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Recently, I reviewed the different levels of chromatin structure. The primary level is nucleosomes, where DNA is bound to histones, and has structural similarity to "beads on a string." The secondary level is a 30nm fiber, and the tertiary level is formed by radially looping the fibers.

I've also been learning about the histone code and how different modifications to the core histones relate to transcriptional regulation. Are these modifications the primary regulation mechanism for chromatin structure? In other words, does chromatin assume the most compact structure possible until histone modifications are made to enable transcription? Or have other regulatory mechanisms unrelated to transcription been discovered and characterized?

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AFAIK chromatin would not assume the most compact structure without topoisomerase activity. –  Ultimate Gobblement Apr 22 '12 at 16:42

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"Are these modifications the primary regulation mechanism for chromatin structure?"

It depends on how you define primary, we might currently think of histone modifications as primary because other regulatory mechanisms have not yet been well studied. Something else you can think of are the various regulatory proteins that interact with histone marks to modify chromatin.

I don't think you should imagine chromatin as assuming "the most compact structure possible until histone modifications are made to enable transcription" but rather histone modifications being a dynamic process with various transcription factors (a class of proteins) coming in and adding/removing histone marks as well as 'remodeling chromatin' (adding/removing nucleosomes)

As a sidenote, I don't believe much is known about the tertiary stage you initially mentioned so maybe that could play a huge role in the regulatory mechanisms of chromatin structure, it has just not been well explored.

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