Introduction
Eukaryotic chromosome DNA (deoxyribonucleic acid) molecules may be 1.7 to 8.5 cm for humans or 7.8 to 520 m for yeast. Eukaryotic organisms are challenged with information storage and packing since mammal cell nuclei (20 to 50 m in diameter) and yeast nuclei (two to six meters in diameter) are so large. Anybody who has ever dealt with knotted yarn or rope may understand how crucial it is to package lengthy strings into a controllable and usable shape. To access a crucial portion of DNA sequences distributed throughout the molecule, DNA must be folded in a certain fashion. As a result, DNA wraps around thousands of globular protein cores rather than folding into a single large ball like yarn or rope, appearing as "beads on a string" in electron micrographs. The smallest packing unit of the chromatin fiber, the "bead" or nucleosome, is made up of 147 bp of DNA wrapped 1.65 times around an octamer core of two H2A/H2B and two H3/H4 heterodimers. The higher-order structures created from the assembled nucleosomes can then be unwrapped as necessary.
What Is The Nucleosome Positioning?
Nucleosome placement refers to the general location of nucleosomes in the genomic DNA sequence. Sequencing-based mapping techniques may pinpoint the locations of specific nucleosomes in a single cell at a particular moment, despite nucleosome placement being a dynamic process. Nevertheless, cell and time-averaged nucleosome locations are often mentioned. Hence, the placement level can range from zero positioning, in which all DNA molecules in a population have nucleosomes placed at every potential genomic site equally, to perfect positioning, in which all DNA molecules in a population have nucleosomes situated at a specified 147 bp length. The idea of nucleosome occupancy indicates the percentage of cells in the population and nucleosome placement are similar yet different.
How DNA Sequence Has a Significant Impact on Nucleosome Placement?
Bending, and hence the creation of nucleosomes, are influenced by two main sequence determinants.
Firstly, the bending characteristics of di-nucleotides vary greatly to start. The face of the helical repeat, which is every ten base pairs and directly interacts with histones, is where bendable di-nucleotides (AT, TA) occur. Recent mapping of nucleosomes in the yeast S. cerevisiae utilizing a cutting-edge H4-S47C-mediated cleavage method that permits accurate mapping of nucleosomes concerning the DNA sequence reveals a striking 10-bp periodicity of bendable di-nucleotides over practically the entire 147-bp region23. The DNA sequence is a key factor in determining the precise location of the histone octamer with regard to the 10 bp helical repeat, and as a result, how nucleosomes are rotationally positioned depends on this information.
Secondly, nucleosome formation is highly inhibited by the homopolymeric sequences poly(dA:dT) and poly(dG: dC), which are both stiff by nature (for various structural reasons). Importantly, poly(dA:dT) tracts are widespread in the genomes of eukaryotes and are especially common in the promoters of several species, including S. cerevisiae. The intrinsic qualities of poly(dA:dT) are critical for nucleosome depletion, promoter accessibility, and transcriptional activity, as will be explored more below.
The above DNA sequence preferences for nucleosomes may be represented as a position-weight matrix that can produce a nucleosome score for any 147-bp section of DNA22, analogous to DNA-binding proteins. These nucleosome scores relate to the relative affinities of 147-bp sequences for histone octamers; these affinities must have an impact on the placement of nucleosomes in vivo. Most DNA sequences will have significantly varying nucleosome scores at adjacent places within a single helical repeat because dinucleotide preferences vary over the 147 bp length of the nucleosome. As a result, there will often be a favoured position(s) inside a helical repeat; this rotational orientation is evident in eukaryotic genomes.
How Crucial Are Poly Tracts for Nucleosome Depletion?
Nucleosomes are synthesized in vitro by salt dialysis using pure histones and genomic DNA, which has been used in investigations to examine the function of DNA sequence in determining nucleosome placements in vivo. Many yeast promoters and terminator regions are lacking in nucleosomes under these circumstances, demonstrating an inherent disadvantage of the DNA sequences for nucleosome synthesis. This idea is supported by the fact that nucleosome depletion at promoters is seen in vivo under a range of circumstances and is unaffected by transcriptional activity. In addition, nucleosome depletion at promoters is maintained in a way that depends on the amount of poly (dA:dT) sequences when artificial chromosomes from heterologous yeast species with vast genomic areas are examined in S. cerevisiae. As a result, the inherent characteristics of poly (dA:dT) sequences have a significant impact on nucleosome depletion at the majority of promoter sequences.
What Function Do Nucleosome Remodelers Have in the Placement of Nucleosomes?
If a yeast crude extract and ATP are added to isolated histones and DNA, certain elements of the in vivo nucleosome positioning pattern may be recreated in vitro45. In a cell-free extract, combining ATP-dependent nucleosome remodelers increases nucleosome depletion at promoters to the level seen in vivo and also produces positioned nucleosomes (i.e., the +1 and 1 nucleosomes) on each side of the nucleosome-depleted areas. Remodeling enzymes might theoretically just let nucleosomes sample different places quickly, bringing about a thermodynamic equilibrium that is absent when nucleosome assembly is carried out by salt dialysis. Although they effectively mobilize nucleosomes, nucleosome assembly processes comprising the yeast RSC46 or the Drosophila ACF33 do not produce the in vivo pattern. These findings reveal that nucleosome-remodeling enzymes play a crucial role in the specificity of nucleosome location and not just in the translocation of nucleosomes to favored intrinsic sites.
How Does Nucleosome Location Impact Cellular Functions Like Transcription?
It is obvious that various variables, including DNA sequence and protein complexes, influence nucleosome packing across the genome. The traditional theory that nucleosomes restrict transcription factors from binding to motifs inside the nucleosomes seems to hold for most transcription factors. Most functional transcription factor binding motifs exist in nucleosome-free areas in vivo, and the places where the main groove faces away from the octamer appear to be enriched for these motifs. Yet, deviations from these general rules frequently have intriguing effects on regulating genes.
Secondly, as was previously mentioned, some transcription factors can remodel nucleosomes on their own. Beautiful in vitro research from the Widom lab demonstrates that the DNA close to the nucleosome's entry/exit point briefly separates from the octamer to reveal any underlying binding sites. It was also demonstrated that binding a transcription factor to a site close to the nucleosome's edge improved the accessibility of additional sites closer to the nucleosome's core. This is particularly intriguing because, even without any direct interaction between the factors on bare DNA, nucleosome occupancy over two motifs can make the binding of one factor reliant on the binding of the other.
Conclusion:
In every DNA-based process that has been researched, the packing of eukaryotic genomes into nucleosomes has a significant effect. Recent advances in genomic technology have made it possible to examine chromatin in greater depth, allowing researchers to explore long-held theories about the connection between sequence, chromatin structure, and control of cellular functions.
