Exonization of active mouse L1s: a driver of transcriptome evolution?

Zemojtel, Tomasz; Penzkofer, Tobias; Schultz, Jörg; Dandekar, Thomas; Badge, Richard; Vingron, Martin
January 2007
BMC Genomics;2007, Vol. 8, p1
Academic Journal
Background: Long interspersed nuclear elements (LINE-1s, L1s) have been recently implicated in the regulation of mammalian transcriptomes. Results: Here, we show that members of the three active mouse L1 subfamilies (A, GF and TF) contain, in addition to those on their sense strands, conserved functional splice sites on their antisense strands, which trigger multiple exonization events. The latter is particularly intriguing in the light of the strong antisense orientation bias of intronic L1s, implying that the toleration of antisense insertions results in an increased potential for exonization. Conclusion: In a genome-wide analysis, we have uncovered evidence suggesting that the mobility of the large number of retrotransposition-competent mouse L1s (~2400 potentially active L1s in NCBIm35) has significant potential to shape the mouse transcriptome by continuously generating insertions into transcriptional units.


Related Articles

  • Complex Transcription Mechanisms in Mammalian Genomes - The Transcriptome of FANTOM3. Katayama, Shintaro; Hayashizaki, Yoshihide // Current Genomics;Dec2005, Vol. 6 Issue 8, p619 

    Systematic analysis of a biological system requires elucidation of its components. However, genome sequencing is only the first step; any analysis of transcription control and further functional genomics require the identification of all transcribed transcripts. FANTOM is the international...

  • Characterization of expressed sequence tags from a full-length enriched cDNA library of Cryptomeria japonica male strobili. Futamura, Norihiro; Totoki, Yasushi; Toyoda, Atsushi; Igasaki, Tomohiro; Nanjo, Tokihiko; Seki, Motoaki; Sakaki, Yoshiyuki; Mari, Adriano; Shinozaki, Kazuo; Shinohara, Kenji // BMC Genomics;2008, Vol. 9, Special section p1 

    Background: Cryptomeria japonica D. Don is one of the most commercially important conifers in Japan. However, the allergic disease caused by its pollen is a severe public health problem in Japan. Since large-scale analysis of expressed sequence tags (ESTs) in the male strobili of C. japonica...

  • Transcriptomics resources for functional genomics. Kawai, Jun; Caminci, Piero; Hayashizaki, Yoshihide // Briefings in Functional Genomics & Proteomics;Sep2007, Vol. 6 Issue 3, p171 

    For the past decade, extensive efforts have been made for establishing cDNA clone resources for various species. The most striking breakthrough has been full-length cDNA technology allowing cloning of intact RNA molecules as cDNA. These transcriptomics resources are providing researchers with...

  • A promoter-level mammalian expression atlas.  // Nature;3/27/2014, Vol. 507 Issue 7493, p462 

    Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal. Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and...

  • Ectopic Overexpression of The Transcription Factor OsGLK1 Induces Chloroplast Development in Non-Green Rice Cells. Nakamura, Hidemitsu; Muramatsu, Masayuki; Hakata, Makoto; Ueno, Osamu; Nagamura, Yoshiaki; Hirochika, Hirohiko; Takano, Makoto; Ichikawa, Hiroaki // Plant & Cell Physiology;Nov2009, Vol. 50 Issue 11, p1933 

    For systematic and genome-wide analyses of rice gene functions, we took advantage of the full-length cDNA overexpresser (FOX) gene-hunting system and generated >12 000 independent FOX-rice lines from >25 000 rice calli treated with the rice-FOX Agrobacterium library. We found two FOX-rice lines...

  • Non-coding antisense transcription detected by conventional and single-stranded cDNA microarray. Vallon-Christersson, Johan; Staaf, Johan; Kvist, Anders; Medstrand, Patrik; Borg, Åke; Rovira, Carlos // BMC Genomics;2007, Vol. 8, p295 

    Background: Recent studies revealed that many mammalian protein-coding genes also transcribe their complementary strands. This phenomenon raises questions regarding the validity of data obtained from double-stranded cDNA microarrays since hybridization to both strands may occur. Here, we wanted...

  • Genome-Wide DNA Methylation Patterns and Transcription Analysis in Sheep Muscle. Couldrey, Christine; Brauning, Rudiger; Bracegirdle, Jeremy; Maclean, Paul; Henderson, Harold V.; McEwan, John C. // PLoS ONE;Jul2014, Vol. 9 Issue 7, p1 

    DNA methylation plays a central role in regulating many aspects of growth and development in mammals through regulating gene expression. The development of next generation sequencing technologies have paved the way for genome-wide, high resolution analysis of DNA methylation landscapes using...

  • Overlapping Protein-Encoding Genes in Pseudomonas fluorescens Pf0-1. Silby, Mark W.; Levy, Stuart B. // PLoS Genetics;Jun2008, Vol. 4 Issue 6, p1 

    The annotated genome sequences of prokaryotes seldom include overlapping genes encoded opposite each other by the same stretch of DNA. However, antisense transcription is becoming recognized as a widespread phenomenon in eukaryotes, and examples have been linked to important biological...

  • Differences in Promoters of Orthologous Genes. Youlian Pan; Sieu Phan; Famili, Fazel; Jaramillo, Maria Luz; Lenferink, Anne Engelina Gesina; Wang, Edwin // Open Bioinformatics Journal;2010, Vol. 4 Issue 2010, p41 

    Human genetic experiments are often conducted based on the orthologous genes in other mammals such as mouse and rat. The resulting conclusions of such experiments are often limited in their applicability to the human situation. This has raised a question as to why the orthologous genes with...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics