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

• RNA transcribed by RNA polymerase III from a number of mammalian SINEs can be polyadenylated in the cell.
• SINEs of this type contain polyadenylation signals (AATAAA) and a transcription terminator in their 3′ end region.
• Sequences located downstream of the promoter box B and upstream of the SINE tail contribute to this type of polyadenylation.
• In many SINEs, the polypyrimidine motif upstream of the AATAAA signals is involved in polyadenylation.

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.