RT Journal Article
SR Electronic
T1 Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 055731
DO 10.1101/055731
A1 Yun Chen
A1 Athma A. Pai
A1 Jan Herudek
A1 Michal Lubas
A1 Nicola Meola
A1 Aino I. Järvelin
A1 Robin Andersson
A1 Vicent Pelechano
A1 Lars M. Steinmetz
A1 Torben Heick Jensen
A1 Albin Sandelin
YR 2016
UL http://biorxiv.org/content/early/2016/07/13/055731.abstract
AB Mammalian transcriptomes are complex and formed by extensive promoter activity. In addition, gene promoters are largely divergent and initiate transcription of reverse-oriented promoter upstream transcripts (PROMPTs). Although PROMPTs are commonly terminated early, influenced by polyadenylation sites, promoters often cluster so that the divergent activity of one might impact another. Here, we find that the distance between promoters strongly correlates with the expression, stability and length of their associated PROMPTs. Adjacent promoters driving divergent mRNA transcription support PROMPT formation, but due to polyadenylation site constraints, these transcripts tend to spread into the neighboring mRNA on the same strand. This mechanism to derive new alternative mRNA transcription start sites (TSSs) is also evident at closely spaced promoters supporting convergent mRNA transcription. We suggest that basic building blocks of divergently transcribed core promoter pairs, in combination with the wealth of TSSs in mammalian genomes, provides a framework with which evolution shapes transcriptomes.