawn from these data?


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Step 1: Examine the control condition where there is no methylation. Note the relative luciferase expression level (490×) as the baseline for comparison.
Step 2: Compare the luciferase expression when methylation occurs outside the luciferase transcription unit. Observe that despite a similar number of methylated CpG sequences (around 100), the expression decreases moderately (to 290× and 250×), indicating some repression but not complete.
Step 3: Analyze the effect of methylation inside the luciferase transcription unit. Notice that even with a similar or slightly higher number of methylated CpG sequences (108 and 134), the expression drops drastically (to 80× and 5×), showing a stronger repression effect when methylation is within the gene region.
Step 4: Look at the condition where the entire plasmid is methylated (12.1 kb, 593 CpG sites). The luciferase expression is almost completely repressed (2×), indicating that extensive methylation across the plasmid strongly inhibits gene expression.
Step 5: Draw a general conclusion that DNA methylation represses gene expression more effectively when it occurs within the transcription unit compared to outside it, and that the extent of methylation correlates with the degree of repression.

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Key Concepts
Here are the essential concepts you must grasp in order to answer the question correctly.
DNA Methylation and Gene Expression
DNA methylation involves adding methyl groups to cytosine bases, often at CpG sites, which typically represses gene transcription. This epigenetic modification can block transcription factor binding or recruit proteins that compact chromatin, reducing gene expression. The data show that methylation inside the transcription unit strongly decreases luciferase expression, highlighting methylation's role in gene silencing.
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Location of Methylation Relative to the Transcription Unit
The position of methylation relative to the gene affects its impact on expression. Methylation outside the transcription unit reduces expression moderately, while methylation within the transcription unit causes a more pronounced repression. This suggests that methylation within coding or promoter regions directly interferes with transcription machinery or elongation.
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Extent of Methylation and Its Effect on Gene Activity
The size and number of methylated CpG sites correlate with the degree of gene repression. Larger methylated patches and higher numbers of methylated CpGs lead to stronger suppression of luciferase activity, as seen with entire plasmid methylation causing near-complete silencing. This indicates a dose-dependent relationship between methylation extent and transcriptional inhibition.
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