title: Intron DNA Sequences Can Be More Important Than the Proximal Promoter in Determining the Site of Transcript Initiation.
abstract: To more precisely define the positions from which certain intronic regulatory sequences increase mRNA accumulation, the effect of aUBIQUITINintron on gene expression was tested from six different positions surrounding the transcription start site (TSS) of a reporter gene fusion inArabidopsis thalianaThe intron increased expression from all transcribed positions but had no effect when upstream of the 5'-most TSS. While this implies that the intron must be transcribed to increase expression, the TSS changed when the intron was located in the 5'-untranslated region (UTR), suggesting that the intron affects transcription initiation. Remarkably, deleting 303 nucleotides of the promoter including all known TSSs and all but 18 nucleotides of the 5'-UTR had virtually no effect on the level of gene expression as long as an intron containing stimulatory sequences was included. Instead, transcription was initiated in normally untranscribed sequences the same distance upstream of the intron as when the promoter was intact. These results suggest that certain intronic DNA sequences play unexpectedly large roles in directing transcription initiation and constitute a previously unrecognized type of downstream regulatory element for genes transcribed by RNA polymerase II.
authors.affiliation: Department of Molecular and Cellular Biology, University of California, Davis, California 95616.
authors.forename: Jenna E
authors.identifier: http://orcid.org/0000-0003-4875-8163
authors.initials: JE
authors.lastname: Gallegos
authors.affiliation: Department of Molecular and Cellular Biology, University of California, Davis, California 95616 abrose@ucdavis.edu.
authors.forename: Alan B
authors.identifier: http://orcid.org/0000-0003-0765-8887
authors.initials: AB
authors.lastname: Rose
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics*; D007438:Introns / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012319:RNA Polymerase II / Q000235:genetics; D024363:Transcription Initiation Site / Q000502:physiology; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions; D029681:Arabidopsis Proteins; D018744:DNA, Plant; D012319:RNA Polymerase II