And they’re off to the races—scientists who want to predict transcription factor efficiency are heading to the genomic track so they can collect measurements of transcription factor mobility. These measurements help the scientists understand why transcription factors (TFs) differ in their ability to search the genome and bind to specific genomic regions, and thereby switch genes on or off with greater or lesser alacrity.
The speed with which a transcription factor finds a specific genomic site is largely a matter of the transcription factor’s search strategy. And a big part of this strategy is sliding, that is, sliding along stretches of DNA. Sliding has been associated with nonspecific binding, as opposed to the specific binding between a transcription factor and the genome site it targets to regulate gene expression.
Nonspecific binding has also been associated with mitotic chromosome binding (MCB). Exploiting this association, scientists based at Ecole Polytechnique Fédérale de Lausanne (EPFL) found a way to predict the efficiency with which different TFs scan the genome in living cells.
Combining quantitative measurements of MCB, transcription factor mobility measurements by fluorescence recovery after photobleaching, single molecule imaging of DNA binding, and mapping of transcription factor binding and chromatin accessibility, the scientists found that co-localization of transcription factors with mitotic chromosomes is a proxy for transcription factor nonspecific DNA binding properties, which regulate transcription factor search efficiency for their specific binding sites and thereby their impact on chromatin accessibility.
Details of the work appeared January 30 in the journal Nature Communications, in an article titled, “Mitotic chromosome binding predicts transcription factor properties in interphase.” The article describes how 501 transcription factors (TFs) were put through their paces.
“TFs associating to mitotic chromosomes are enriched in DNA-rich compartments in interphase and display slower mobility in interphase and mitosis,” the article’s authors wrote. “Remarkably, MCB correlates with relative TF on-rates and genome-wide specific site occupancy, but not with TF residence times.”
They found that different TFs vary by three orders of magnitude in their ability to find their sites. Thus, TF with strong nonspecific DNA binding properties associate with mitotic chromosomes, move slowly in the nucleus, and are particularly efficient at finding the specific sequences they need to bind to regulate gene expression.
“Transcription factors differ largely in their ability to scan the genome to find their specific binding sites, and these differences can be predicted by simply looking at how much they bind to mitotic chromosomes,” said David Suter, the article’s senior author and a bioengineer at EPFL. “Transcription factors that are the most efficient in searching the genome could be able to drive broad changes in gene expression patterns even when expressed at low concentrations, and can, therefore, be particularly important for cell fate decision processes.”
The EPFL scientists suggested that DNA sliding may be most effective if it is used when the TF is getting close to the finish line. “Experimental and computational modeling studies thus converge on a TF search model that combines 3D diffusion and facilitated diffusion, the latter resulting from local 1D search mediated by sliding along DNA, local jumps or hopping, and transfer between genomically distant but physically close segments of DNA (intersegment transfer).”