Interview for Faculty Position

Single-Cell Biophysical Study on Nucleosome-Depleted Region and Gene Regulation

Lu Bai

Rockefeller University

Precise gene regulation is crucial for cell proliferation and differentiation, yet the genomic features that control transcription noise are poorly understood. In eukaryotic cells, nucleosome positioning on promoters plays an important role in transcription. Recent genome-wide nucleosome mapping revealed that >90% of yeast promoters, as well as many promoters in higher eukaryotes, contain nucleosome-depleted-regions (NDRs). I hypothesized that NDRs in promoters strongly affect transcription levels and noise, and my research has focused on the formation mechanism and functional consequence of NDR on a cell-cycle regulated yeast promoter, CLN2. I discovered two sets of DNA-binding factors in the CLN2pr NDR: activators and Nucleosome-depleting factors (NDFs), with the latter responsible for the NDR formation. Disruption of the NDFs, or spatial separation of the two sets of factors, brings nucleosome(s) onto the activator binding sites. By assaying transcription in single cells using time-lapse fluorescence microscopy, I found that the promoters with nucleosome-covered activator binding sites are bimodal: strong activation in some cell cycles and none in the others. In contrast, the same binding sites localized in NDR lead to reliable activation once-per-cycle. My results strongly support the role of the NDR in suppressing gene expression noise and provide insight for how to build a functional promoter.