Final answer:
SINEs (Short Interspersed Nuclear Elements) are non-autonomous non-LTR retrotransposons that require the transcriptional machinery of LINEs to move within the genome. They influence genetic variation and can contribute to exon shuffling.
Step-by-step explanation:
What are SINEs (Short Interspersed Nuclear Elements)?
Short Interspersed Nuclear Elements (SINEs) are a subclass of non-LTR retrotransposons found within eukaryotic genomes. Unlike their relatives, the Long Interspersed Nuclear Elements (LINEs), SINEs do not encode the enzymes needed for their own transposition, which makes them non-autonomous elements. They depend on the transposition machinery of autonomous retrotransposons, particularly that of LINEs, to move within the genome.
SINEs are transcribed by RNA polymerase III, similarly to tRNAs and 5S rRNA. During the target-site primed retrotransposition, if a LINE is transcribed concurrently, its enzymes become available, and the integration of the SINE occurs. The LINE's integrase-endonuclease makes a cut in one DNA strand at the new insertion site, allowing the SINE cDNA to use the 3'OH end of the cut strand to start reverse transcription by the LINE reverse transcriptase. The end result of this process is the insertion of a new copy of the SINE into a new location in the genome.
SINEs can influence genomic structure and function in various ways. For instance, Alu elements, which are a type of SINE, are often found within introns and can contribute to genetic variation and evolution through mechanisms such as exon shuffling. This happens when the presence of similar SINEs in the introns of different genes leads to unequal crossing over between those genes.