Introduction

Image Source: Roberto Facenda/Flickr (Creative Commons Attribution Share Alike)

Compared to prokaryotes, eukaryotes have enormous genomes. For example, inside each of your cells is a genome containing more than 3 billion base pairs. Lined up, that's more than six feet (~2 meters) of DNA.

Fitting that much DNA in a cell nucleus (average width: 5 micrometers) is like fitting a string the length of the Empire State building underneath your fingernail! How do our cells store these extremely long, information-packed molecules?

The answer, in one word: Chromatin.

Chromatin -- found only in the cells of eukaryotic organisms -- is the complex of DNA and a specialized suite of of proteins that are organized in beads, wrapped with DNA, and the string folded, at multiple scales, to allow the DNA to be packaged into the neat nuclear structures called chromosomes that we see through the microscope. But chromatin is about more than just solving a storage problem. In the past few decades, scientists have come to increasingly appreciate the role of chromatin, and of modifications to the histone proteins central to chromatin structure, in regulating gene expression. The packaging is even as a mechanism for heritable changes in phenotype that don't involve actual changes to the genome sequence. The study of such mechanisms makes up an exciting, and rapidly growing, branch of biology called epigenetics.

In this section of the site, we'll take a brief look at chromatin as a regulator of gene expression in some ways complementary to transcription factors. And we'll see how the techniques used in the modENCODE project have helped to broaden our understanding of the system.

Strings, Beads, and Nucleosomes

Image Source: Reprinted by perimisson from Macmillan Publishers Ltd: Nature 421, 448-453 (23 January 2003), copyright 2003.

To fit our genomes into a tiny cell, the DNA of each chromosome is coiled, compacted, and coiled up some more. At the primary level of compaction, the DNA is wrapped around a group of special proteins called histones. When DNA wraps around a group of histones, it forms a nucleosome. You can think of the system as DNA "thread" wound around a protein "spool". The first scientists who saw nucleosomes with an electron microscope remarked that they looked like "beads on a string," though we now know that nucleosomes are more like "string wrapped around beads."

Each nucleosome is made of four different histones -- H2A, H2B, H3, and H4. Two molecules of each histone come together to form an octamer. (Note the prefix "octa" -- an octamer is just a complex made of eight proteins.) The DNA string wraps around the histone octamer bead to create the nucleosome.

So the process of fitting all of that DNA into a tiny cell nucleus begins with wrapping the DNA around histones into a nucleosome. But it doesn't end there -- the chain of nucleosomes coils around a central axis to get even more compact. As depicted in the diagram at the right, the packaging actually takes place at a number of scales:

  • The DNA wraps around histone octamers to form a "beads on string" fiber approximately 10 nanometers (nm) in width.
  • The beads-on-string structure in turn coils into a 30-nm-diameter fiber that packs the nucleosomes more closely together.
  • During cellular interphase -- the period in which the cell is not actively dividing -- "scaffold" proteins fold the 30-nm fibers into a somewhat more compact structure to fit within the nucleus.
  • During cell division, the chromatin, through the action of additional scaffold proteins, is radically packed and condensed to form the metaphase chromosome that divides and passes the DNA carrying the genetic code to the two daughter cells.

You might be starting to see a problem here. You already know that the genome contains important information -- the instructions for making all of the proteins of your cells. If the DNA is all twisted up on itself, how can the cell access that information so it can make proteins?

Getting at the Data: Histone Modification

Image Source: Richard Wheeler/Wikimedia Commons (Creative Commons Attribution Share Alike)

At the end of the holiday season, you may store your holiday decorations away in a closet or garage. You don't need them immediately at hand in the house, since you don't use them regularly -- but you know where they are in storage, and can find them when you need them.

Something very similar is happening in your cells. Cells have ways of opening up the DNA to be read -- or of hiding it so that it isn't read by mistake. And different types of cells have different sets of genes that are accessible for transcription, and other sets of genes that they have closed up and stored away. That's why your nerve cells are so different from your muscle cells, even though both types of cells contain exactly the same genome with exactly the same DNA code. And, just as you can push or slide boxes out of the way in your garage or closet to get at the holiday decorations when you need them, the cell can remove or slide nucleosomes so that RNA polymerase can get to a gene it needs to transcribe.

One way that cells can open or close a certain gene is by modifying the histones around which the DNA is wrapped. The ends of histone proteins form so-called "tails", and certain chemical groups can attach to those tails, changing their chemical properties and affecting how the tails interact with the DNA. Sometimes, chemical modification of histones makes a whole region of the genome easier to access –- sort of like putting the boxes you use most often on a lower shelf, or at the front of the closet. Other times, these chemical markers are labels that can be read by other proteins, as you might label a box with a marker to make it easier to find what you need.

Image Source: Reprinted by perimisson from Macmillan Publishers Ltd: Nature Reviews Neuroscience 8, 355-367 (May 2007), copyright 2007.

Examples of chemical modifications to histones are methylation, acetylation, or phosphorylation (the names just refer to the types of chemical group that is attached – methyl, acetyl, phosphate, etc.). These modifications can be added and removed by special enzymes, so that each type of cell can organize its genome to make it easier to synthesize the proteins that cell type uses most often. These enzymes can also change the modifications as the organism develops, or in response to the environment -- for example, in response to a hormone signal or temperature change.

These histone modifications can directly affect how tightly DNA binds to histones. In unmodified histones, the positively charged (basic) histone tails bind very tightly to the negatively charged (acidic) DNA. Some modifications, like the acetylation of a lysine, help neutralize the positive charge of the histone tails. This means the tails bind the DNA less tightly, and the chromatin is more open. Acetylation is thus a histone modification that is associated with genes that are very active, and expressed at high levels. (Check out an animation that illustrates how acetylation weakens the binding between DNA and the histone octamer, making it easier to disassemble the nucleosome.)

As already noted, other histone modifications work differently -- instead of directly affecting how tightly the tails bind to DNA, they are instead interpreted by other proteins. These modifications are believed to be part of a histone code, which is "read" by proteins that respond by making the chromatin either more open or more compact, depending on the specific histone modification.

Vignette: modENCODE, the Fly, and Chromatin States

Image source: Mr.checker/Wikimedia Commons (Creative Commons Attribution Share Alike)

The modENCODE scientists worked hard to understand how chromatin functions in model organisms like flies and worms. This has uncovered a lot of important and useful information about how chromatin is structured in general, which can be applied to other organisms, including humans. It's time to drill down into some of this work. Click on the image to the right to explore what detailed work in the fly has taught us about chromatin.

Thought Questions

  1. Why would modifications like acetylation, that make histones bind to DNA less tightly, affect how active a gene is?
  2. Imagine a gene that encodes a protein important for developing the axons of neurons. There are histones binding your DNA coding for this gene in every cell. Do you think these histones are more likely to be acetylated in your skin cells, brain cells, or the cells of your immune system?
  3. What effect do you think histone deacetylases have on gene expression, in general?
  4. Why would we study chromatin in flies and worms? Can you think of living organisms that might not be helpful for studying chromatin structure?