Researchers at MIT have discovered that the physical order of genes along DNA influences the activity of neighboring genes. Turning one gene on can boost or suppress nearby genes. Genes positioned upstream, meaning before the active gene, are often stimulated. Genes positioned downstream, meaning after it, are usually inhibited. These effects result from local unwinding and rewinding of the DNA double helix during gene transcription.
Transcription is the process in which an enzyme called RNA polymerase copies a gene into messenger RNA. This unwinding loosens DNA structure upstream and tightens it downstream, affecting how easily the enzyme can access neighboring genes.
Gene syntax determines coordinated control of synthetic gene circuits
The arrangement of genes, which the researchers term “gene syntax,” offers a new way to design synthetic gene circuits. These are artificial networks of genes engineered into cells to produce desired proteins or behaviors in a controlled manner. The scientists tested three main arrangements in human cells and stem cells. In divergent circuits, where two genes point away from each other, both genes showed increased activity. In tandem circuits, where one gene follows directly after another, the upstream gene often suppressed the downstream gene. Effects reached up to 25-fold changes in gene expression and extended across distances of up to 2,000 base pairs.
Imaging revealed that active genes create tightly twisted DNA structures called plectonemes downstream. These act like knots in a cord and hinder RNA polymerase binding. A new insertion tool named STRAIGHT-IN Dual enabled precise placement of gene pairs.
This physical approach complements traditional biochemical methods for controlling synthetic gene circuits. In testing, a divergent arrangement greatly increased production of segments of a novel yellow fever antibody. The strategy also improved earlier circuits designed for gene therapy and cell reprogramming. It opens possibilities for dynamic synthetic gene circuits such as toggle switches that flip between states, oscillators that cycle on and off, or pulse generators.
The study shows how engineers can achieve more precise and coordinated control in synthetic gene circuits for medical and biotechnology applications. This research is published in Science.