title: Polyadenylation of RNA transcribed from mammalian SINEs by RNA polymerase III: Complex requirements for nucleotide sequences.
abstract: It is generally accepted that only transcripts synthesized by RNA polymerase II (e.g., mRNA) were subject to AAUAAA-dependent polyadenylation. However, we previously showed that RNA transcribed by RNA polymerase III (pol III) from mouse B2 SINE could be polyadenylated in an AAUAAA-dependent manner. Many species of mammalian SINEs end with the pol III transcriptional terminator (TTTTT) and contain hexamers AATAAA in their A-rich tail. Such SINEs were united into Class T(+), whereas SINEs lacking the terminator and AATAAA sequences were classified as T(-). Here we studied the structural features of SINE pol III transcripts that are necessary for their polyadenylation. Eight and six SINE families from classes T(+) and T(-), respectively, were analyzed. The replacement of AATAAA with AACAAA in T(+) SINEs abolished the RNA polyadenylation. Interestingly, insertion of the polyadenylation signal (AATAAA) and pol III transcription terminator in T(-) SINEs did not result in polyadenylation. The detailed analysis of three T(+) SINEs (B2, DIP, and VES) revealed areas important for the polyadenylation of their pol III transcripts: the polyadenylation signal and terminator in A-rich tail, β region positioned immediately downstream of the box B of pol III promoter, and τ region located upstream of the tail. In DIP and VES (but not in B2), the τ region is a polypyrimidine motif which is also characteristic of many other T(+) SINEs. Most likely, SINEs of different mammals acquired these structural features independently as a result of parallel evolution.
authors.affiliation: Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russian Federation.
authors.forename: Olga R
authors.initials: OR
authors.lastname: Borodulina
authors.affiliation: Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russian Federation.
authors.forename: Julia S
authors.initials: JS
authors.lastname: Golubchikova
authors.affiliation: Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russian Federation.
authors.forename: Ilia G
authors.initials: IG
authors.lastname: Ustyantsev
authors.affiliation: Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russian Federation. Electronic address: kramerov@eimb.ru.
authors.forename: Dmitri A
authors.initials: DA
authors.lastname: Kramerov
mesh_terms: D000818:Animals; D001483:Base Sequence; D051379:Mice; D011061:Poly A / Q000235:genetics; D026723:Polyadenylation / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012313:RNA / Q000235:genetics; D012320:RNA Polymerase III / Q000235:genetics*; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D011061:Poly A; D012313:RNA; D012320:RNA Polymerase III
keywords: Mammals; Non-coding RNA; Polyadenylation; RNA polymerase III; SINE; Signal nucleotide sequences