Long + Short Interspersed Nuclear Elements (LINEs + SINEs) make up approximately 21% + 11% of the human genome, respectively. They are non-long terminal repeat (non-LTR) retrotransposons, which means they are transposons that reintegrate themselves within genomes via RNA intermediates (hence, retro), + they are not flanked by long terminal repeats (hence, non-LTR). Note that, in contrast to DNA transposons, retrotransposons use a copy + paste mechanism, thereby extending the genome + repeating within it. LINE's + SINE's only occur in eukaryotic genomes + are hypothesised to have co-evolved.
Approximately 6000bp long
Are known as autonomous transposons
Divided into five groups
Insertions of LINEs in to genes are known to cause at least 100 diseases, such as epithelial cell cancer.
Some open reading frames (ORF) in each LINE encode a reverse transcriptase/endonuclease and an RNA-binding protein which facilitate it's integration into an alternate locus in the genome. For example, there are two ORFs in group L1 sequences, separated by a 63bp spacer and followed by a poly-A tail.
The vast majority of LINEs have mutated so much over millions of years (including 5' truncations + internal rearrangements) that they are no longer retrotransposition-competent; the exception is group L1. Around 100 out of 500,000 L1 sequences remain active in humans.
The FASTA sequence found with accession no. L19092 in GenBank is an example of a full-length human L1 sequence. BLAST-ing this sequence reveals that is is located on chromosomes 1, 2, 3, 4 + many more!
Some groups have sub-families which can be identified by specific unique sub-sequences. For example, the L1 Ta (transcribed, subset a) sub-family can be recognised by* the following 19-mer: 5′-CCTAATGCTAGATGACACA-3′.
Fun fact: On average, two people differ by 285 L1 insertions!
Read about SINEs in my next blog post here.
Hancks, D.C. and Kazazian, H.H., 2016. Roles for retrotransposon insertions in human disease. Mobile DNA, 7(1), p.9. [Highly recommended.]
*Myers, J.S., Vincent, B.J., Udall, H., Watkins, W.S., Morrish, T.A., Kilroy, G.E., Swergold, G.D., Henke, J., Henke, L., Moran, J.V. and Jorde, L.B., 2002. A comprehensive analysis of recently integrated human Ta L1 elements. The American Journal of Human Genetics, 71(2), pp.312-326.
Singer, M.F., 1982. SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell, 28(3), pp.433-434.
Brouha, B., Schustak, J., Badge, R.M., Lutz-Prigge, S., Farley, A.H., Moran, J.V. and Kazazian, H.H., 2003. Hot L1s account for the bulk of retrotransposition in the human population. Proceedings of the National Academy of Sciences, 100(9), pp.5280-5285.