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12

From a brief survey of the literature, it seems Kawasaki and Taira have been largely vindicated by the community before and since their paper. The retraction was by Taira alone, Kawasaki refused to co-sign because he maintained the data were valid. From the retraction it seems the reason for the retraction was a lost lab book. Prior to the Kawasaki and ...


4

Jon Wilkins has a nice introduction to imprinting. He does a nice job of introducing the idea methylation and how these patterns are maintained during development and cell division. Further, he links to some interesting papers on the subject.


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It is difficult to draw any conclusion without further experimentation. There may be many other factors that prevent the expression of the gene including factors like post-transcriptional regulators. Some histone modifications like the ones you are mentioning are also a bit dicey and there can be bivalent modifications too. However, if there is a strong ...


1

The authors obviously meant to write that the histones associated with the promoter become deacetylated. They cannot mean the promoter itself as that is DNA. What they wrote is not shorthand or acceptable alternative usage, but just a mistake — published papers often contain typos and mistakes of this sort. Probably the authors meant to write the ...


1

We have a more recent study, Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin and they seem to suggest that in accordance with your '05 paper, H3K36me3 in part contributes to the formation of tightly packed, inaccessible chromatin. You'll see there's a lot of crosstalk, but you would also think that ...


1

ChIP-seq isn't perfect. Even between technical replicates, you get a fair amount of variation, especially for broad marks like those you're using. It's rather uncommon to see people use H3K79me2 and H3K36me3 to determine if a gene's expressed or not. Using H3K4me3 and H3K27ac or H3ac is a more common method of marking promoters of transcribed genes. 40 ...


1

It is not simple MS, it is tandem MS. They send the sample through multiple MS and they fragment it between them. So they can get info about the molecular structure as well, not just the mass/charge of the molecule. A quote from your article: MS/MS spectra of the methylated H3 protein (top down) and fragments upon electron transfer dissociation ...


1

Histone methylation is regulated by a variety of of events, including transcriptional activation and repression, relative location of the histone in the chromatin (pericentric or not, hetero- vs. euchromatin, etc.), X-inactivation, the cell's point in the cell cycle, and others. A variety of signaling pathways can lead to the (in)activation of HMTs. I found ...


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I can get the ball rolling.. Found a nice paper which looks at this phenomenon in yeast. So as a primer, 8 histone proteins come together to make a spool of sorts which DNA wraps around: Histone proteins have many sequence variants, and each one of them can be covalently modified with methyl, acyl, phospho, SUMO, adp and many other sorts of chemical ...



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