title: Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality.
abstract: Active human promoters produce promoter-upstream transcripts (PROMPTs). Why these RNAs are coupled to decay, whereas their neighboring promoter-downstream mRNAs are not, is unknown. Here high-throughput sequencing demonstrates that PROMPTs generally initiate in the antisense direction closely upstream of the transcription start sites (TSSs) of their associated genes. PROMPT TSSs share features with mRNA-producing TSSs, including stalled RNA polymerase II (RNAPII) and the production of small TSS-associated RNAs. Notably, motif analyses around PROMPT 3' ends reveal polyadenylation (pA)-like signals. Mutagenesis studies demonstrate that PROMPT pA signals are functional but linked to RNA degradation. Moreover, pA signals are under-represented in promoter-downstream versus promoter-upstream regions, thus allowing for more efficient RNAPII progress in the sense direction from gene promoters. We conclude that asymmetric sequence distribution around human gene promoters serves to provide a directional RNA output from an otherwise bidirectional transcription process.
authors.affiliation: Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
authors.forename: Evgenia
authors.initials: E
authors.lastname: Ntini
authors.forename: Aino I
authors.initials: AI
authors.lastname: Järvelin
authors.forename: Jette
authors.initials: J
authors.lastname: Bornholdt
authors.forename: Yun
authors.initials: Y
authors.lastname: Chen
authors.forename: Mette
authors.initials: M
authors.lastname: Boyd
authors.forename: Mette
authors.initials: M
authors.lastname: Jørgensen
authors.forename: Robin
authors.initials: R
authors.lastname: Andersson
authors.forename: Ilka
authors.initials: I
authors.lastname: Hoof
authors.forename: Aleks
authors.initials: A
authors.lastname: Schein
authors.forename: Peter R
authors.initials: PR
authors.lastname: Andersen
authors.forename: Pia K
authors.initials: PK
authors.lastname: Andersen
authors.forename: Pascal
authors.initials: P
authors.lastname: Preker
authors.forename: Eivind
authors.initials: E
authors.lastname: Valen
authors.forename: Xiaobei
authors.initials: X
authors.lastname: Zhao
authors.forename: Vicent
authors.initials: V
authors.lastname: Pelechano
authors.forename: Lars M
authors.initials: LM
authors.lastname: Steinmetz
authors.forename: Albin
authors.initials: A
authors.lastname: Sandelin
authors.forename: Torben Heick
authors.initials: TH
authors.lastname: Jensen
mesh_terms: D001483:Base Sequence; D015152:Blotting, Northern; D006367:HeLa Cells; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000235:genetics; D026723:Polyadenylation / Q000235:genetics / Q000502:physiology*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism; D020871:RNA Stability / Q000235:genetics / Q000502:physiology*; D024363:Transcription Initiation Site / Q000502:physiology; D014158:Transcription, Genetic / Q000235:genetics / Q000502:physiology*
chemical_list: D009841:Oligonucleotides; D012319:RNA Polymerase II