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I am confused on a detail in a paper I am reading and am not sure whether I am misunderstanding the wording or misunderstanding the concept. I am including the whole abstract of this paper for background:

Epigenetic regulation of uterine biology by transcription factor KLF11 via posttranslational histone deacetylation of cytochrome p450 metabolic enzymes.

Zheng Y, Tabbaa ZM, Khan Z, Schoolmeester JK, El-Nashar S, Famuyide A, Keeney GL, Daftary GS.

Abstract:

Endocrine regulation of uterine biology is critical for embryo receptivity and human reproduction. Uterine endometrium depends on extrinsic sex steroid input and hence likely has mechanisms that enable adaptation to hormonal variation. Emerging evidence suggests that sex steroid bioavailability in the endometrium is determined by adjusting their metabolic rate and fate via regulation of cytochrome (CYP) p450 enzymes. The CYP enzymes are targeted by ubiquitously expressed Sp/Krüppel-like (Sp/KLF) transcription factors. Specifically, KLF11 is highly expressed in reproductive tissues, regulates an array of endocrine/metabolic pathways via epigenetic histone-based mechanisms and, when aberrantly expressed, is associated with diabetes and reproductive tract diseases, such as leiomyoma and endometriosis. Using KLF11 as a model to investigate epigenetic regulation of endometrial first-pass metabolism, we evaluated the expression of a comprehensive array of metabolic enzymes in Ishikawa cells. KLF11 repressed most endometrial CYP enzymes. To characterize KLF11-recruited epigenetic regulatory mechanisms, we focused on the estrogen-metabolizing enzyme CYP3A4. KLF11 expression declined in secretory phase endometrial epithelium associated with increased CYP3A4 expression. Additionally, KLF11 bound to CYP3A4 promoter GC elements and thereby repressed promoter, message, protein as well as enzymatic function. This repression was epigenetically mediated, because KLF11 colocalized with and recruited the corepressor SIN3A/histone deacetylase resulting in selective deacetylation of the CYP3A4 promoter. Repression was reversed by a mutation in KLF11 that abrogated cofactor recruitment and binding. This repression was also pharmacologically reversible with an histone deacetylase inhibitor. Pharmacological alteration of endometrial metabolism could have long-term translational implications on human reproduction and uterine disease.

Citation:

Zheng Y, Tabbaa ZM, Khan Z, Schoolmeester JK, El-Nashar S, Famuyide A, et al. Epigenetic regulation of uterine biology by transcription factor KLF11 via posttranslational histone deacetylation of cytochrome p450 metabolic enzymes. Endocrinology. 2014;155:4507–20.

My question is on the fourth-to-last sentence of this abstract specifically:

"This repression was epigenetically mediated, because KLF11 colocalized with and recruited the corepressor SIN3A/histone deacetylase resulting in selective deacetylation of the CYP3A4 promoter."

This sentence seems to say that SIN3A/histone deacetylase is deacetylating the CYP3A4 promoter itself (i.e. it is deacetylating a region of DNA directly). However, shouldn't a histone deacetylase be deacetylating a histone, not a region of DNA? Am I misunderstanding the mechanism? Or is "deacetylation of the CYP3A4 promoter" really a short-hand way of saying "deacetylation of a histone that is associated with the CYP3A4 promoter"?

Thanks in advance for your help!

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    $\begingroup$ The promoter sequence is wrapped by histones, which a modified (look at figure 3). "KLF11 binds distinct nuclear cofactor complexes that posttranslationally modify promoter histones to epigenetically alter the chromatin state, gene expression levels, and activity" $\endgroup$ – Gergana Vandova Apr 15 '16 at 19:57
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    $\begingroup$ Thanks @GerganaVandova. Just to make sure I am understanding the wording correctly: is it always ok to refer to a histone modification as a modification of the corresponding gene (as the authors seem to do in the abstract)? For example, if we were talking about histone methylation, it would be confusing to phrase a statement as "methylation of XYZ123 promoter" (since DNA methylation and histone methylation are two separate phenomena). Is it acceptable in the case of histone acetylation, since there's no such thing as DNA acetylation (as far as I know)? Hope this question makes sense! $\endgroup$ – mshum Apr 15 '16 at 20:21
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    $\begingroup$ I would say yes, it is probably acceptable, but I agree that the authors should have been more clear by stating that changing the acetylation state of the histones wrapping the promoter affects the expression of the gene from that promoter. $\endgroup$ – Gergana Vandova Apr 15 '16 at 20:43
  • $\begingroup$ @Georgana Vandova. I've edited the title of this question, deleted my own comment and turned it into an answer. That way the question can be answered and eventually taken off the unanswered list. As your comment is more extensive you might like to do likewise (and perhaps reconsider your attitude to the acceptability of the statement). $\endgroup$ – David Apr 17 '16 at 21:29
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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 technically correct form of words but lost a phrase. Or perhaps they had exceeded the limit to the number of words allowed in the summary, and so they went through trimming, but trimmed too much.

Why didn’t the referees pick this up? Of course they should have, but they were probably more concerned with the contents of the paper and whether the experiments described by the authors justified their conclusions. They are busy scientists and probably doing the job voluntarily.

In conclusion, scientists are human, scientific writing is difficult, and everyone makes mistakes. But we should still try to convey our ideas as clearly as possible, and certainly not copy something that is technically incorrect or ambiguous, just because it has made it into print.

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This is all about DNA-Protein interactions. The promoter region of the DNA is interacting with the Histone modifications, which are controlled by other proteins.

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