Sines

SINEs, or short interspersed nuclear elements, are a class of small, non-autonomous retrotransposons found in many eukaryotic genomes. They are typically 100–300 base pairs long and do not encode proteins, including reverse transcriptase. Because they lack their own enzymatic machinery, SINEs rely on the activity of autonomous retrotransposons, most notably LINE-1, to mobilize. SINEs are transcribed by RNA polymerase III from internal promoter sequences and insert into new genomic locations via an RNA intermediate that is reverse-transcribed and integrated through target-primed reverse transcription.

In mammals, SINEs have contributed significantly to genome composition and evolution. Alu elements in humans are the most abundant SINEs, with roughly 1–1.5 million copies, making up about 10–11% of the genome. Rodent genomes feature B1 elements, and older families such as MIRs are present but largely inactive. SINEs are found in intergenic regions as well as introns and exons, where insertions can disrupt genes, alter transcription, or create new splice sites (exonization). They can also serve as regulatory motifs or sources of recombination, influencing genome structure and expression patterns.

Because they lack coding potential, SINE activity is largely controlled by host defense mechanisms, including DNA methylation and small RNA pathways. Their mobilization and inheritance are typically studied through genome-wide sequencing and annotation tools, with RepeatMasker being a common resource. Insertional mutagenesis by SINEs has been implicated in various genetic diseases and cancers, making their study relevant to medicine as well as evolution.