Chromatin Chapter 1: DNA Organization, the Nucleosome, and Histones

Chromatin is one of those things that I never really paid any attention until I suddenly realized how important and interesting it is.  How is it that so much information (DNA) can be stored in such a small space (the nucleus)?  How is it that this information is used when it is so tightly packaged?  It may sound nerdy, but I’m still in awe at how important chromatin really is.  This next set of posts will explore the basics of chromatin and begin to touch on the effects it has on genes and cells.  I’ve already mentioned how it affects DNA repair, but the process has even more far-reaching effects.

DNA Organization

Chemically, DNA and RNA are composed of sugar phosphate backbones with nitrogenous bases attached.  The sugar comes in the form of ribose (in the case of RNA) or deoxyribose (in the case of DNA).  Deoxyribose lacks the 2’ hydroxyl group on ribose.  The ribose / deoxyribose sugars are connected via a phosphate linkage (PO₄) via the 3’ and 5’ hydroxyl groups.  The 1’ hydroxyl group is where the nitrogenous base attached.  Purines contain a purine ring and come in the form of adenine and guanine.  Pyrimidines consist of cytosine, uracil, and thymine.  The ribose / deoxyribose connected to the base and the phosphate are considered nucleic acids.

Nearly everyone knows the famous story of Watson and Crick and their discovery of the structure of DNA.  They hypothesized (correctly so) that DNA consists of a double-helix held together by the hydrogen bonds formed by the nitrogenous bases (adenine to thymine; guanine to cytosine).  This double helix is antiparrallel, right-handed, and has polarity: the 5’ end is attached to a phosphate group, while the 3’ end consists of a free hydroxyl group.  The helix turns once every 10.5 bases at a total distance of 36 Å, with a 3.4-Å rise per base and a width of 20 Å.  The entire helix is negatively charged due to the phosphate groups that connect the sugars. 

DNA does not exist in the cell as a free-floating molecule.  Instead, it is shaped and organized by chromatin, the makeup of the chromosomes consisting of the DNA itself and the attached proteins.  In the case of humans, unraveled DNA measures about two meters in length, but cell nuclei are, at most, 10 μm.  Therefore, the cell must attain a 10,000-fold compaction while still performing all the requirements for the cell.  To accomplish this, the cell uses the chromatin hierarchy, composed of five orders of organization.

The Nucleosome

The first order of chromatin packaging is the nucleosome, the most basic organization mechanism used to compact the DNA.  The nucleosome packages 147 bp of DNA wrapped on “beads” of eight histone proteins (making an octamer). These octamers are positioned at intervals on the DNA, and,  if the DNA is spread, the  nucleosomes attached to the DNA look like beads on a string.  The nucleosome consists of histones H2A, H2B, H3, and H4, and nucleosomes are attached to each other by linker histone H1.  Linker and nucleosomal histones are made throughout S phase, when new DNA is synthesized and must be compacted.   Histones can be modified in several ways to affect the structure and dynamics of the DNA.  The proteins have largely been conserved through evolutionary history but variants do exist.  These variants are synthesized mostly during interphase and insert into mature chromatin via chromatin remodeling complexes.  One of these variants, H2A.Z,  limits chromatin condensation; another variant H2A.X is involved in DSB response.  H3.3 can be found in long-term active chromatin.  In general, these variants are involved in changes in chromatin that remain for long periods of time in the cell. 

In addition to histones, a number of other proteins bind DNA and are included in the chromatin.  Namely, the high mobility group proteins (HMGs), polymerases, and DNA repair enzymes interact with the DNA and the chromatin. 

The DNA itself is wrapped around the nucleosome 1.75 times, with about 60 bp of DNA between nucleosomes and associated with linker histone H1.  The nucleosomes contain groves that fit the DNA between H2B and H4 and H4 and H3.  The octamer itself exists as two H2A/H2B dimers and one H4-H3-H3-H4 tetramer.