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Long interspersed nuclear element

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Long interspersed elements (LINEs) are a group of non-LTR retrotransposons which are widespread in the genome of many eukaryotes.[1]

History of discovery

The first description of an approximately 6.4 kb long LINE-derived seequence was published by J. Adams et al. in 1980.[2]

Types of LINE elements

The LINE-1/L1-element is the only element that is still active in the human genome today. It is found in all mammals.[3] However, remnants of L2 and L3 elements are also found in the human genome.[citation needed]

Structure

A typical L1 element is approximately 6,000 base pairs long and consists of two non-overlapping open reading frames (ORF) which are flanked by UTR and target side duplications.

First ORF

The first ORF encodes a RNA-binding protein of 500 amino acid lengths that weighs 40 kDA. This protein contains a leucine zipper motif and functions as a chaperone.[4]

Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition.

Second ORF

The second ORF encodes a protein-complex has endonuclease and reverse transcriptase activity. The encoded protein has a molecular weight of 150 kDA.

Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon

UTR

The 5' Untranslated region (UTR) of the L1 element contains an strong, internal RNA Polymerase II transcription promoter in sense[5] and a less strong anti-sense promoter.[6]

Incidence

In human

In the first human genome draft the fraction of LINE elements of the human genome was given as 21% and their copy number as 850,000. The non-autonomous SINE elements which depend on L1 elements for their proliferation make up 13% of the human genome and have a copy number of around 1.5 million.[7]

Propagation Mechanism: Target Primed Reverse Transcription

LINE elements propagate by a so-called target primed reverse transcription mechanism. This mechanism was first described for the R2 element from Bombyx mori: A specific nick on one of the DNA strands at the target site is generated by the endonuclease encoded by the R2 element. Thus, a 3'OH group is freed for the R2 reverse transcriptase to prime reverse transcription of the LINE RNA transcript. Following the reverse transcription the target strand is cleaved and the thus created cDNA integrated[8]

Regulation of LINE activity

It has been shown that host cells regulate L1 retrotransposition activity, for example through epigenetic silencing. For example, the RNA interference (RNAi) mechanism of small interfering RNAs derived from L1 sequences can cause suppression of L1 retrotransposition.[9]

References

  1. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1016/S0959-440X(98)80067-5, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1016/S0959-440X(98)80067-5 instead.
  2. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1093/nar/8.24.6113, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1093/nar/8.24.6113 instead.
  3. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1038/nature06936, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1038/nature06936 instead.
  4. ^ Attention: This template ({{cite doi}}) is deprecated. To cite the publication identified by doi:10.1186/gb-2013-14-3-r22, please use {{cite journal}} (if it was published in a bona fide academic journal, otherwise {{cite report}} with |doi=10.1186/gb-2013-14-3-r22 instead.
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  6. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 16877819, please use {{cite journal}} with |pmid=16877819 instead.
  7. ^ Lander ES, Linton LM, Birren B; et al. (February 2001). "Initial sequencing and analysis of the human genome". Nature. 409 (6822): 860–921. doi:10.1038/35057062. PMID 11237011. {{cite journal}}: Explicit use of et al. in: |author= (help); Unknown parameter |displayauthors= ignored (|display-authors= suggested) (help)CS1 maint: multiple names: authors list (link)
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  9. ^ Attention: This template ({{cite pmid}}) is deprecated. To cite the publication identified by PMID 16936727, please use {{cite journal}} with |pmid=16936727 instead.
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