Human gene promoters are intrinsically bidirectional

R Andersson, Y Chen, L Core, JT Lis, A Sandelin… - Molecular cell, 2015 - cell.com
Molecular cell, 2015cell.com
A recent Molecular Cell paper by Duttke et al. concluded that ''human promoters are
intrinsically directional''(Duttke et al., 2015). This, at least on the surface, contradicts earlier
observations (Almada et al., 2013; Core et al., 2008; Ntini et al., 2013; Seila et al., 2008). As
part of the disagreement could be based on a different usage of scientific terms, we find it
important to contribute our perspective, hoping to reach common definitions. In addition, we
present a reconsideration of an important question asked by Duttke et al., namely whether …
A recent Molecular Cell paper by Duttke et al. concluded that ‘‘human promoters are intrinsically directional’’(Duttke et al., 2015). This, at least on the surface, contradicts earlier observations (Almada et al., 2013; Core et al., 2008; Ntini et al., 2013; Seila et al., 2008). As part of the disagreement could be based on a different usage of scientific terms, we find it important to contribute our perspective, hoping to reach common definitions. In addition, we present a reconsideration of an important question asked by Duttke et al., namely whether divergent transcription is a generic feature of human promoters. A core promoter has been classically defined by biochemical studies as the minimal region of DNA required to support assembly of a general transcription complex and initiate transcription. This activity is often encompassed by the±50 bp surrounding the transcription start site (TSS)(Kadonaga, 2012). Core promoters rarely act alone in vivo, requiring nearby transcription factor binding to regulate their activity. Therefore, the term ‘‘promoter’’often includes more extended upstream regions that contribute to regulation of initiation at the core promoter. The terms ‘‘core promoter,’’‘‘TSS,’’and ‘‘promoter’’have at times been used interchangeably in the literature, which in light of current genomic data is likely to cause confusion.
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