title: Widespread promoter-mediated coordination of transcription and mRNA degradation.
abstract: BACKGROUND
  Previous work showed that mRNA degradation is coordinated with transcription in yeast, and in several genes the control of mRNA degradation was linked to promoter elements through two different mechanisms. Here we show at the genomic scale that the coordination of transcription and mRNA degradation is promoter-dependent in yeast and is also observed in humans.
  
  
  RESULTS
  We first demonstrate that swapping upstream cis-regulatory sequences between two yeast species affects both transcription and mRNA degradation and suggest that while some cis-regulatory elements control either transcription or degradation, multiple other elements enhance both processes. Second, we show that adjacent yeast genes that share a promoter (through divergent orientation) have increased similarity in their patterns of mRNA degradation, providing independent evidence for the promoter-mediated coupling of transcription to mRNA degradation. Finally, analysis of the differences in mRNA degradation rates between mammalian cell types or mammalian species suggests a similar coordination between transcription and mRNA degradation in humans.
  
  
  CONCLUSIONS
  Our results extend previous studies and suggest a pervasive promoter-mediated coordination between transcription and mRNA degradation in yeast. The diverse genes and regulatory elements associated with this coordination suggest that it is generated by a global mechanism of gene regulation and modulated by gene-specific mechanisms. The observation of a similar coupling in mammals raises the possibility that coupling of transcription and mRNA degradation may reflect an evolutionarily conserved phenomenon in gene regulation.
authors.forename: Mally
authors.initials: M
authors.lastname: Dori-Bachash
authors.forename: Ophir
authors.initials: O
authors.lastname: Shalem
authors.forename: Yair S
authors.initials: YS
authors.lastname: Manor
authors.forename: Yitzhak
authors.initials: Y
authors.lastname: Pilpel
authors.forename: Itay
authors.initials: I
authors.lastname: Tirosh
mesh_terms: D020121:5' Untranslated Regions; D000818:Animals; D006801:Humans; D051379:Mice; D011401:Promoter Regions, Genetic; D020871:RNA Stability; D012333:RNA, Messenger / Q000378:metabolism*; D012440:Saccharomyces / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D020121:5' Untranslated Regions; D012333:RNA, Messenger