Transcription factors (TFs) regulate gene expression by interacting with DNA in a sequence-specific manner. High-throughput in vitro technologies, such as protein-binding microarrays1–6 and HT-SELEX (high-throughput systematic evolution of ligands by exponential enrichment)7,8, have revealed the DNA-binding specificities of hundreds of TFs. However, they have limited ability to reliably identify lower-affinity DNA binding sites, which are increasingly recognized as important for precise spatiotemporal control of gene expression9–19. Here, to address this limitation, we developed protein affinity to DNA by in vitro transcription and RNA sequencing (PADIT-seq), with which we comprehensively assayed the binding preferences of six TFs to all possible ten-base-pair DNA sequences, detecting hundreds of novel, lower-affinity binding sites. The expanded repertoire of lower-affinity binding sites revealed that nucleotides flanking high-affinity DNA binding sites create overlapping lower-affinit

Gene redundancy complicates systematic characterization of gene function as single-gene deletions may not produce discernible phenotypes. We report dual transposon sequencing (dual Tn-seq), a platform...

Staphylococcus aureus, a Gram-positive bacterium, is a pathogen capable of infecting nearly all host tissues, causing severe morbidity and mortality. Antibiotic resistant S. aureus are abundant, and…

Animals harbor divergent microbiota, including various Bifidobacterium species, yet their evolutionary relationships and functional adaptations remain…

Bona fide gene clusters for archaella are widespread across a bacterial phylum and encode functional motility machinery.