Gene expression, the process of turning a gene into a functional product, is not a steady stream. For many genes, it occurs in intermittent pulses known as transcriptional bursting. During a burst, a gene rapidly produces messenger RNA (mRNA) molecules and then falls silent before becoming active again, contrasting the older view of transcription as a constant process.
This process is understood through a two-state model, where a gene switches between an active “on” state and a silent “off” state. Transcription only happens during the “on” periods. The timing and output of each burst are irregular and stochastic, meaning they are subject to random fluctuations, a defining feature of gene operation in individual cells.
This bursting is a common mode of gene expression in organisms from bacteria to humans, representing a dynamic view of how genetic information is used. Understanding this behavior is important for comprehending how cells regulate functions, respond to their environment, and generate diversity. The intermittent activity creates variability with significant consequences for cellular processes.
The Mechanics of Gene Bursts
A primary factor in transcriptional bursting is the changing structure of chromatin, the complex of DNA and proteins that packages genetic material. For a gene to be transcribed, this tightly coiled chromatin must loosen to make the DNA accessible. This dynamic opening and closing of chromatin contributes to the gene’s switching between active and inactive states.
A gene’s promoter region acts as a landing pad for the proteins that initiate transcription, functioning as a molecular switch. This switch flips between a “permissive” state, where transcription can occur, and a “restrictive” state, where it is blocked. The transition is governed by the binding and unbinding of specific proteins called transcription factors, which play a large part in modulating this switch.
The binding of transcription factors to DNA is transient. When the right combination assembles at the promoter, they recruit RNA polymerase, the enzyme that synthesizes mRNA. This recruitment can lead to multiple rounds of transcription in quick succession, which constitutes a burst. Afterward, the transcription factor complex may disassemble or the chromatin may become compact again, ending the burst.
Distant genetic elements called enhancers also help orchestrate bursts. Though far from the gene, enhancers can physically contact the promoter through DNA looping. These fleeting contacts help trigger transcription-permissive environments, sometimes involving protein- and RNA-rich droplets called biomolecular condensates. The transient nature of these interactions contributes to the bursting pattern of gene activity.
Detecting Transcriptional Bursts
Scientists visualize and quantify gene expression in individual cells using techniques like single-molecule RNA Fluorescence In Situ Hybridization (smFISH). This technique allows researchers to label and count individual mRNA molecules in chemically preserved cells. By fluorescently tagging probes that bind specifically to the mRNA of interest, scientists see bright dots under a microscope, with each dot representing a single mRNA molecule. This provides a snapshot of gene activity at a specific moment.
By analyzing a large population of cells with smFISH, researchers observe the distribution of mRNA counts. Cells in a burst show many mRNA molecules, often clustered at the gene, while silent cells have few or none. From this data, scientists can calculate the average number of mRNAs produced during a burst (burst size). They can also estimate how often bursts occur (burst frequency).
Live-cell imaging captures bursting dynamics in real-time. A common approach, using systems like MS2 or PP7, involves genetically engineering a cell in two ways. First, the gene of interest is modified to include repeating sequences in its mRNA. Second, the cell is made to produce a fluorescent protein that binds to these sequences. As the gene is transcribed, the new mRNA glows, allowing scientists to watch mRNA production as bright spots in a living cell.
Live-cell imaging allows researchers to track the appearance and disappearance of fluorescent transcription sites. This provides direct measurements of the duration of the “on” and “off” periods. From this, they can precisely quantify burst frequency and the number of mRNAs made per burst. These techniques confirm that gene expression occurs in discrete pulses.
Biological Impact of Pulsatile Gene Activity
Pulsatile gene expression creates variability in protein and RNA levels from one cell to another. Even in a genetically identical population, the random timing of bursts ensures each cell has a slightly different internal composition. This “noise” in gene expression is a feature cells can use for adaptation and survival.
Cell-to-cell variability is important in cellular decision-making, such as stem cell differentiation. Varying levels of regulatory proteins, driven by bursting, can push individual cells toward different fates. A cell that experiences a large burst of a developmental gene might commit to a specific lineage, while its neighbor remains undifferentiated. This allows a population to explore different possibilities, increasing the chance of survival in a changing environment.
During development, transcriptional bursting contributes to the patterns and structures in a growing organism. Regulatory networks can finely tune the frequency and size of bursts to ensure proteins are produced in the right amounts at the right times. For example, the pulsatile expression of genes for tissue formation helps establish sharp boundaries and distinct cell types.
The regulation of bursting kinetics is linked to cellular health, and its dysregulation can be associated with disease. Changes in burst frequency or size can alter the average level of a gene’s product and the degree of variability in a cell population. In some cancers, for instance, altered bursting dynamics of genes that control cell growth can lead to a more heterogeneous tumor, where some cells may be more resistant to therapy or more likely to metastasize.