Questions tagged [histone]

Basic (positively charged) proteins that help in compacting the genomic DNA in the form of chromatin, by forming nucleosomes.

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Can untargeted metabolomics detect epigenomic changes such as methylation?

My main focus is transcriptomics analysis and very recently I have also started working on metabolomics. From my transcriptomic data it looks like there is a gene/protein that could potentially ...
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How do you read the histone code?

I took it upon myself to research how methylation/acetylation affects histone tails via post-translational modifications. However, I find myself confused about how to "read" this histone code, ...
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DNA methylation in different positions

I'm trying to understand how does DNA methylation and histone methylation status of promoters differs given their position in a gene? Does position affect whether they are repressive or activating?
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When does histone synthesis occur in relation to DNA replication?

Do histones have to be synthesized before DNA is replicated to allow the DNA to coil around histones?
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Western blot transfer issues

I am having some issues with transfer efficiency to nitrocellulose membranes. To get all the technical info out of the way: Transfer method: Wet, tank transfer overnight at 30V with normal tris-...
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Why DNA needs histones to be packaged and ordered?

I know that histones are proteins that package and order the DNA into structural units called nucleosomes, my question is Why DNA needs histones to be packaged and ordered ? Why DNA cannot do that by ...
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Can one talk about deacetylation of a promoter rather than associated histone?

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 ...
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What's the difference between CREs and DHSs?

I would like to know what's the difference between cis-regulating elements and DNase I–hypersensitive sites, in order to produce a meaningful segregation of non coding elements affecting gene ...
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H3K36me3 role in RNA polymerase II elongation

I found a paper describing the association of RNA polymerase II with the histone methyltransferase Set2 that methylates H3K36. At the end they say: While our results strongly implicate K36 ...
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ChIP-seq for histone modification not in agreement with RNA-seq for expression

I have ChIP-seq for H3K79me2 and H3K36me3 and RNA-seq data for treated and untreated samples. Those two histones mark active genes. Lets say, hypothetically, a peak caller finds differential sites at ...
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Through which mechanisms did the Drosophila Histone Cluster evolve?

The Drosophila Histone Cluster is a gene cluster that contains more than a hundred copies of a sequence that encodes several histone proteins. These copies are very similar. My question is what ...
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Are there histones present in the cytoplasm?

In this paper the authors depleted core histone heterodimers H3-H4 at 90 % from the cytoplasm of Xenopus oocytes. They state that their concentration is in the order of 6 uM. My question is, are ...
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SNPs in DNase hypersensitive and histone marks sites

I am investigating a role of SNPs in DNase hypersensitive sites and in the DNA regions of histone marks and have some questions about it. SNPs in DNase hypersensitive sites might mean that those SNPs ...
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In what sense is the "histone code" a code?

Since I started learning about molecular cell biology, I have witnessed an increasing amount of attention to this thing called a "histone code." However, unlike the central dogma of molecular cell ...
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Nucleosome wrapping direction

Does anyone know which direction the nucleosomes are wrapped? I wonder: Relative to the B-DNA double helix twist direction (right-hand) Relative to the neighbor nucleosomes. Do they alternate to ...
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Function of heparin and dextran sulfate for removing proteins

From this article : The reaction was terminated and the histones, and most nonhistones, were removed by adding the nuclease-treated chromosomes to a solution containing dextran sulfate (2 mg/ml)...
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What signals histone methyl transferases to function?

I wanted to find out if anyone knows what stimulates histone methyltransferases to function? I know that it is a process still trying to be understood, but I can't find anything that seems to direct ...
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How are epigenetic marks transmitted during cell division?

As far as I know, this is one of the biggest questions in the epigenetic field: how are the epigenetic marks like histone modifications propagated through cell division? A lot is already known about ...
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Histone marks mechanism

I am slightly confused about the mechanisms that makes histone modifications associate with gene expression. That is, H3K36me3 is believed to be present in actively transcribed genes, H3K27me3 in ...
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How does "inheritance of methylation" of DNA and/or histones work?

What are the current models/ideas describing the mechanisms explaining inheritance of methylation on DNA resp. histone level? Is there evidance of this "setup" information being really duplicated/...
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Regulation of chromatin structure

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 ...
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What is the functional and structural distinction between core (H2A, H2B, H3,H4) and linker(H1/H5) histones?

Many explanations of histone biochemistry isn't quite elucidating for the undergraduate student. How does histone structure (dimers, octomers) relate to their specific functions as core or linker ...
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Can siRNA induce DNA methylation in mammalian cells?

Some years ago Hiroaki Kawasaki and Kazunari Taira published an article called "Induction of DNA methylation and gene silencing by short interfering RNAs in human cells" in Nature: In plants, ...
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What are the mechanism binding histone code with alternative splicing?

There are some bioinformatical considerations showing that there is a significant correlation of some between histone code and alternative splicing; but what are the hypothesis about the underlying ...
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