Universality of core promoter elements?

Arising from B. J. Venters & B. F. Pugh Nature 502, 53–58 (2013); doi:10.1038/nature12535 How cells locate the regions to initiate transcription is an open question, because core promoter elements (CPEs) are found in only a small fraction of core promoters1,2,3,4. A recent study5 measured 159,117 DNA binding regions of transcription factor IIB (TFIIB) by ChIP-exo (chromatin immunoprecipitation with lambda exonuclease digestion followed by high-throughput sequencing) in human cells, found four degenerate CPEs—upstream and downstream TFIIB recognition elements (BREu and BREd), TATA and initiator element (INR)—in nearly all of them, and concluded that these regions represent sites of transcription initiation marked by universal CPEs. We show that the claimed universality of CPEs is explained by the low specificities of the patterns used and that the same match frequencies are obtained with two negative controls (randomized sequences and scrambled patterns). Our analyses also cast doubt on the biological significance of most of the 150,753 non-messenger-RNA-associated ChIP-exo peaks, 72% of which lie within repetitive regions. There is a Retraction accompanying this Brief Communication Arising by Venters, B. J. & Pugh, B. F. Nature 511, http://dx.doi.org/10.1038/nature13588 (2014).