The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression
Roughly, when were cells, nuclei, chromosomes, and DNA discovered? .. Illustrate the relationship between the membranes of the endoplasmic . They are discovered by inserting test sequences next to a reporter gene (e.g., white) to see if. Twenty-three correlation matrices, one for each chromosome, were then . enrichment of housekeeping genes in CODs (hypergeometric test p. chromatin folding, and of the relationship between chromosome structure The role of ubiquitination of histone H2A has been tested in the yeast.
The scaffold has a diffuse, fibrous texture except in i where part of one arm appears to have become artefactually condensed during spreading and dehydration.
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Micrograph in a reproduced with permission from DuPraw ; be and f reproduced from Marsden and Laemmli with permission from Elsevier; c and d reproduced from Paulson and Laemmli with permission from Elsevier; g reproduced from Roth and Gall with permission from The Rockefeller University Press; h and i reproduced from Paulson with permission from Springer.
Condensin regulates the structure of the vertebrate mitotic chromosome. The condensin complex is present in the axial region of each chromatid. Condensin acts on this region to constrain the stretch, possibly by catenating the centromeric DNA. In the absence of condensin fthe centromeric chromatin can be abnormally pulled by the attached microtubules arrows causing defects in executing mitosis.
Chromosomes, white; microtubules, green. Condensin loads onto the chromosomes early in mitosis and is essential for maintaining their structure and organisation, but it is not essential for global chromatin compaction. RCA regulates mitotic chromatin compaction and its activity is mediated by protein phosphorylation. Specialised chromosome structures and chromosome organisation in interphase.
The two sister chromatids white are held together at the centromere and this defines the region where the kinetochore is assembled. The inner kinetochore red lies underneath the outer kinetochore greenwhich mediates the interaction with the spindle microtubules blue. Each sister chromatid contains a single linear DNA molecule and the terminal ends are called telomeres pink. Courtesy of J Dorrens, University of Edinburgh. In a hybrid chicken cell containing one CHO Chinese hamster ovary chromosome, hybridisation with CHO genomic DNA reveals that the single CHO chromosome present in the cell f is not dispersed within the interphase nucleus e but maintains a compact organisation and a distinct territory.
Journal of Cell Biology Holt, Rinehart and Winston. Earnshaw WC and Rothfield N Identification of a family of human centromere proteins using autoimmune sera from patients with scleroderma.
Nature Reviews Genetics 8: Biochemical and Biophysical Research Communications Hirano T and Mitchison TJ Topoisomerase II does not play a scaffolding role in the organization of mitotic chromosomes assembled in Xenopus egg extracts. PLoS One 5 9: Annual Review of Cell and Developmental Biology Mitchison TJ Microtubule dynamics and kinetochore function in mitosis.
Annual Reviews of Cell Biology 4: Journal of Biological Chemistry You have an adenine, a guanine, thymine, thymine, cytosine, cytosine.
The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression
So what just happened? By separating and then just attracting their complementary bases, we just duplicated this molecule, right? We'll do the microbiology of it in the future, but this is just to get the idea.
This is how the DNA makes copies of itself. And especially when we talk about mitosis and meiosis, I might say, oh, this is the stage where the replication has occurred. Now, the other thing that you'll hear a lot, and I talked about this in the DNA video, is transcription.
In the DNA video, I didn't focus much on how does DNA duplicate itself, but one of the beautiful things about this double helix design is it really is that easy to duplicate itself. You just split the two strips, the two helices, and then they essentially become a template for the other one, and then you have a duplicate.
Now, transcription is what needs to occur for this DNA eventually to turn into proteins, but transcription is the intermediate step.
And then that mRNA leaves the nucleus of the cell and goes out to the ribosomes, and I'll talk about that in a second.
So we can do the same thing. So this guy, once again during transcription, will also split apart. So that was one split there and then the other split is right there.
And actually, maybe it makes more sense just to do one-half of it, so let me delete that. Let's say that we're just going to transcribe the green side right here. Let me erase all this stuff right-- nope, wrong color. Let me erase this stuff right here. Now, what happens is instead of having deoxyribonucleic acid nucleotides pair up with this DNA strand, you have ribonucleic acid, or RNA pair up with this. And I'll do RNA in magneta. So the RNA will pair up with it.
And so thymine on the DNA side will pair up with adenine. Guanine, now, when we talk about RNA, instead of thymine, we have uracil, uracil, cytosine, cytosine, and it just keeps going. That mRNA separates, and it leaves the nucleus. It leaves the nucleus, and then you have translation. The transfer RNA were kind of the trucks that drove up the amino acids to the mRNA, and this all occurs inside these parts of the cell called the ribosome.
