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You can reuse this answer Creative Commons License. A Schematic representation of human p53FL and its deletion mutants. B Pull-down assay for p53 binding to the histone complex. Lane 1 indicates protein markers. Finally, we tested whether the N-terminal region of p53 affects the nucleosome binding.
Therefore, the N-terminal region of p53 may contribute to its specific binding to the nucleosome, by binding to the H3-H4 tetramer.
A histone acetyltransferase, p, reportedly binds to the TAD1 and TAD2 domains of the p53 N-terminal region, and may induce the p53 target gene expression 32 , Therefore, the p53 N-terminal region may function to connect p to histones in the nucleosome via p53 multimer formation.
A well-characterized pioneer transcription factor, FoxA1, also interacts with the histone H3-H4 complex to induce an open chromatin configuration The histone binding by p53 may be a common feature for a group of pioneer transcription factors.
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Oxford University Press is a department of the University of Oxford. Enrol and complete the course for a free statement of participation or digital badge if available. We have seen how in the eubacterial chromosome, bending DNA serves to facilitate its compaction.
A similar process occurs in eukaryotic cells in that DNA is bent and wrapped around a protein unit. In this case, the core unit is a protein—DNA complex termed a nucleosome. In order to understand how the nucleosome is assembled, we first need to study the structure of the individual histones that it contains. Each histone protein folds to give the histone fold motif as shown in Figure The next stage is the dimerisation of two of these folded histones through the crossing-over of the two central helices domains II.
This structure resembles a small cylinder with the eight N-terminal tails protruding freely from it. Between and bp of DNA can be wrapped in two turns around the histone octamer unit to form the nucleosome, the structure of which is shown in Figure The DNA wraps around the histone octamer rather like a thread wrapped around a spool. The many interactions between the negatively charged DNA backbone and the positively charged histone proteins serve to stabilise the structure.
Note that the interaction between the histone proteins and the DNA is not sequence-specific; thus the histone octamer is able to bind DNA of any sequence. As the DNA wraps around the octamer, torsional stress is introduced into it such that for every nucleosome, two left-handed superhelical turns are introduced into the DNA.
If you look back at Figure 11b , you can see that one conformation adopted by supercoiled DNA is a solenoid. The DNA wrapped around an octamer adopts just such a conformation. Thus supercoiling of DNA is accommodated or maintained by the nucleosomes. The location of a nucleosome along any particular stretch of duplex DNA, such as relative to regulatory elements in a gene's promoter, is called translational positioning.
This positioning determines whether any segment of DNA lies within a nucleosome or within the linker region. The DNA that is wrapped around the histone octamer is inaccessible to many chemicals and enzymes, fulfilling a primary objective of DNA packaging.
This protection of DNA can be exploited as a means of determining which part of any one region of DNA is or isn't associated with the octamer. If chromatin is isolated from a eukaryotic nucleus and treated with a nuclease that cleaves the DNA double helix, the DNA helix will be cleaved where it is unprotected, i.
An analysis of the DNA isolated from this preparation using agarose gel electrophoresis reveals a ladder of nucleosomal fragments Figure 29c. Figure 29 : a Pictorial representation showing nucleosomes along a DNA strand top being treated with a nuclease that cleaves between nucleosomes red arrows to generate DNA chains carrying one, two or three nucleosomes.
The DNA from two chromatin samples treated in this way is shown, analysed by gel electrophoresis, revealing a ladder of fragments that correspond to different lengths of DNA. The fragments in successive bands differ in length by a stretch of DNA equivalent to one nucleosome repeat length bp. Shown for comparison is the result of micrococcal nuclease digestion of naked DNA: a smear of fragments due to random cleavage. The positioning of the nucleosome relative to the rotation of the DNA helix is called rotational positioning.
If the position of the helix on the octamer is such that the bases of a particular region are facing into the core unit, the recognition site will not be accessible Figure Consider the Zif protein Figure What would the effect be if the 9 bp recognition sequence was positioned as in Figure 30b?
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