AU Kierra Franklin

Text Book – Epigenetic Cancer Therapy

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Chapter 10 – Synthetic biology and cell engineering—deriving new insights into cancer epigenetics.
Franklin KA, Haynes KA. (2023) Translational Epigenetics: Epigenetic Cancer Therapy (Second Edition). Academic Press. pp 195-210

The latest edition of Epigenetic Cancer Therapy includes a chapter that explores how scientists are using synthetic biology and cell engineering techniques, collectively known as epigenetic engineering, to develop powerful tools for understanding and manipulating the regulation of genes in cancer cells. In this chapter, we explain how four general technologies in epigenetic engineering have been used in cancer research. The first two technologies are genetic reporters and protein reporters, which allow us to closely monitor the changes in gene expression inside living cells. The other two technologies are epigenome editing and epigenome actuation. Epigenome editing enables scientists to make precise changes to the chemical modifications on the DNA and proteins that affect gene activity. Epigenome actuation, on the other hand, involves using synthetic molecules to activate or deactivate groups of genes in cancer cells. One exciting aspect of epigenome editing and actuation is that they offer advantages over traditional epigenetic drugs and genetic knockdowns when studying cancer epigenetics. Combining cell engineering with cancer research has the potential to revolutionize our understanding of cancer and may lead to the development of more effective therapies in the future.

Perspective – Trends in Biochem Sci – Adding post-translational modifications and protein-protein interactions to protein schematics

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TIBS_2022_reviewAdding post-translational modifications and protein-protein interactions to protein schematics.
Pandy N, Franklin KA, Haynes KA, Rapé M, Cristea IM. (2023) Trends Biochem Sci. 48: 407–409.
PMID: 37059055

In this “TrendsTalk” of the Special series: Scientific Figure Development, Dr. Karmella Haynes and Kierra Franklin and other recent TiBS authors share their thoughts on aspects to consider when creating figures that depict proteins, post-translational modifications (PTMs), and important protein–protein interactions (PPIs) in protein complexes

Review – Trends in Biochem Sci – Beyond the marks: reader-effectors as drivers of epigenetics and chromatin engineering

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TIBS_2022_reviewBeyond the marks: reader-effectors as drivers of epigenetics and chromatin engineering
Franklin KA, Shields C, Haynes KA. (2022) Trends Biochem Sci. 47: 417–432. Free access (until June 3, 2022)
PMID: 35267540 | PMCID: PMC9074927

Epigenetics is a process where changes in gene expression are inherited through cell divisions and in some cases across familial generations. As more links between epigenetics and human development and disease have emerged, scientists have become more interested in controlling epigenetic states using molecular technologies including protein engineering. In this review, we discuss a relatively new substrate for epigenetic engineering, a class of gene regulators called “reader-effectors.” These are different from DNA-binding transcription factors in that a single reader-effector type can engage at multiple sites through interactions with biochemical marks (“signals”) on chromatin, the protein/DNA structure that organizes the genome. So far, scientists have used “epigenome editing” to generate or erase signals to alter epigenetic states. Relatively little has been done to control how these signals are transduced into outputs, such as gene regulation, to ultimately control cell behavior. We discuss what natural systems have taught us about the mechanism of two basic composable parts, the “reader” and “effector” domains,  and discuss potential of reader-effector engineering, a technique we call “epigenome actuation.”