Genomic DNA from the nematode worm Caenorhabditis elegans is organized by nucleosomes in the manner typical of eukaryotic genomes, with 145 bp encircling each nucleosome and approximately 55 bp in linker DNA. When C. elegans chromatin is carefully isolated, stripped of nonhistone proteins, and placed in an appropriate buffer, the chromatin decondenses to the 10-nm fiber structure. Suppose researchers mix a sample of 10-nm–fiber chromatin with a large amount of the enzyme DNase I that randomly cleaves DNA in regions not protected by bound protein. Next, they remove the nucleosomes, separate the DNA fragments by gel electrophoresis, and stain all the DNA fragments in the gel. How do the expected results support the 10-nm–fiber model of chromatin?

Verified step by step guidance

1. Understand the structure of chromatin: In eukaryotic cells, DNA is wrapped around histone proteins to form nucleosomes, which are the basic units of chromatin. Each nucleosome consists of approximately 145 base pairs (bp) of DNA wrapped around a histone octamer, with linker DNA of about 55 bp connecting adjacent nucleosomes.
2. Recognize the role of DNase I: DNase I is an enzyme that cleaves DNA at random sites, but it cannot cut DNA that is tightly bound to proteins, such as the DNA wrapped around histones in nucleosomes. Therefore, DNase I will preferentially cut the linker DNA between nucleosomes.
3. Predict the pattern of DNA fragments: When the chromatin is treated with DNase I, the enzyme will cleave the linker DNA, resulting in DNA fragments that correspond to the length of DNA protected by nucleosomes. This means you would expect to see DNA fragments of approximately 145 bp, which is the length of DNA wrapped around each nucleosome.
4. Analyze the gel electrophoresis results: After DNase I treatment, the DNA fragments are separated by size using gel electrophoresis. If the 10-nm fiber model is correct, the gel should show a prominent band at around 145 bp, indicating the presence of nucleosome-protected DNA fragments.
5. Interpret the results in the context of chromatin structure: The presence of a distinct band at 145 bp supports the 10-nm fiber model of chromatin, as it demonstrates that the DNA is organized into nucleosomes with linker DNA that is susceptible to DNase I cleavage. This pattern confirms the regular spacing and protection of DNA by nucleosomes in the chromatin structure.

Key Concepts

Nucleosome Structure

Nucleosomes are the fundamental units of chromatin, consisting of a segment of DNA wrapped around a core of histone proteins. Each nucleosome typically contains about 145 base pairs of DNA, which helps package the DNA into a compact structure. This organization is crucial for regulating gene expression and DNA accessibility, as the positioning of nucleosomes can either expose or shield DNA sequences from transcription factors and other regulatory proteins.

10-nm Fiber Model

The 10-nm fiber, also known as 'beads on a string,' represents the initial level of chromatin organization where nucleosomes are spaced along the DNA strand. This structure is essential for understanding how DNA is compacted within the nucleus while still allowing for some accessibility for transcription and replication. The presence of linker DNA between nucleosomes contributes to this fiber's flexibility and dynamic nature, which is important for chromatin remodeling.

DNase I Sensitivity

DNase I is an enzyme that cleaves DNA at sites that are not protected by bound proteins, such as histones in nucleosomes. When chromatin is treated with DNase I, the resulting DNA fragments can indicate the accessibility of the chromatin structure. If the 10-nm fiber model is accurate, we would expect to see specific patterns of DNA cleavage that reflect the positions of nucleosomes and linker DNA, supporting the idea that the chromatin is organized in a way that allows for both protection and accessibility.