Polyadenylation of RNA transcribed from mammalian SINEs by RNA polymerase III: Complex requirements for nucleotide sequences

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, beta region positioned immediately downstream of the box B of pol III promoter, and T region located upstream of the tail. In DIP and VES (but not in B2), the T 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. (C) 2015 Elsevier B.V. All rights reserved.