Nuclear organization refers to the spatial organization of chromatin within a cell nucleus during interphase. There are many different levels and scales of nuclear organization. At the smallest scale, DNA is packaged into units called nucleosomes, which compact DNA about 7-fold. In addition, nucleosomes protect DNA from damage and carry epigenetic information. Positions of nucleosomes determine accessibility of DNA to transcription factors. At the intermediate scale, DNA looping can physically bring together DNA elements that would otherwise be separated by large distances. These interactions allow regulatory signals to cross over large genomic distances—for example, from enhancers to promoters. At a larger scale, chromosomes are organized into two compartments labelled A ("active") and B ("inactive"), which are further subdivided into sub-compartments. At the largest scale, entire chromosomes segregate into distinct regions called chromosome territories. Chromosome organization is dynamically-maintained at all scales. Individual nucleosomes undergo constant thermal motion and nucleosome breathing. At intermediate scales, an active process of loop extrusion creates dynamic loops and Topologically Associating Domains (TADs).
Importance Each human cell contains around two metres of DNA, which must be tightly folded to fit inside the cell nucleus. However, in order for the cell to function, proteins must be able to access the sequence information contained within the DNA, in spite of its tightly-packed nature. Hence, the cell has a number of mechanisms in place to control how DNA is organized. Moreover, nuclear organization can play a role in establishing cell identity. Cells within an organism have near identical nucleic acid sequences, but often exhibit different phenotypes. One way in which this individuality occurs is through changes in genome architecture, which can alter the expression of different sets of genes. These alterations can have a downstream effect on cellular functions such as cell cycle facilitation, DNA replication, nuclear transport, and alteration of nuclear structure. Controlled changes in nuclear organization are essential for proper cellular function.
History and methodology The organization of chromosomes into distinct regions within the nucleus was first proposed in 1885 by Carl Rabl. Later in 1909, with the help of the microscopy technology at the time, Theodor Boveri coined the termed chromosome territories after observing that chromosomes occupy individually distinct nuclear regions. Since then, mapping genome architecture has become a major topic of interest. Over the last ten years, rapid methodological developments have greatly advanced understanding in this field. Large-scale DNA organization can be assessed with DNA imaging using fluorescent tags, such as DNA Fluorescence in situ hybridization (FISH), and specialized microscopes. Additionally, high-throughput sequencing technologies such as Chromosome Conformation Capture-based methods can measure how often DNA regions are in close proximity. At the same time, progress in genome-editing techniques (such as CRISPR/Cas9, ZFNs, and TALENs) have made it easier to test the organizational function of specific DNA regions and proteins. There is also growing interest in the rheological properties of the interchromosomal space, studied by the means of Fluorescence Correlation Spectroscopy and its variants.
Architectural proteins Architectural proteins regulate chromatin structure by establishing physical interactions between DNA elements. These proteins tend to be highly conserved across a majority of eukaryotic species. In mammals, key architectural proteins include:
Histones: DNA is wrapped around histones to form nucleosomes, which are basic units of chromatin structure. Each nucleosome consists of 8 histone protein subunits, around which roughly 147 DNA base pairs are wrapped in 1.67 left-handed turns. Nucleosomes provide about 7-fold initial linear compaction of DNA. The concentration and specific composition of histones used can determine local chromatin structure. For example, euchromatin is a form of chromatin with low nucleosome concentration - here, the DNA is exposed, promoting interactions with gene expression, replication, and organizational machinery. In contrast, heterochromatin has high nucleosome concentration and is associated with repression of gene expression and replication, as the necessary proteins cannot interact with the DNA. Chromatin remodeling enzymes: These enzymes are responsible for promoting euchromatin or heterochromatin formation by a number of processes, particularly modifying histone tails or physically moving the nucleosomes. This in turn, helps regulate gene expression, replication, and how the chromatin interacts with architectural factors. The list of chromatin remodeling enzymes is extensive and many have specific roles within the nucleus. For example, in 2016 Wiechens et al. identified two human enzymes, SNF2H and SNF2L, that are active in regulating CTCF binding and therefore affect genome organization and transcription of many genes. CCCTC-binding factor (CTCF), or 11-zinc finger protein, is considered the most prominent player in linking genome organization with gene expression. CTCF interacts with specific DNA sequences and a variety of other architectural proteins, chiefly cohesin - these behaviours allow it to mediate DNA looping, thus acting as transcriptional repressor, activator, and insulator. Furthermore, CTCF is often found at self-interacting domain boundaries, and can anchor the chromatin to the nuclear lamina. CTCF is also involved in V(D)J recombination. Cohesin: The cohesin complex was initially discovered as a key player in mitosis, binding sister chromatids together to ensure proper segregation. However, cohesin has since been linked to many more functions within the cell. It has been found to help facilitate DNA repair and recombination, meiotic chromosome pairing and orientation, chromosome condensation, DNA replication, gene expression, and genome architecture. Cohesin is a heterodimer composed of the proteins SMC1 and SMC3 in combination with the SCC1 and SCC3 proteins. The entire complex is loaded onto DNA by the NIPBL-MAU2 complex in a ring-like fashion.
Levels of nuclear organization
Nucleosome fiber
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