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Question: You hypothesise that EV cargo from aged cells can play a role in changing the epigenetic landscape of stem cells. Outline an experimental design that would enable you to explore the influence of EVs on histone modifications using ChIP-seq. Include a hypothesis, rationale, methodology, what you will quantify and why, and how will you interpret the data in 700 words
. Hypothesis: Exosomes released from aged cells can alter the epigenetic landscape of stem cells through modifications of histone proteins. Rationale: Epigenetic modifications are heritable changes in gene expression that occur without changes in the primary DNA sequence. Histone modifications are one type of epigenetic modification and are critical for proper gene expression. Research has demonstrated that aging is associated with an alteration of histone proteins; however, the mechanisms by which aging can influence epigenetic changes are still unclear. Exosomes are extracellular vesicles released by both healthy and aged cells, which may contain RNA and proteins that can influence cell behavior and gene expression. It is possible that exosomes released from aged cells could contain proteins capable of altering the epigenetic landscape of a cell. This experiment aims to explore the influence of exosomes on histone modifications in the context of stem cells. Methodology: To explore the influence of exosomes on histone modifications, ChIP-seq will be used. ChIP-seq stands for chromatin immunoprecipitation-sequencing and is used to identify and quantify the frequency of binding sites for a given transcription factor, histone modification, or other DNA binding proteins. In this experiment, ChIP-seq will be used to quantify the frequency of histone modifications in stem cells after treatment with exosomes. Specifically, stem cells will be grown under culture conditions and differentiated into a muscle lineage. Then, the cells will be divided into two groups. The first group of cells will be exposed to exosomes derived from aged cells, while the second group will serve as a control and be exposed to exosomes derived from healthy cells. Following exposure, the cells will be collected, and ChIP-seq will be performed to quantify the frequency of histone modifications in the two groups. What will be quantified and why: Histone modifications will be quantified with ChIP-seq to explore the influence of exosomes on epigenetic modifications. Histone modifications are critical for transcription regulation and proper gene expression, and ChIP-seq is the most accurate method for measuring changes in the frequency of histone modifications. How the data will be interpreted: The goal of the experiment is to determine whether exosomes released from aged cells can influence the epigenetic landscape of stem cells. To interpret the results, the frequency of each histone modification in the group
Jan. 16, 2023, 5:05 a.m.
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