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Chromatin regulation at the frontier of synthetic biology

Key Points

  • Synthetic approaches are increasingly being applied to study and harness chromatin biology.

  • Residue-specific histone modifications and site-specific chromatin modifications provide powerful approaches to address key questions about the 'histone code' and chromatin-based gene expression 'memory'.

  • The synthetic positioning of nucleosomes enables fine-tuning of gene expression and can drive complex nonlinear gene expression programmes.

  • Chromatin exhibits spatial spreading of histone marks and gene regulation. The boundaries of these spatial regions can be synthetically controlled using both protein and DNA sequence elements.

  • Long-range chromatin interactions have been synthetically recapitulated, providing insights into their roles in gene regulation and development, as well as potential approaches to control gene expression.

  • Continued collaboration between chromatin biology and engineering will reveal mechanisms underlying gene regulation and the computational potential of chromatin. It will also provide a quantitative framework to harness chromatin in cellular engineering applications.

Abstract

As synthetic biology approaches are extended to diverse applications throughout medicine, biotechnology and basic biological research, there is an increasing need to engineer yeast, plant and mammalian cells. Eukaryotic genomes are regulated by the diverse biochemical and biophysical states of chromatin, which brings distinct challenges, as well as opportunities, over applications in bacteria. Recent synthetic approaches, including 'epigenome editing', have allowed the direct and functional dissection of many aspects of physiological chromatin regulation. These studies lay the foundation for biomedical and biotechnological engineering applications that could take advantage of the unique combinatorial and spatiotemporal layers of chromatin regulation to create synthetic systems of unprecedented sophistication.

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Figure 1: Regulatory features of chromatin at multiple length scales.
Figure 2: Synthetic control of biochemical chromatin modifications.
Figure 3: Synthetic spatial control of chromatin.
Figure 4: Potential applications of synthetic chromatin biology.

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Acknowledgements

This work was supported by a US National Institutes of Health (NIH)-National Institute of General Medical Sciences (NIGMS) Ruth L. Kirschstein Postdoctoral Fellowship (A.J.K.), an NIH Director's Pioneer Award (J.K.J.), a Defense Advanced Research Projects Agency grant (J.K.J., A.S.K., and J.J.C.), start-up funds from the Department of Biomedical Engineering at Boston University (A.S.K.), a National Science Foundation CAREER Award (A.S.K.), a NIH R24 (J.J.C.), the Wyss Institute for Biologically Inspired Engineering (J.J.C.) and the Howard Hughes Medical Institute (J.J.C.). Owing to space limitations, the authors regret that many important publications were not able to be discussed in this Review.

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Correspondence to James J. Collins.

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Competing interests

J.K.J. is a consultant for Horizon Discovery. J.K.J. has financial interests in Editas Medicine and Transposagen Biopharmaceuticals. J.K.J.'s interests were reviewed and are managed by Massachusetts General Hospital and Partners HealthCare in accordance with their conflict of interest policies. A.J.K., A.S.K. and J.J.C. declare no competing interests.

PowerPoint slides

Glossary

Nucleosomes

Octamer protein complexes in which an octamer is comprised of two copies each of H3, H4, H2A and H2B histone proteins.

Non-coding RNAs

Functional RNA molecules that are not translated into proteins.

Lysine acetylation

A post-translational modification in which an acetyl group reacts with the primary amine on the side chain of a lysine residue.

Correlation

A relationship between two or more variables. The correlation between the occupancy of a chromatin modification and transcriptional activity does not directly prove that the modification causes transcriptional activity, or vice versa.

Pleiotropy

The phenomenon whereby one gene influences multiple other seemingly unrelated genes or traits.

Unnatural amino acid

An amino acid that is not naturally encoded or found in the genetic code of an organism.

Chemical ligation

A chemical reaction that links a fully chemically derived peptide to the end of a recombinant protein.

Zinc-finger

(ZF). A small protein structural motif coordinated to one or more zinc ions that stabilize its fold.

Transcription activator-like effector

(TALE). A bacterial protein with a variable number of 34-amino-acid repeats, of which 2 residues specify binding to a DNA base.

CRISPR

(Clustered regularly interspaced short palindromic repeat). An important part of a prokaryotic adaptive immune system that uses short RNAs to guide the CRISPR-associated 9 (Cas9) nuclease to specific targets, which cleaves foreign DNA elements such as plasmids and phage genomes.

RNA interference

(RNAi). A biological process that inhibits gene expression through RNA molecules interacting and interfering with specific mRNA molecules.

FKBP–FRB

A protein pair consisting of FKBP and FRB, which dimerize by mutually binding to the small molecule rapamycin.

PYL–ABI

A protein pair consisting of PYL and ABI, which dimerize by mutually binding to abscisic acid.

Avidity

The accumulated strength of multiple affinities from multivalent non-covalent binding interactions.

Cry2 and CIB1

(Cryptochrome 2 and cryptochrome-interacting basic helix–loop–helix 1). A pair of proteins that dimerize at the subsecond timescale upon blue-light exposure and that dissociate on the minute timescale.

Nuclear lamina

A dense fibrillar network of intermediate filament proteins at the periphery of the nucleus.

Telomeres

The regions at the ends of chromosomes comprised of repetitive nucleotide sequences that are typically repressed by heterochromatin.

Auxotrophic markers

Genes absent in an organism that normally produce organic compounds required for survival of the organism.

Yeast knockout library

A collection of yeast strains, each of which harbour a knockout allele for a single gene. Strains are either haploid and have a non-essential gene knocked out, or diploid and have the knockout allele in a heterozygous state.

β-globin

A subunit of the major haemoglobin complex found in adult mammals.

Locus control region

(LCR). A genomic region that enhances the expression of genes from a distance.

Kinetochores

The protein structures assembled on the centromere to which spindle fibres attach during cell division to pull sister chromatids apart.

Centromeres

The genetic loci on chromosomes that link sister chromatids during mitosis and on which kinetochores assemble.

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Keung, A., Joung, J., Khalil, A. et al. Chromatin regulation at the frontier of synthetic biology. Nat Rev Genet 16, 159–171 (2015). https://doi.org/10.1038/nrg3900

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