NOVA scienceNOW: Epigenetics
Epigenetics is a field of research
that investigates heritable information carried in the cell that is not
directly coded by DNA. The prefix epi, which comes from both Latin and Greek, means
"above" or "outside." The term epigenetics refers to
mechanisms controlling gene expression that are independent of the DNA sequence
Methyl groups are one kind of chemical known to have an
epigenetic effect. Methyl groups occur naturally, and the body obtains them
through food and as natural products of metabolism. They enable the
nucleus's very tightly wound chromatin to uncoil. Since they originate
outside the DNA, methyl groups are considered epigenetic factors. Today, you
will build a model of chromatin and explore how chromatin can be chemically
influenced by factors originating from "outside" the DNA.
Build a model of chromatin. Gather the materials you need
to make a model similar to the one your teacher demonstrated. Mark and assemble
the three tubes as follows:
Make the first "DNA" tube: Using a ballpoint pen, mark
the length of the tube using combinations of the letters A, C, T, G. The
letters should be large and in random order. You can repeat letters, and two of
the same letter can be next to each other. These letters represent the amino
acids of the nucleotides (A for Adenine, C for Cytosine, T for Thymine, and G
Make the second "DNA" tube: Lay a
second length of tubing alongside the first tube. Where you've written an
A on the first tube, mark a T on the second; where there's a T on the
first, write an A on the second. Similarly, where you've written a C on
the first, mark a G on the second; where there's a G on the first, mark a
C on the second.
Make the "histone" tube: Using a colored marker, put
dots or stripes along the length of the third tube.
Hold the ends of the three tubes together, keeping them as parallel
as possible (i.e., no twists, overlaps, or kinks). It does not matter which
tube is next to which. Wrap tape around the ends, securing the tubes together.
Repeat with the other end of the tubes. You should end up with a single 24-inch
unit made up of three strands.
Twist the tubes. With
one person holding each end of the triple bundle, begin twisting it into a
spiral. When it begins to form knots, continue to twist slowly while pulling
gently outward. Maintain tension so that the first spiral of knots forms into a
secondary spiral of knots.
Show how epigenetic factors control the behavior of
chromatin. Use your model to show how chromatin uncoils to reveal the sequence
of the nucleotides so they can be "read" by enzymes and then
transcribed by messenger RNA.
Select a zone about six inches long near the middle of the twisted
tubes. Mark this zone by attaching a binder clip to the "histone"
tube at each end of the zone. The clips represent chemicals called methyl groups
that are able to attach to the histone complex.
Have a third person from your group work to carefully uncoil the
three tubes in the six-inch zone marked off by the clips.
Once this zone is uncoiled, read the sequence of base pair letters
on the DNA tubes. This models the way that enzymes would "read" DNA
base pairs to transcribe messenger RNA.
After reading the base pair
sequence, carefully recoil the three tubes and remove the clips.
Write your answers on a separate sheet of
Why can it be difficult for enzymes to "read"
DNA base pairs in a coiled nucleosome?
In your own words, explain the process of how methyl tags
(represented by the binder clips) help chromatin uncoil to reveal the base
pairs in a nucleosome.
How are methyl groups examples of an epigenetic factor?
What would happen if methyl groups stayed attached to the
nucleosome forever and kept it continuously open?
List some ways that a nucleosome stuck in
"continuous reading" mode might become unstuck.
List some strengths and weaknesses of this
activity's model of the DNA–chromatin complex.
Why might high-level exposures in early life to factors
that lead to the accumulation of methyl groups have health consequences much
later in life?