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Ch. 11 - Gene Mutation, DNA Repair, and Homologous Recombination
Sanders - Genetic Analysis: An Integrated Approach 3rd Edition
Sanders3rd EditionGenetic Analysis: An Integrated ApproachISBN: 9780135564172Not the one you use?Change textbook
All textbooksSanders 3rd EditionCh. 11 - Gene Mutation, DNA Repair, and Homologous RecombinationProblem 36c
Chapter 11, Problem 36c

A geneticist searching for mutations uses the restriction endonucleases SmaI and PvuII to search for mutations that eliminate restriction sites. SmaI will not cleave DNA with CpG methylation. It cleaves DNA at the restriction digestion sequence ↓ 5′−CCC GGG−3′ 3′−GGG CCC−3′ ↑ PvuII is not sensitive to CpG methylation. It cleaves DNA at the restriction sequence ↓ 5′−CAG CTG−3′ 3′−GTC GAC−5′ ↑ Explain why CpG dinucleotides are hotspots of mutation.

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CpG dinucleotides are hotspots of mutation because the cytosine (C) in CpG sequences is often methylated to form 5-methylcytosine. This methylation is a normal epigenetic modification that plays a role in gene regulation.
5-methylcytosine is chemically unstable and prone to spontaneous deamination. When deamination occurs, the 5-methylcytosine is converted into thymine (T), resulting in a C-to-T transition mutation.
The repair mechanisms in the cell may fail to recognize this mutation because the resulting T pairs with A during DNA replication, making the mutation permanent if not corrected.
CpG dinucleotides are underrepresented in the genome because of this high mutation rate. However, they are still critical in regulatory regions, and mutations in these sites can have significant effects on gene expression and function.
In the context of the problem, the presence of CpG methylation can prevent the SmaI enzyme from cleaving DNA at its recognition site, which could be used to detect mutations that eliminate or alter CpG sites.

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Key Concepts

Here are the essential concepts you must grasp in order to answer the question correctly.

CpG Dinucleotides

CpG dinucleotides are pairs of cytosine (C) and guanine (G) nucleotides linked by a phosphate bond, often found in the promoter regions of genes. They are significant in gene regulation and are typically subject to methylation, which can silence gene expression. The methylation of cytosine in CpG sites can lead to deamination, converting methylated cytosine to thymine, thus creating mutations.
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Methylation and Mutation

Methylation is a biochemical process where a methyl group is added to the DNA molecule, often affecting gene expression without altering the sequence. In the context of CpG dinucleotides, methylation can lead to instability and increased mutation rates, as the deamination of 5-methylcytosine is more likely to occur than that of unmethylated cytosine, resulting in a higher frequency of mutations in these regions.
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Restriction Endonucleases

Restriction endonucleases are enzymes that cut DNA at specific sequences, which can be used to analyze genetic material. Different enzymes have varying sensitivities to DNA modifications, such as methylation. For instance, SmaI is inhibited by methylation at CpG sites, while PvuII is not, making these enzymes useful tools for identifying mutations that affect restriction sites and understanding the role of methylation in mutation hotspots.
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Related Practice
Textbook Question
Ataxia telangiectasia (OMIM 208900) is a human inherited disorder characterized by poor coordination (ataxia), red marks on the face (telangiectasia), increased sensitivity to X-rays and other radiation, and an increased susceptibility to cancer. Recent studies have shown that this disorder occurs as a result of mutation of the ATM gene. Propose a mechanism for how a mutation in the ATM gene leads to the characteristics associated with the disorder. Be sure to relate the symptoms of this disorder to functions of the ATM protein. Further, explain why DNA repair mechanisms cannot correct this problem.
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Textbook Question

A geneticist searching for mutations uses the restriction endonucleases SmaI and PvuII to search for mutations that eliminate restriction sites. SmaI will not cleave DNA with CpG methylation. It cleaves DNA at the restriction digestion sequence ↓ 5′−CCC GGG−3′ 3′−GGG CCC−3′ ↑ PvuII is not sensitive to CpG methylation. It cleaves DNA at the restriction sequence ↓ 5′−CAG CTG−3′ 3′−GTC GAC−5′ ↑ What common feature do SmaI and PvuII share that would be useful to a researcher searching for mutations that disrupt restriction digestion?

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Textbook Question

A geneticist searching for mutations uses the restriction endonucleases SmaI and PvuII to search for mutations that eliminate restriction sites. SmaI will not cleave DNA with CpG methylation. It cleaves DNA at the restriction digestion sequence ↓ 5′−CCC GGG−3′ 3′−GGG CCC−3′ ↑ PvuII is not sensitive to CpG methylation. It cleaves DNA at the restriction sequence ↓ 5′−CAG CTG−3′ 3′−GTC GAC−5′ ↑ What process is the researcher intending to detect with the use of these restriction enzymes?

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Textbook Question

In a mouse-breeding experiment a new mutation called Dumbo is identified. A mouse with the Dumbo mutation has very large ears. It is produced by two parental mice with normal ear size. Based on this information, can you tell whether the Dumbo mutation is a regulatory mutation or a mutation of a protein-coding gene? Why or why not?

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Textbook Question

Considering the Dumbo mutation in Problem 37, what kinds of additional evidence would help you determine whether Dumbo is a mutation of a regulatory sequence or of a protein-coding gene?

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Textbook Question

Thinking back to the discussion of gain-of-function and loss-of-function mutations, explain why gain-of-function mutations are often dominant and why loss-of-function mutations are often recessive. Give an example of a type of gain-of-function mutation that is dominant and of a loss-of-function mutation that is recessive.

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