Tail Wags Dog’s SINE: Retropositional Mechanisms of Can SINE Depend on Its A-Tail Structure

Abstract

SINEs, non-autonomous short retrotransposons, are widespread in mammalian genomes. Their transcripts are generated by RNA polymerase III (pol III). Transcripts of certain SINEs can be polyadenylated, which requires polyadenylation and pol III termination signals in their sequences. Our sequence analysis divided Can SINEs in canids into four subfamilies, older a1 and a2 and younger b1 and b2. Can_b2 and to a lesser extent Can_b1 remained retrotranspositionally active, while the amplification of Can_a1 and Can_a2 ceased long ago. An extraordinarily high Can amplification was revealed in different dog breeds. Functional polyadenylation signals were analyzed in Can subfamilies, particularly in fractions of recently amplified, i.e., active copies. The transcription of various Can constructs transfected into HeLa cells proposed AATAAA and (TC)n as functional polyadenylation signals. Our analysis indicates that older Can subfamilies (a1, a2, and b1) with an active transcription terminator were amplified by the T+ mechanism (with polyadenylation of pol III transcripts). In the currently active Can_b2 subfamily, the amplification mechanisms with (T+) and without the polyadenylation of pol III transcripts (T−) irregularly alternate. The active transcription terminator tends to shorten, which renders it nonfunctional and favors a switch to the T− retrotransposition. The activity of a truncated terminator is occasionally restored by its elongation, which rehabilitates the T+ retrotransposition for a particular SINE copy.

SINE Insertion in the Pig Carbonic Anhydrase 5B (CA5B) Gene Is Associated with Changes in Gene Expression and Phenotypic Variation

“…This is consistent with our analysis (TSD sequence: CAATTTATTT). Kosushkin suggests that these TSD regions may be responsible for the tandem repeats in the A-tails [ 33 ]. Several studies have confirmed that the (AAAT) n repeat polymorphism in the Alu sequence of the Neurofibromatosis-1 ( NF1 ) gene is related to racial differentiation in autism patients and has a regulatory effect on gene expression [ 34 , 35 , 36 ].…”

Alu antisense RNA ameliorates methylglyoxal-induced human lens epithelial cell apoptosis by enhancing antioxidant defense

“…In the eye, the ROS causes cellular damage that induces cataract formation [16] . Short interspersed nuclear elements (SINEs) occupy approximately 10% of the mammalian genome [17][18] . Alu elements are the main SINEs in the human genome [17][18][19] .…”

“…Short interspersed nuclear elements (SINEs) occupy approximately 10% of the mammalian genome [17][18] . Alu elements are the main SINEs in the human genome [17][18][19] . These Alu elements can be transcribed into Alu RNA.…”

SINEs as Potential Expression Cassettes: Impact of Deletions and Insertions on Polyadenylation and Lifetime of B2 and Ves SINE Transcripts Generated by RNA Polymerase III

“…SINEs are important factors in genome evolution and function. Their integration into genes including their introns and regulatory regions can affect gene function, i.e., induce deleterious mutations [3,5,6]. At the same time, many other SINE insertions into introns 2 of 14 or regulatory regions do not induce negative effects on gene function but can modulate it and upregulate transcription [7][8][9] as well as splicing [3,10,11] or polyadenylation [12,13] of mRNA.…”