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Research Proposal
Megha Sevalia
Intern Mentor I
2017-2018
Title:​ Epigenetics: A Small Change Can Make a Big Difference

Introduction and Overview of Research:

This research project will consider epigenetic effects on a specific series of lab
experiments relating to mutations on the phospho sixs of SET 5 on the enzyme lysine. The
quantitative, experimental research conducted through lab experiments will seek to find the
genetic regulation, stability, and localization, and then connect the conclusion to lifestyle or
environmental factors, explored through the literature review. The outcome of the research will
be a model to visualize the results of the research, along with written description with the
necessary information. It will be presented to students with a background in beginner genetics as
an introduction to epigenetics, which is not currently covered in most curriculums.

Background and Rationale:

Epigenetics is a rapidly upcoming field in which a previously denied concept emerged as
possible. Previously, DNA was considered uncontrollable, left only changeable by the processes
of natural selection, random assortment, and chance mutations (“The epigenome learns from its
experiences”). However, new ideas suggest that lifestyle factors could have effects on repressing
the transcription of DNA through methylation, or through histone methyltransferases (H. Green,
2012). Through either process, DNA from one generation remains in an inaccessible state from
the beginning of a newer generation’s lifespan, preventing the manifestation of the trait, which
could have been shown had the initial repression not happened (Green, 2017). This is done
through the methylation of certain genes, in which the DNA and histones remain tightly packed.
To explore this faster, the following specific example will be used, along with
experimentation regarding it. The enzyme lysine and histone modifying enzymes catalyze the
transfer of methyl groups to the lysine, which changes proteins from serines to alanines. The
(histone methyltransferase) enzyme is called SET (Su(var)3-9, Enhancer of Zeste, Trithorax) 5,
and its regulation, its methylation of other proteins, whether protein stability of SET 5 changes
with the mutations, and whether the localization (areas where it methylates the lysines) of SET 5
is changing are also still being questioned ​(Green, 2017)​. This overall process changes which
DNAs are wrapped around histones to form chromatin, and unable to have genetic expression or
stability. In order to do this, scientists utilize vectors inserted in artificially created holes in the
nuclear membrane with SET 5 and mutated DNA. This is then placed into bacterial cells, which
have natural mechanisms to imbibe the new DNA, and culture colonies of the new traits,
allowing the scientists the ability to observe genetic expression (E. Green, 2012). They can also
run DNA through gel electrophoresis and western blotting to figure out how the mutated DNA
affects the new gene expression and proteins, by finding the lengths of the new DNA.
Epigenetics is an important concept because it is a concept in the largely controversial
genetic research realm which people can take measures to control through ethically
unquestionable ways (“The epigenome learns from its experiences”). Epigenetics works at a
molecular level, but the phenotypic effects are large, and the causes are as well. Due to this, it
would be beneficial to share the ways in which people can adjust their lifestyles as to preserve
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their genetic code. The concept also has many interesting possibilities for future medical
advances, which is something that people might be interested in investing in for the future. The
specific lab research will hopefully show the results of an epigenetic change as positive or
negative, and will connect to a specific lifestyle factor in support of the better outcome.

Research and Methodology:

Research Questions:​ How does epigenetics affect DNA? How do mutations in the phospho sixs
of SET 5 effect lysine, and DNA regulation/ silencing? How do environmental stressors
influence the process? How do lifestyle stressors influence epigenetics?
Research Hypothesis: ​Unhealthy lifestyle influences create stressors which lead to harmful
epigenetic changes in the DNA. Stressors cause mutations to influence the process and silence
DNA, regulating genomic function. The mutations in the phospho sixs of SET 5 will cause DNA
silencing.
So far a lot of the experiments are showing a null hypothesis in that the mutations are not
causing the DNA silencing, which is still analyzable, as it shows the stability of the gene despite
a certain environmental condition changing in increasingly large increments. Other trends will be
discovered as the experiments continue, and the environmental connections will be made later in
the year.
Research Design Model:
The research design will be experimental research and the results will be quantitative.
This design model makes the most sense as the research is conducted in a lab with physical
results, which can be analyzed to form direct causal relationships. The research will include a
series of experiments relating to SET 5. The independent variables will consist of the different
mutations which exist in the phospho sixes of lysine. The dependent variables will be the effects
the mutations have on DNA regulation, silencing, localization, and stability.
Data Collection:
The data collection will be the experiments that are conducted at the lab during the
internship. This data will lead to a molecular conclusion hopefully, which will then be connected
to the broader research about epigenetics and lifestyle stress factors done through the literature
review through acquired knowledge of epigenetic mechanisms. While the literature review and
connections may already exist in connection to other mechanisms, the results discovered in the
lab will be original and the connections to lifestyle factors will be made under the guidance of
the mentor, who is experienced in doing so.

Product Objectives:
The product of this research will be some sort of model with a flier description. This
product aligns nicely with the research because as it is done at the molecular level, it is hard to
picture or present the information to an audience who does not specifically know the details of
genetics. A model will help them picture the project and the flier will include any other crucial
information needed. Originally, I had planned to do a physical model, which is still a possibility.
However, I have found ways to create an online model using prezi or other websites, which
might be easier to present. The product will be presented to students with a background in
genetics, such as AP Biology, and will provide information about the general epigenetic process,
the lab research, and any personal implications proposed as a result of the experiments. I might
also give the product to my mentor for her beginner students or for the lab. The product will be
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presented in a presentation format, but will show them the connection between the molecular
changes and the physical manifestations.

Logistical Considerations:
The limitations that exist are that as the outcome has to be built within the school ear, the
research at the lab may not be finished in the same time limit. There would still be information to
present, but possibly not a conclusion, so the presentation will just be a bit of a cliff hanger and
end with the possibilities that could be found in the future. The resources required will be the lab
materials and my time spent conducting the experiments. Time spent with an online product may
also be required, or craft materials may be required instead. The product materials will cost
money, but the data collection is funded by the internship through grants and the school. I will
probably need the permission of my mentor to share my final product, but it should be easy to
get. In third quarter, a timeline will be added that outlines the data collection, product
development, and audience distribution.

References:
The epigenome learns from its experiences. (n.d.). ​Learn Genetics: Genetic Science Learning
Center.​ Retrieved October 05, 2017, from
http://learn.genetics.utah.edu/content/epigenetics/

Green, E. M., Mas, G., Young, N. L., Garcia, B. A., & Gozani, O. (2012). Methylation of H4
lysines 5, 8 and 12 by yeast Set5 calibrates chromatin stress responses. ​Brief
Communications: Nature, Structure, and Molecular Biology,​ ​19​(3), 361-363.

Green, E. (2017, October 18). Personal Interview.

Green, H. [SciShow]. (2012, January 22). ​Epigenetics​ [Video File].

https://www.youtube.com/watch?v=kp1bZEUgqVI