Williams LAB @ UC Berkeley

1. What is epigenetics & how does it work?

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Epigenetics is the study of heritable information that is not contained within the DNA sequence of the genome. One example of this is DNA methylation - a reversible chemical modification to DNA that can be added or removed by specialized enzymes. DNA methylation can profoundly affect how a DNA sequence functions. Two genes with identical sequences can produce very different traits, depending on whether or not methylation is added to the DNA. Below is an example of a gene that changes the leaf surface when its DNA methylation is removed:

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In the Williams lab, we are interested in understanding how this epigenetic information is regulated and maintained by cells:

• How do the enzymes that add and remove DNA methylation find which sequences to act upon with precision?

• How do DNA methylation patterns get accurately inherited over many generations?

• How do these mechanisms function during the development of tissues and organs?

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2. How do cells recognize different DNA sequences?

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Each eukaryotic genome contains an enormously complex array of genetic information. DNA sequences can exhibit a huge diversity of functions and regulations. For example, genes encoding proteins can be highly expressed in all cells, or turned on precisely at particular times or in cell types. Repetitive DNA is often transcriptionally silent, as expressing repetitive sequences can cause problems for the cell. We are interested in understanding how the myriad sequences of the genome are perceived:

• How is repetitive DNA recognized?

• How are important genes protected from silencing?

• How do different DNA sequences regulate their epigenetic state?

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3. How does epigenetics influence cell identity and regeneration?

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Every cell within an organism contains the same genome sequence, yet cells can differentiate into diverse and specialized cell types. The cells of many plant species show an extraordinary ability to be flexible, reversing or changing their specialized cell identity in response to certain conditions. In the Williams lab, we are fascinated by how this happens at the level of perceiving and processing genetic and epigenetic information. 

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The information to make different cell types is accessible to every cell - so what determines the conditions under which cells can change their state? How are some plant species able to do this much better than others?

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Answering these questions could have a large impact on the world, by changing how we can get different plant species to regenerate. Regenerating whole plants from a few cells is a critical part of the process of plant engineering. The inability to regenerate many types of plants is a significant hurdle to our ability to use gene editing technologies (such as CRISPR/Cas9) to improve these plants to meet future challenges. Mitigating the effects of global climate change on agriculture and environments across the world will likely require the creative and nimble use of gene editing, which will require an understanding of how to regenerate gene edited plants. In the Williams lab, we are motivated to help unlock the secrets of plant regeneration to expand our ability to improve important plants to meet global challenges.

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