BMCB625:Nucleosome Coding

(Homework) Questions

Jon

No question here (it is implied), however, I want you all to think about nuclesome mobility.

Also if you have time play around with the following pdb file: 1kx3.pdb

This one is slightly higher resolution, and referred to in their paper more. It has about 3 times the number of water molecules added in: 1kx5.pdb --Chayne 15:41, 14 May 2007 (EDT)

Chris

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Mahta

Q1. To determine binding affinities of their DNA sequences (Fig 1c-1e)(sequences with additional dinucleotide motifs, removed dinucleotide motifs, and disrupted spacing between the motifs) the authors use the core histone tetramer H3(2)H4(2). Do you think this is a valid approach for determining binding affinity? Why or why not?

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Larry

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Chayne

Q: Why might the following quote from the article be, strictly-speaking, an overstatement (from page 777): "Overall, our results establish that genomes encode the positioning and stability of nucleosomes in regions that are critical for gene regulation...", and what is the significance of the caveat in that statement "...critical for gene regulation..."?

A: The positioning of nucleosomes are dependent upon many factors, such as DNA methylation, competition with other DNA binding proteins, modification state of histones, local concentration of other nucleosomes, etc. Of this, the genome sequence seems only to be a single piece of the information that determines nucleosome position. As such, specific sequence motifs that favor nucleosome architecture do so by contributing a limited amount of local thermodynamic stability, making the free-energy change associated with placing a nucleosome at that position either more negative or less positive. Conceptually, the sequence can provide energy "depressions" for nucleosome structure to "fall into", and if isolated from all other factors, will statistically favor nucleosome formation. In the physiological context of all of the factors that determine nucleosome position, this may or may not be significant, dependent of the relative magnitude of this thermodynamic quantity compared to the other forces that are present at any point in time to determine chromatin structure.

I call their sentence fragment "...critical for gene regulation..." a caveat because it seems that this model is most robust for genes that are critically regulated, that is genes that would most likely be found in a heterochromatic state. This suggests that the cell must provide more robust levels of signalling (forces) to remodel that chromatin into a euchromatic state. Thus, the thermodynamic stability offered by the sequence specifc motif at that position results in a stronger silent "default" state, making the gene more tightly regulated. This could be contrasted to, perhaps, genes that undergo position-effect variegation. Perhaps the sequence specific motifs are not as strong, thus the factors that determine the nucleosome positions when those genes are down-regulated might be more variable, without a significant "default" energy depression to stabilize nucleosome structures. PEV might also arise even if the sequences provide energy terms identical to more critically regulated genes, but are regularly being outweighed by the other myriad forces that regulate transcription, eg a high level of expression of transcription factors that compete with the nucleosomes for binding at a gene locus, or even a change in temperature. (Le Chatelier's principle). --Chayne 22:39, 13 May 2007 (EDT)

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