#DOTD: Long Interspersed Nuclear Element

24 Aug 2017

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.

 

LINEs

  • 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.

 

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References:

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.

https://en.wikipedia.org/wiki/Retrotransposon#Non-LTR_retrotransposons

https://en.wikipedia.org/wiki/Long_interspersed_nuclear_element

https://en.wikipedia.org/wiki/Short_interspersed_nuclear_elements_(SINEs)

https://en.wikipedia.org/wiki/Alu_element

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.

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