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Yes, nucleosomes are completely unwound. Histone chaperones such as FACT (for H2A/H2B) and ASF1, CAF-1, HIRA, Nucleophosmin etc (for H3/H4), associate with RNA Pol II and handle the displaced nucleosomes. As you surmised, the histone octamer complex is disassembled, into the H3/H4 tetramer and two H2A/H2B dimers. Right behind the elongating Pol II, the ...
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The fact that there is no inter-strand cross-linking between different double strands might be just because the cross-linker cannot bridge the distance between amines of different bases on different double strands.
The formaldehyde based linking of nucleobases has been described by Chaw et al. (1980) where formaldehyde bridged a gap of app. 3 angstroms (2x ...
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Percentage of euchromatin varies between cell types and organisms. It has been shown that upto 88% of the human genome is transcribed; a phenomenon called pervasive transcription [1]. Highly specialized cells may have a lower percentage of transcribed regions and in females one entire X-chromosome is silenced (some regions in the silenced-X do show ...
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Most cancers involve, in addition to genetic changes, a whole suite of epigenetic changes that orchestrate changes in transcriptional profiles. Additionally, multiple epigenetic modifiers (Eg - EZH2) are associated with worse prognoses.
There is also the fact that chromatin modification machinery is very highly mutated in cancers; examples include EP300 - a ...
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Just to add very recent new information to the first answer: the initial steps of RNA Pol II transcription through a nucleosome have now been revealed at the structural level by cryoEM.
See these two articles:
https://doi.org/10.1126/science.aau9904
https://doi.org/10.1101/437574
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Good question. Anchor regions are regions that connect to the nuclear matrix. More specifically, in eukaryotic organisms, chromatin is anchored to the nuclear matrix by short DNA sequences of about 100-2,000 bp called matrix attachment regions or MAR. To answer the second part of your question, there are many categories (and opinions about those categories) ...
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Chromatin state refers to the marks (i.e. methylated DNA, histone modifications, euchromatin v. heterochromatin) found at specific loci and is often referred to as open (readily bound by DNA binding proteins, like transcription factors) or closed (inaccessible to most factors).
Chromatin interactions can include the binding of transcription factors and ...
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@ThoH.Ho and @Thawn. When banding chromosomes they are first treated with trypsin before staining with Giemsa dye. My understanding, and I have worked in the field of cytogenetics for quite a while, is that chromatin condensation due to gene content IS the reason for differential banding patterns. Gene rich/ high GC content areas, with more open chromatin, ...
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Looking at the article, I think they could leave out the word "targeted".
I think they used it because what is being enriched is not a promoter DNA, but the section of promoter DNA bound to the protein and antibody.
I suppose they could use "...enriched 4.1-fold more FOLR1 Promoter DNA-CIC protein complex,..."
It is a little awkward or ...
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I would suggest in the future doing a small amount of research before asking. For example, the wikipedia page for euchromatin says this:
Euchromatin participates in the active transcription of DNA to mRNA products. The unfolded structure allows gene regulatory proteins and RNA polymerase complexes to bind to the DNA sequence, which can then initiate the ...
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Re:
In particular, if the underlying DNA structure is changing, then
wouldn’t we expect the progeny to inherit these epigenetic changes?
Why is it so remarkable?
Given the context of the quote, the "variegation" part of the phrase refers to gene expression sometimes being turned off by influence of newly-nearby heterochromatin. The extent to ...
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This is a fascinating question, and I spent a fair amount of time looking into it. From what I've been able to find regarding the relationship between metabolics and epigenetics, it seems that metabolites drive epigenetic changes, not the other way around.
This can be shown quite well by looking at cell differentiation and induced pluripotent stem cells. ...
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The "histone code" is not like the genetic code where one codon in an ORF always is translated to a single amino acid. It's closer to something like GC content or CpG islands: a single instance doesn't tell you anything, but enrichment over some finite window may be biologically significant.
You may want to review the basics, starting with the Wikipedia ...
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Chromosome condensation seems to be primarily driven by epigenetic factors like methylation and histone modifications, not GC content. However, high GC content is associated with gene rich regions and gene expression generally requires open chromatin. In other words high GC content correlates with genes, and genes being expressed correlate with open ...
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There is a phase between meiosis 1 and meiosis 2 called Interkinesis.
During this phase centrosomes or centriole pairs undergo replication in animal cells, which is important for bringing true haploidy.
Refer - meiosis-ii
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I am unsure that how much does it answer your question, but have a look at the homepage of DeltaSVM - In his work, Lee et al. have used similar datasets (only for GRCH37 I reckon) and I am sure they will address some of your queries.
As you yourself can better determine which dataset(s) are ones you need.
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The compaction of DNA into chromatin is a very complex process that involves not only DNA, but on the histone code. Some may say that the histone code plays more of a role in chromatin state To develop a screen you would have understand the act of methylation, acetylation, ubiquitination, and phosphorylation of all modifiable histone residues. The ...
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So, after the restriction digestion, the sample consists of DNA fragments with 5' overhangs. These are filled in by Klenow DNA polymerase, adding biotin-dCTP to both ends of each fragment. Then the fragments are ligated under conditions (ie low DNA concentration) such that ligation between non-crosslinked DNA is less likely. This reduced ligation efficiency (...
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If by "satellite chromosomes" you mean "satellite repeats", then:
Not always. There many types of satellites, such as telomeric, centromeric (like gamma, alpha, beta satellites), simple repeats (CT)n.
It is still an open question. Some say they are important for chromosome structure (e.g., centromeres). Sometimes satellites get transcribed as might act ...
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So my answer was deleted because it "didn't answer your question." Except that it did. The article linked here, Gene expression, chromosome position and lamin A/C mutations, is an entire paper devoted to what we knew as of 2011 about lamins and gene expression, with references. Your question was not a simple question, and article details how ...
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