Figure 1

A 10-bp periodic signal is present downstream of human transcription start sites. (a) Average compositional profiles around 13,622 human promoters. A 1,000-bp region on either side of each TSS was extracted from the genome and the 13,622 sequences were aligned at the TSS (base +1 is the first transcribed base). The average composition at each base-pair position is shown on the y-axis. Inset: average compositional profile of purine-purine and pyrimidine-pyrimidine dinucleotides between positions +40 and +200. The raw signal is shown in orange and a 3-bp smoothed distribution is shown in purple (RR) and dark green (YY). (b) DNA sequences of the +1 nucleosome contain the periodic signal. Sequence tags from nucleosome-bound DNA obtained by a ChIP-seq experiment [23] were remapped to the human genome and their density was smoothed with a sliding 70-bp window (see Materials and methods). Tags mapped to the forward (magenta) and the reverse (cyan) strand mark the 5' and 3' ends of nucleosome bound DNA fragments, respectively. Counter-phased RR (purple) and YY (green) dinucleotide frequencies, and base pair coordinates are as in (a).