RT Journal
A1 Lubliner, Shai
A1 Regev, Ifat
A1 Lotan-Pompan, Maya
A1 Edelheit, Sarit
A1 Weinberger, Adina
A1 Segal, Eran
T1 Core promoter sequence in yeast is a major determinant of expression level
JF Genome Research 
JO Genome Research 
YR 2015 
FD July 01 
VO 25 
IS 7 
SP 1008 
OP 1017 
DO 10.1101/gr.188193.114 
UL http://genome.cshlp.org/content/25/7/1008.abstract 
AB The core promoter is the regulatory sequence to which RNA polymerase is recruited and where it acts to initiate transcription. Here, we present the first comprehensive study of yeast core promoters, providing massively parallel measurements of core promoter activity and of TSS locations and relative usage for thousands of native and designed sequences. We found core promoter activity to be highly correlated to the activity of the entire promoter and that sequence variation in different core promoter regions substantially tunes its activity in a predictable way. We also show that location, orientation, and flanking bases critically affect TATA element function, that transcription initiation in highly active core promoters is focused within a narrow region, that poly(dA:dT) orientation has a functional consequence at the 3′ end of promoters, and that orthologous core promoters across yeast species have conserved activities. Our results demonstrate the importance of core promoters in the quantitative study of gene regulation.