Roles of intragenic and intergenic L1s in mouse and human.

Chumpol Ngamphiw,Apiwat Mutirangura,Sissades Tongsima,Robert Feil

doi:10.1371/journal.pone.0113434

Abstract

Long INterspersed Element-1 (LINE-1 or L1) is a retrotransposable element that has shaped the evolution of mammalian genomes. There is increasing evidence that transcriptionally active L1 could have been co-opted through evolution to play various roles including X-inactivation, homologous recombination and gene regulation. Here, we compare putatively active L1 distributions in the mouse with human. L1 density is higher in the mouse except for the Y-chromosome. L1 density is the highest in X-chromosome, implying an X-inactivation role. L1 is more common outside genes (intergenic) except for the Y-chromosome in both species. The structure of mouse L1 is distinguished from human L1 by the presence of a 200 bp repeat in the 5′ UTR of the former. We found that mouse intragenic L1 has significantly higher repeat copy numbers than intergenic L1, suggesting that this is important for control of L1 expression. Furthermore, a significant association between the presence of intragenic L1s and down-regulated genes in early embryogenesis was found in both species. In conclusion, the distribution of L1 in the mouse genome points to biological roles of L1 in mouse similar to human.

Highlights

The Long INterspersed Element-1 (LINE-1 or L1) is a retrotransposable element, which constitutes 18–20% of mammalian genomes [1,2]
The frequencies of L1s differ among closely related mammalian lineages [3,4] and active L1s may still be a major driver of mammalian genome evolution
Intragenic L1 density is lower than intergenic for autosomes and X chromosome of both species, whereas the density of intragenic L1s is greater in the Y chromosome of both species (Figure 1C)

Summary

Introduction

The Long INterspersed Element-1 (LINE-1 or L1) is a retrotransposable element, which constitutes 18–20% of mammalian genomes [1,2]. The frequencies of L1s differ among closely related mammalian lineages [3,4] and active L1s may still be a major driver of mammalian genome evolution. There are about 500,000 copies of L1 in the human genome, whereas the mouse genome has almost 600,000 copies [1,2]. A full-length human L1 (,6,000 nucleotides) is shorter than that of mouse (,7,000 nucleotides). The RNA transcribed from active full-length L1s comprises both ORFs flanked by 59 and 39 UTRs with a poly-A tail [5,6]

Methods

Results

Discussion

Conclusion