Structural Biochemistry/30nm chromatin fibers

Presence of 30nm Chromatin fibers, essential?

It is essential for eukaryotic genomes to be folded and compacted to fit within the restricted volume of the nucleus. A question arise from this that whether 30nm chromatin fiber must be present or not to constitute the template for active genomic material.

30nm chromatin fiber models

The molecular model of the 30nm fiber includes the one-start solenoid, two-start helix zigzag, the cross-linker, and supranucleosome. These models were based on EM of buffer-extracted chromatin fibers and micrococcal nuclease-digested material.

One-start solenoid

Solenoid model shows that 10nm fiber coils around a central axis of symmetry with nucleosome which is packed face-to-face and the six or seven nucleosome is packed every helical turn. This model is supported by a molecular tweezers experiment that provides sub-pico Newton force resolution. From the experiment, a conclusion is drawn that the 30nm fiber follows a regular helical structure.

Two-start helix zigzag

This model predicts zigzagging pattern of two nucleosomes. Later, the zigzagging of two nucleosomes will turn coil into a helical conformation. This model is demonstrated by the crystal packing of the structure of the tetranucleosome.

Cross-linker

It is similar to the two-start helix zigzag model but what is different is the linker DNA crisscrosses back and forth across the helical axis. This model requires folding complexity and precision in linker length and nucleosome spacing.

Supranucleosome model

The Supranucleosome model requires clumps of nucleosomes which are separated by linker sequences.

Existence of 30nm fibers in interphase nuclei

The 30nm fiber was observed in starfish sperm by EM studies and ESI (electron spectroscopic imaging). It was shown that 10nm fiber was folded and twisted into a fiber and the fiber was about 30nm in width. However, cryo-EM studies demonstrated that the 30nm fibers were not present in the fully condensed chromatin, and it was proved by the absence of a 30nm peak in the power spectrum.

Techniques that prove the existence of 30nm fibers in interphase nuclei

EM

It relies on heavy metal contrast agent, and thus is hard to visualize chromatin fibers.

ESI

It is a high-contrast technique and since it does not rely on the heavy metal contrast agent, but on the only electrons that have interacted with specific elements. Most of the chromatin is observed as 10nm fibers rather than 30nm. This technique proves that majority of genome is compacted into 10nm chromatin fibers.

3C technique

This technique utilizes the chromosome conformation capture. Based on this technique, it was also observed that the yeast genome was not compacted into 30nm fiber, but instead as an extended fiber. However, this technique is quite limited to the long-range chromatin interaction from a locus of interest.

FISH(fluorescence in situ hybridization)

This technique uses fluorescent probes that bind to only those parts of the chromosomes. This technique lacks high resolution to exclude a highly bent and kinked 10nm fiber from a less bent or kinked 30nm fiber.

Conclusion

There are variety of models and techniques to observe the presence of the 30nm fibers but it has been more observed that highly compacted chromatin fiber like 30nm fibers are not necessarily present for any gene regulation such as folding of DNA. Instead, 10 nm chromatin can be condensed enough into compacted domains through frequent bending and making 10nm fibers close to each other. In other words, it does not require to have 30nm fibers but is sufficient to have 10 nm chromatin fibers that is organized in genome to explain the complexities of nuclear organization and gene regulation.

References

Fussner E, Ching RW, Bazett-Jones DP. "Living without 30nm chromatin fibers." http://www.ncbi.nlm.nih.gov/pubmed?term=Living%20without%2030nm%20chromatin%20fibers.