DNA bendability regulates transcription factor pioneer binding to nucleosomes
Date:
Xiao Liu1,2, Luca Mariani2, Martha L Bulyk2,3
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 2Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 3Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
The nucleosome is a complex formed by 147 DNA bases wrapped around a histone octamer for 1.65 turns. Being the fundamental unit of chromatin packaging, nucleosomes regulate gene expression by posing a barrier to transcription factors (TFs) binding to DNA. Recent studies have investigated how TFs can access nucleosomal DNA (“TF pioneer binding”), unveiling different interaction modes including binding at nucleosome ends, dyad and spanning gyres. Furthermore, single molecule looping assays revealed that the nucleosomal DNA ends unwrap asymmetrically with the stiffer half being more prone to opening. We hypothesized that this asymmetric unwrapping facilitates TF pioneer binding by exposing the less bendable half.
To test this hypothesis, we analyzed the DNA bendability of in vitro nucleosomal libraries bound by TFs and histone octamers from published NCAP-SELEX datasets for 154 TFs. To quantitatively evaluate the bendability of DNA sequences assembled into nucleosomes, we employed DNAcycP, an existing deep learning model based on loop-seq datasets. Loop-seq experiments measure the ability of 100-bp sequences to form loops (“DNA cyclizability”), creating a proxy for nucleosomal DNA bendability. Consistent with our hypothesis, we discovered that most TFs prefer binding at nucleosome ends adjacent to the less cyclizable ends, a trend that we did not observe in DNA libraries selected exclusively by either TFs or histone octamers. This behavior is also less pronounced for TFs which bind more strongly at the nucleosome dyad, suggesting that TFs capable of overcoming the histone octamer barriers do not rely on the nucleosome unwrapping for pioneer binding. We further analyzed the nucleosomal sequences selected by the gyre-spanning binding factor T(Brachyury). We noticed that sequences bound by T on a single gyre exhibit cyclizability asymmetry, while sequences with T spanning across two gyres do not. This agrees with our hypothesis that DNA bendability differences underlie the exposure of TF binding sites at the ends of nucleosomes. Integrated analyses of MNase-seq data with ChIP-seq data for C/EBP TFs support our model for how bendability regulates pioneer binding of TFs.
In summary, we found that TF binding sites at nucleosome ends adjacent to sequences with low bendability are preferentially exposed, and propose a model for how genomic sequence composition ~100-bp away from TF DNA binding sites on nucleosomes can influence TF binding through nucleosome dynamics.