A single human cell contains about 6.5 feet of DNA that must be packed into a microscopic nucleus. This feat of data compression is not just a matter of stuffing it in; the organization is highly regulated. The way DNA is folded and arranged determines which parts of the genetic code are accessible and which are kept in storage. This precise organization is fundamental to how a cell functions, as the structure of this packaging holds the instructions for how and when to read the genetic code.
The Fundamentals of DNA Packaging
To solve the storage problem, the cell winds its DNA around proteins called histones, much like a thread is wrapped around a spool. The DNA is the thread, and a core of eight histone proteins acts as the spool. This combined structure, a segment of DNA wrapped around a histone core, is called a nucleosome.
The resulting “beads-on-a-string” structure is known as chromatin. A nucleosome includes about 147 base pairs of DNA wrapped around the histone octamer. This unit of compaction is then further coiled and folded into more complex structures, allowing the DNA to be contained within the nucleus.
The arrangement of nucleosomes is the first level of DNA organization. It transforms the linear DNA molecule into a three-dimensional structure. This initial folding is not merely for compaction, as it sets the stage for all subsequent layers of genetic control.
Defining Nucleosome Phasing
The spacing of nucleosomes is often not arbitrary. Nucleosome phasing refers to the regular arrangement of nucleosomes along the DNA, where they are positioned with a consistent and repeating interval. This creates a predictable pattern of occupancy along a specific stretch of the genome.
This regularity is defined by the length of the DNA that connects one nucleosome to the next, known as linker DNA. In a phased array, the linker DNA segments have a relatively uniform length. For instance, nucleosomes might be positioned so that the linker DNA is consistently 20 base pairs long, creating a periodic pattern in contrast to a random arrangement.
The result is an ordered chromatin architecture in specific regions of the genome. This ordered array means that the position of one nucleosome provides information about the likely position of its neighbors. This predictability is an active feature of the genome with significant implications for how the DNA sequence can be accessed.
Mechanisms Establishing Nucleosome Positions
The placement of nucleosomes is established through several mechanisms. One is the barrier model, where DNA-binding proteins like transcription factors bind to specific DNA sequences. These proteins act as physical obstacles, preventing a nucleosome from forming at that location. Nucleosomes then assemble in an ordered pattern extending outward from this barrier.
Another factor is the DNA sequence itself, a concept called statistical positioning. DNA is not uniformly flexible, as some sequences bend more easily than others. Sequences that are rigid are less favorable for wrapping around the histone core, while more flexible sequences are preferred. For example, A-T base pairs are more easily bent and often found on the inside of the wrapped DNA.
These processes are complemented by chromatin remodelers. These enzyme complexes use energy to physically alter the chromatin landscape. They can slide nucleosomes along the DNA, eject them, or help assemble them in specific locations. This dynamic action allows the cell to establish and alter nucleosome phasing in response to various signals.
The Role of Phasing in Gene Regulation
The structured arrangement of nucleosomes is a mechanism for controlling gene activity. The positioning of nucleosomes can either conceal or reveal important stretches of DNA. When a regulatory sequence, such as a promoter, is wrapped within a nucleosome, it is hidden from the cellular machinery. This positioning can keep the associated gene in an “off” state.
A feature often found at the beginning of active genes is a Nucleosome-Depleted Region (NDR). This is a gap in the regular array of nucleosomes, creating an open stretch of DNA. This NDR acts as an accessible landing pad for transcription factors and RNA polymerase, the enzyme that transcribes a gene into RNA. The presence of an NDR indicates that a gene is poised for expression.
Nucleosome phasing organizes the genome into functional domains. The positioned nucleosomes flanking an NDR help to define its boundaries and can influence how efficiently transcription is initiated. By sliding nucleosomes, the cell can fine-tune the accessibility of these regulatory sites, turning genes on or off.
Methods for Studying Nucleosome Architecture
Scientists map the locations of nucleosomes using a technique called Micrococcal Nuclease sequencing (MNase-seq). The method uses the enzyme Micrococcal Nuclease (MNase) to cut the exposed linker DNA between nucleosomes. The DNA wrapped tightly around the histone core is protected from this digestion.
The process involves treating chromatin with MNase until most of the linker DNA is degraded, leaving behind the nucleosome-bound DNA fragments. These protected fragments, each approximately 147 base pairs long, are then collected. They are identified using high-throughput DNA sequencing, which generates millions of sequences corresponding to nucleosome locations.
By aligning these sequences to a reference genome, researchers create a map of nucleosome occupancy. This map reveals the positions of individual nucleosomes with high accuracy. It allows scientists to identify phased arrays, locate Nucleosome-Depleted Regions, and observe how nucleosome patterns change in different cell types or conditions.