But the translation is essentially going from the mRNA to the proteins, and we saw how that happened. You have this guy-- let me make a copy here. Let me actually copy the whole thing. This guy separates, leaves the nucleus, and then you had those little tRNA trucks that essentially drive up.Chromosomes, Chromatids, Chromatin, etc.
So maybe I have some tRNA. Let's see, adenine, adenine, guanine, and guanine. A codon has three base pairs, and attached to it, it has some amino acid. And then you have some other piece of tRNA. Let's say it's a uracil, cytosine, adenine. And attached to that, it has a different amino acid. Then the amino acids attach to each other, and then they form this long chain of amino acids, which is a protein, and the proteins form these weird and complicated shapes.
So just to kind of make sure you understand, so if we start with DNA, and we're essentially making copies of DNA, this is replication. You are transcribing the information from one form to another: Now, when the mRNA leaves the nucleus of the cell, and I've talked-- well, let me just draw a cell just to hit the point home, if this is a whole cell, and we'll do the structure of a cell in the future.
If that's the whole cell, the nucleus is the center.
That's where all the DNA is sitting in there, and all of the replication and the transcription occurs in here, but then the mRNA leaves the cell, and then inside the ribosomes, which we'll talk about more in the future, you have translation occur and the proteins get formed.
So mRNA to protein is translation. You're translating from the genetic code, so to speak, to the protein code. So this is translation. So these are just good words to make sure you get clear and make sure you're using the right word when you're talking about the different processes.
Now, the other part of the vocabulary of DNA, which, when I first learned it, I found tremendously confusing, are the words chromosome. I'll write them down here because you can already appreciate how confusing they are: So a chromosome, we already talked about. You can have DNA. You can have a strand of DNA. That's a double helix. This strand, if I were to zoom in, is actually two different helices, and, of course, they have their base pairs joined up.
I'll just draw some base pairs joined up like that. So I want to be clear, when I draw this little green line here, it's actually a double helix. Now, that double helix gets wrapped around proteins that are called histones. So let's say it gets wrapped like there, and it gets wrapped around like that, and it gets wrapped around like that, and you have here these things called histones, which are these proteins.
Chromosomes, chromatids and chromatin
Now, this structure, when you talk about the DNA in combination with the proteins that kind of give it structure and then these proteins are actually wrapped around more and more, and eventually, depending on what stage we are in the cell's life, you have different structures.
But when you talk about the nucleic acid, which is the DNA, and you combine that with the proteins, you're talking about the chromatin. And the idea, chromatin was first used-- because when people look at a cell, every time I've drawn these cell nucleuses so far, I've drawn these very well defined-- I'll use the word.
So let's say this is a cell's nucleus. I've been drawing very well-defined structures here.
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So that's one, and then this could be another one, maybe it's shorter, and then it has its homologous chromosome. So I've been drawing these chromosomes, right? And each of these chromosomes I did in the last video are essentially these long structures of DNA, long chains of DNA kind of wrapped tightly around each other.
So when I drew it like that, if we zoomed in, you'd see one strand and it's really just wrapped around itself like this. And then its homologous chromosome-- and remember, in the variation video, I talked about the homologous chromosome that essentially codes for the same genes but has a different version.
If the blue came from the dad, the red came from the mom, but it's coding for essentially the same genes.
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So when we talk about this one chain, let's say this one chain that I got from my dad of DNA in this structure, we refer to that as a chromosome. Now, if we refer generally-- and I want to be clear here. DNA only takes this shape at certain stages of its life when it's actually replicating itself-- not when it's replicating. Before the cell can divide, DNA takes this very well-defined shape. Most of the cell's life, when the DNA is actually doing its work, when it's actually creating proteins or proteins are being essentially transcribed and translated from the DNA, the DNA isn't all bundled up like this.
Because if it was bundled up like, it would be very hard for the replication and the transcription machinery to get onto the DNA and make the proteins and do whatever else. Normally, DNA-- let me draw that same nucleus. Normally, you can't even see it with a normal light microscope. It's so thin that the DNA strand is just completely separated around the cell.
I'm drawing it here so you can try to-- maybe the other one is like this, right? And then you have that shorter strand that's like this. And so you can't even see it. It's not in this well-defined structure. This is the way it normally is. And they have the other short strand that's like that.
So you would just see this kind of big mess of a combination of DNA and proteins, and this is what people essentially refer to as chromatin.