Questions tagged [chromatin]
Chromatin is the complex of DNA, histones, and other scaffolding proteins that make up the chromosomes, which in eukaryotes is located in the nucleus of the cell.
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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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How much is known about dinosaur DNA condensation and crosslinking?
The conclusion section of Bailleul et al. (2020) Evidence of proteins, chromosomes and chemical markers of DNA in exceptionally preserved dinosaur cartilage is:
The identification of chemical markers ...
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Do nucleosomes ever completely unwrap during transcription?
In eukaryotic transcription will the nucleosomes ever completely unwind the DNA and the histone complex disassemble? If an operon is more 160 base pairs it seems it must.
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DNA-DNA cross-linking with formaldehyde?
The 3C (chromosome conformation capture) technology for studying chromatin 3D organization starts by a cross-linking step using formaldehyde to find segments of DNA interacting. In my understanding ...
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What is the mechanism by which lamins regulate gene expression?
The heterochromatin is generally localized at the nuclear periphery (also near nuclear lamina), whereas active genes are preferentially found in the nuclear interior.
Children with Hutchinson-...
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What happens after the purification step in Hi-C sequencing?
I am a statistician reading an article on Hi-C, and I am trying to better understand one of the steps in the DNA isolation and sequencing process.
Since I'm a statistician, please try to avoid too ...
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Bacterial chromatin binding data?
I'm looking for data - maybe CHP^2 data that shows chromatin binding to a prokaryotic genome under some specific conditions. Can anyone point me to a source?
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Transcriptionally-mediated DNA damage
I'm researching the genetics of brain cancer, and finding a huge number of mutations in voltage-gated channels. It stands to reason that some of this DNA damage is due to the DNA being transcribed ...
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Why is it important to study chromatin to understand cancer?
Many labs and many projects in biology institutes and university departments have been starting to study chromatin. Chromatin states, chromatin interactions, chromatin loopings, chromatin behaviours, ...
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What are "anchor regions" in the human genome?
I've been reading this paper entitled "A high-resolution map of the three-dimensional chromatin interactome in human cells", about interactome in 3D chromatin.
We next applied the above algorithm ...
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How can chromatin state be measured?
I have some RNA-Seq data and I'd like to align it to the physical genome and see which sections of chromatin are geometrically open and being transcribed. The data are already sequence-aligned, and ...
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In chromatin, what are the differences among states, interactions, and structures?
I am new to the study of chromatin, and I am trying to understand what people mean when they write about chromatin states, chromatin interactions, and chromatin structures.
What are the difference ...
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Chromatin shearing: what is it and what are the effects of high-sensitivity?
I am reading a paper which discusses a complex (MSL-DCC) involved in dosage compensation of the drosophila X-chromosome. Descriptions of the complex's structure and function are given in the papers ...
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Heterochromatin v Euchromatin. Which is more abundant?
So I was just reading that whether heterochromatin or euchromatin is more abundant in a particular human cell depends on how active that cell is. But considering that most of the 25,000 or so genes in ...
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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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Why does cell waste energy in meiosis, between meiosis 1&2
As far as I have learnt about meiosis I have read that anaphase 1 is followed by telophase 2 where chromosomes change back to reticulum.but in the very next stage i.e prophase 2 they again start ...
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Dnase data for GRCh38
This question below turned to be completely faulty. I don't have to do anything with DNase data for GRCh38.
I asked it because of the file count difference between hg38 and hg37, which I thought to be ...
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Properties of Satellite Chromosomes
I have some questions regarding Satellite chromsomes which could not be resolved by a google search.
Does the satellite consist of telomeric sequences ?
If not, What is the function of a satellite ? ...
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Why are GC-rich regions less condensed than GC-poor regions?
As far as I know, chromatin consists of two kinds:
Heterochromatin is more condensed so translational factors have less access to this region, and this region is poor in GC.
Euchromatin is less ...
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Meaning of the word "targeted" in a description of chromatin immunoprecipitation
From a research paper:
The ChIP assay demonstrated that CIC physically binds to the promoter region of FOLR1, PCFT and RFC1.
Compared with IgG control antibody, CIC antibody enriched 4.1-fold more ...
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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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Are there limitations in using DNase I hypersensitive sites (DHSs) to identify candidate enhancers?
Candidate enhancer regions are often defined in studies by DHSs and/or certain chromatin marks. I was wondering if DHSs are exhaustive for identifying possible enhancer regions, and if there is any ...
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what chromatin factors are the most potent supressors of meiotic crossover?
I think linker histone H1 is probably involved, but the literature is scant. What else prevents crossovers from becoming hyper-frequent during meiosis?
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4DGenome or another comprehensive database of chromatin interactions
I'm searching for the most comprehensive source of chromatin interactions to support enhancer targets (data such like Hi-C, ChIA-PET, IM-PET, 5C, 4C, 3C, etc.) and my question according that could be ...
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Why are odd numbers of chromosomes (triploidy, pentaploidy) less common than even ones (tetraploidy, hexaploidy)?
Perhaps there is an obvious reason, and I know that most organisms that are either exclusively sexual or at least capable of sexual reproduction are diploid, but....
Is there a specific reason ...
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What’s so remarkable about position effect variegation?
I am reading Albert et. al’s Molecular Biology of the Cell and at one point the authors discuss the idea of “position effect variegation.” They mention that through events of DNA relocation, it’s ...
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Transcription when Chromosomes are Condensed
Are genes transcribed just as well when chromosomes are condensed?
I want to design a screen that depends on genes not transcribed when chromosomes are condensed (to identify cells that can't ...
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What is the structure of heterochromatin?
A short article about euchromatin and heterochromatin mentions that the structure of heterochromatin usually depicted in images "has never been visualized in vivo, and its existence is ...
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Mitotic chromosome condensation screen
If I want to screen for mutant yeast (S. cerevisiae) colonies that have defects in mitotic chromosome condensation, can I screen for colonies arrested in Mid-M phase? Would that work?
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Can Euchromatin convert into Heterochromatin?
I know that Heterochromatin can convert into Euchromatin but is the reverse possible? If yes, then How?
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