Nucleosome fiber The organization of DNA within the nucleus begins with the 10 nm fiber, a "beads-on-a-string" structure made of nucleosomes connected by 20-60bp
linkers. A fiber of nucleosomes is interrupted by regions of
accessible DNA, which are 100-1000bp long regions devoid of nucleosomes. Transcription factors bind within accessible DNA to displace nucleosomes and form
cis-regulatory elements. Sites of accessible DNA are typically probed by
ATAC-seq or
DNase-Seq experimental methods. A 30 nm fiber has long been proposed as the next layer of chromatin organization. While 30 nm fiber is often visible
in vitro under high salt concentration, its existence
in vivo has been questioned in many recent studies. Instead, these studies point towards a disordered fiber with a width of 20 to 50 nm.
Loop extrusion and DNA loops The process of loop extrusion by
SMC complexes dynamically creates chromatin loops ranging in size from 50-100kb in yeast to up to several Mb in mammals. There is strong support for loop extrusion in yeast, mammals, and
nematodes. In mammals, loop extrusion is responsible for the formation of
topologically associating domains and loops between
CTCF sites, as well as for bringing promoters and enhancers together. CTCF sites serve as boundaries of
insulated neighborhoods or
topologically associating domains. The presence of loop extrusion in
fruit flies is debated and the formation of DNA loops may be mediated by a different process of boundary element pairing.
Chromosomal domains Topologically associating domains Self-interacting (or self-associating) domains are found in many organisms. In eukaryotes, they have been usually referred to as
TADs irrespective of the mechanism of their formation. TADs have a higher ratio of chromosomal contacts within the domain than outside it. They are formed through the help of architectural proteins. In many organisms, TADs correlate with
regulation of gene expression, and enhancers and promoters within a TAD interact at higher frequency. The boundaries of LADs, like self-interacting domains, are enriched in transcriptional elements and architectural protein binding sites. NADs are associated with nucleolus function. The nucleolus is the largest sub-organelle within the nucleus and is the principal site for rRNA transcription. It also acts in signal recognition particle biosynthesis, protein sequestration, and viral replication. The nucleolus forms around rDNA genes from different chromosomes. However, only a subset of rDNA genes is transcribed at a time and do so by looping into the interior of the nucleolus. The rest of the genes lay on the periphery of the sub-nuclear organelle in silenced heterochromatin state. Researchers noticed that the whole genome could be split into two spatial compartments, labelled "A" and "B", where regions in compartment A tend to interact preferentially with A compartment-associated regions than B compartment-associated ones. Similarly, regions in compartment B tend to associate with other B compartment-associated regions. A/B compartment interactions span larger genomic regions than TADs and LADs and represent a network connecting regions of open and expression-active chromatin ("A" compartments) or closed and expression-inactive chromatin ("B" compartments). A compartments tend to be gene-rich, have high
GC-content, contain histone markers for active transcription, and usually displace the interior of the nucleus. As well, they are typically made up of self-interacting domains and contain early replication origins. B compartments, on the other hand, tend to be gene-poor,
compact, contain histone markers for gene silencing, and lie on the nuclear periphery. They consist mostly of LADs and contain late replication origins. The fact that compartments self-interact is consistent with the idea that the nucleus localizes proteins and other factors such as
long non-coding RNA (lncRNA) in regions suited for their individual roles. An example of this is the presence of multiple
transcription factories throughout the nuclear interior. These factories are associated with elevated levels of transcription due to the high concentration of transcription factors (such as transcription protein machinery, active genes, regulatory elements, and nascent RNA). Around 95% of active genes are transcribed within transcription factories. Each factory can transcribe multiple genes – these genes need not have similar product functions, nor do they need to lie on the same chromosome. Finally, the co-localization of genes within transcription factories is known to depend on cell type.
Chromosome territories during
prometaphase in
fibroblast cells The last level of organization concerns the distinct positioning of individual chromosomes within the nucleus. The region occupied by a chromosome is called a chromosome territory (CT). Among eukaryotes, CTs have several common properties. First, although chromosomal locations are not the same across cells within a population, there is some preference among individual chromosomes for particular regions. For example, large, gene-poor chromosomes are commonly located on the periphery near the nuclear lamina while smaller, gene-rich chromosomes group closer to the center of the nucleus. Second, individual chromosome preference is variable among different cell types. For example, the X-chromosome has shown to localize to the periphery more often in liver cells than in kidney cells. Another conserved property of chromosome territories is that homologous chromosomes tend to be far apart from one another during cell interphase. The final characteristic is that the position of individual chromosomes during each cell cycle stays relatively the same until the start of mitosis. The mechanisms and reasons behind chromosome territory characteristics is still unknown and further experimentation is needed. == References ==