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Construction of a Synthetic, Chromatin-Based Epigenetic System in Human Cells

62 Pages Posted: 13 Apr 2018   Sneak Peek Status: Review Complete

Minhee Park

Boston University - Biological Design Center; Boston University - Department of Biomedical Engineering

Nikit Patel

Boston University - Biological Design Center; Boston University - Department of Biomedical Engineering

Albert J. Keung

North Carolina State University - Department of Chemical and Biomolecular Engineering

Ahmad S. Khalil

Boston University - Biological Design Center; Boston University - Department of Biomedical Engineering; Harvard University - Wyss Institute for Biologically Inspired Engineering

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Abstract

The chromatin landscape of DNA and histone modifications represents a fundamental layer of cellular regulation. These modifications, which are implicated in gene regulation and even complex properties such as epigenetic programs, allow eukaryotic organisms to expand information content beyond DNA sequence. Despite its rich regulatory potential, our ability to manipulate this landscape in living cells remains limited. Here we exploit DNA adenine methylation (m6A), a modification rarely found in metazoan genomes, to construct a fully synthetic chromatin system in human cells. Our system is composed of three functional modules that mediate m6A operations: (1) synthetic initiator module to place m6A at specific genomic sites; (2) synthetic readout module to recognize m6A and mediate m6A-dependent transcriptional logic; (3) propagation module that implements “read-write”, a mechanism proposed to underlie chromatin spreading and epigenetic maintenance across cellular systems. Together with a quantitative model, we combine these modules to construct regulatory circuits that drive spatial m6A propagation to regulate distal genes, and enable epigenetic memory of transcriptional states. These epigenetic functions are engineered de novo and do not make use of endogenous mechanisms, providing evidence that complex behaviors like memory can be programmed using specific molecular mechanisms at the chromatin level. Our work establishes a synthetic, chromatin ‘programming language’ to expand the regulatory potential of the genome and engineer epigenetic functions in mammalian cells.

Suggested Citation

Park, Minhee and Patel, Nikit and Keung, Albert J. and Khalil, Ahmad S., Construction of a Synthetic, Chromatin-Based Epigenetic System in Human Cells (2018). Available at SSRN: https://ssrn.com/abstract=3155804 or http://dx.doi.org/10.2139/ssrn.3155804
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Minhee Park

Boston University - Biological Design Center

610 Commonwealth Ave.
Kilachand Center
Boston, MA 02215
United States

Boston University - Department of Biomedical Engineering

595 Commonwealth Avenue
Boston, MA 02215
United States

Nikit Patel

Boston University - Biological Design Center

610 Commonwealth Ave.
Kilachand Center
Boston, MA 02215
United States

Boston University - Department of Biomedical Engineering

595 Commonwealth Avenue
Boston, MA 02215
United States

Albert J. Keung

North Carolina State University - Department of Chemical and Biomolecular Engineering ( email )

Centennial Campus Box 7905
911 Partners Way
Raleigh, NC 27695
United States

Ahmad S. Khalil (Contact Author)

Boston University - Biological Design Center ( email )

610 Commonwealth Ave.
Kilachand Center
Boston, MA 02215
United States

Boston University - Department of Biomedical Engineering ( email )

595 Commonwealth Avenue
Boston, MA 02215
United States

Harvard University - Wyss Institute for Biologically Inspired Engineering ( email )

3 Blackfan Circle
Center for Life Science Bldg.
Boston, MA 02115
United States