Episode #125 of the Stack Overflow podcast is here. We talk Tilde Club and mechanical keyboards. Listen now
9

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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A large number of prokaryotes do indeed have nucleosome-like structures. The most well studied is H-NS in E. coli, Salmonella and some other deltaproteobacteria. H-NS like molecules have also been found in mycoplasma (Lsr2). One of its roles is to bind AT-rich DNA and silence transcription. The binding is usually to suppress the expression of foreign DNA ...


4

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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"Are these modifications the primary regulation mechanism for chromatin structure?" It depends on how you define primary, we might currently think of histone modifications as primary because other regulatory mechanisms have not yet been well studied. Something else you can think of are the various regulatory proteins that interact with histone marks to ...


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There seems to be some solid evidence that transcription promotes mutation because the untranscribed strand is able to form secondary structures which expose bases to chemical mutagenesis. Here is a recent paper about transcription-associated mutagenesis: Kim H et al.(2010) Transcription-associated mutagenesis increases protein sequence diversity more ...


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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 ...


2

Starting out with RNA data is great, since you already have fully spliced entities, despite being in a different dynamic regime. As the chromatin landscape itself is dynamic and High throughput data exploration has only begun in the last decade, consider the following tools and results with care... You may find the following tools helpful: Archalign , ...


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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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Shear forces are experienced by all molecules, and molecular complexes when they are treated roughly. So, for example, if you have a solution of high molecular weight DNA it will be very viscous, but if you treat it roughly by pipetting up and down through a narrow aperture the DNA strands will suffer shear forces strong enough to break covalent bonds and ...


1

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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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 lamins are ...


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