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We identified >100,000 promoter regions, including known transcription start sites (TSSs) of protein-coding genes, lncRNA, pseudogenes and others (Figure 1). We filtered the promoters to retain only those with a region that was significantly enriched in the STARR-seq assay (Figure 2). Over 90% of the retained promoters contained transcription factor binding sites (TFBSs) (Figure 3) and 69% of them were occupied by multiple transcription factors, compared to 28% of all promoters (1.5-fold enrichment; Fisher’s exact test; P value 4e−17). The most enriched motifs among these TFBSs were for the TATA-binding protein (TBP), which is known to play an important role in the initiation of transcription, transcription initiation complex formation, and transcriptional elongation [ 35 ]. Interestingly, the enrichment of TBP was significantly correlated with the enrichment of its target motifs (Pearson’s correlation coefficient 0.50), suggesting that TBP plays a role in the RNA generation of most genes. Intuitively, TBP should promote transcriptional initiation and elongation and, thus, its binding should increase RNA abundance. This TBP enrichment correlated with the enrichment of several other TFs, including NKX2-5, GATA2, HAND1, ETS1 and ELF1, which are known to regulate cardiovascular development and have important roles in the early heart [ 35 – 40 ]. Furthermore, overlapping with the known promoters, we identified new candidate promoters with similar readout profiles (Figure 3). In particular, GATA2 and NKX2-5 were enriched in the promoter regions of many genes known to be involved in cardiovascular development. Our data revealed a subset of candidate promoters that were enriched in the identified TFs and that appear to respond to transcriptional regulatory programs.

In this study, we report the first draft genome sequence of Kp PHL644, a bacterium isolated from the anaerobic bioreactor sludge of an activated sludge sewage treatment plant. Kp PHL644 represented a single spiral-shaped cell with a diameter of approximately 0.5 μm and a circular chromosome with a size of 4.38 Mb. Genome analysis revealed that Kp PHL644 shared several features, including multidrug resistance to different antibiotics, resistance to killing by hydrogen peroxide, and low doubling time, with Klebsiella pneumoniae. The final genome sequence of this strain will provide a valuable source for understanding the biology and ecology of the human-associated lineage, which has emerged as a dominant source of antibiotic resistance in hospitals worldwide. In this paper, we used a very recently developed program, STARRPeaker, to identify regulatory regions under the influence of a TF. However, this program can be readily extended to other organisms and cells. For example, STARRPeaker only requires STARR-seq data and its target annotation information, so it is compatible with all organism and cell types in which STARR-seq data can be generated. Currently, the abundance of RNA is measured using RNA sequencing technology. We anticipate that future technologies will permit higher sensitivity measurement of RNA expression in cells. One of such systems is single-molecule sequencing, which allows measuring every RNA transcript in a cell [ 33 ]. Another technology, known as smARTseq [ 34, 35 ], is one of the most efficient ways to produce massive amounts of purified full-length RNA molecules from whole-cell extracts in a single experiment. This technology allows generating a large number of RNA molecules with various sequences and structures from a single preparation. Third, the platforms that measure RNA abundance, RNA-Seq and smARTseq, are not limited to detecting transcripts of genes; they can be used to detect any RNAs in a cell. Finally, fluorescence reporters on guide RNAs can also be used to measure the spatial and temporal expression pattern of a TF as it performs its function [ 21, 36, 37 ]. All these technologies provide an opportunity to delineate regulatory regions corresponding to TF target genes on the basis of the protein’s influence. 5ec8ef588b





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