1512–1521 Nucleic Acids Research, 2006, Vol. 34, No. 5 doi:10.1093/nar/gkl027 LINE-1 RNA splicing and influences on mammalian gene expression Victoria P. Belancio, Dale J. Hedges and Prescott Deininger* Tulane Cancer Center, SL66 and Department of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, USA Received December 27, 2005; Revised and Accepted February 17, 2006 ABSTRACT Long interspersed element-1 elements compose on average one-fifth of mammalian genomes. The expression and retrotransposition of L1 is restricted by a number of cellular mechanisms in order to limit their damage in both germ-line and somatic cells. L1 transcription is largely suppressed in most tissues, but L1 mRNA and/or proteins are still detectable in testes, a number of specific somatic cell types, and malignancies. Down-regulation of L1 expression via premature polyadenylation has been found to be a secondary mechanism of limiting L1 expression. We demonstrate that mammalian L1 elements contain numerous functional splice donor and acceptor sites. Efficient usage of some of these sites results in extensive and complex splicing of L1. Several splice variants of both the human and mouse L1 elements undergo retrotransposition. Some of the spliced L1 mRNAs can potentially contribute to expression of open reading frame 2-related products and therefore have implications for the mobility of SINEs even if they are incompetent for L1 retrotransposition. Analysis of the human EST database revealed that L1 elements also participate in splicing events with other genes. Such contribution of functional splice sites by L1 may result in disruption of normal gene expression or formation of alternative mRNA transcripts. INTRODUCTION Long interspersed element-1 or LINE-1 (L1) is a non-long terminal repeat (non-LTR), autonomous retroelement cur- rently active in mammalian genomes that composes 17 and 20% of the human and mouse genomes, respectively (1,2). L1 inserts in the forward orientation are depleted in genes, prob- ably due to their deleterious effects on gene expression (3–5). Even though L1 activity has been detected in somatic cells (6–9), L1 is believed to undergo preferential expression and retrotransposition in the germ-line (10,11). Suppression of L1 activity is partly attributed to promoter regulation, either through tissue-speciﬁc transcription factors (12,13), or methylation of the L1 promoter that is often released upon malignant transformation (14–16). L1 expression is also attenuated via premature polyadenylation at internal poly- adenylation [poly(A)] sites (17). This mechanism is redundant and cannot be easily overcome by removal of a few internal poly(A) signals. A model of hindered polymerase II elongation along the A-rich L1 sequence was put forward as an additional explanation for poor expression through L1 elements (18). L1 transcription uses an internal RNA pol II promoter to encode a full-length (FL) L1 bicistronic mRNA that produce open reading frame (ORF) 1 and 2 proteins that are essential for retrotransposition (19). This FL transcript is retrotransposi- tionally competent (20), generating new L1 copies via target- primed reverse transcription (21). The majority of the 500 000 L1 copies found in mammalian genomes are 50 truncated (1) and/or rearranged (1,22). Thus, only about 100 human ele- ments are capable of expressing full-length RNA that codes for functional ORF1 and ORF2 proteins (23). The signals necessary for RNA splicing include both cis elements and trans factors, some of which are more conserved and well characterized then others. RNA splicing [reviewed in (24)] involves a splice donor site (SD or 50 splice), a splice acceptor site (SA or 30 splice) and a conserved cis element 20–50 bp 50 to the SA site. Trans-acting factors include ﬁve snRNAs (U1, U2, U4, U5 and U6) and at least 150 iden- tiﬁed proteins that form a functional spliceosome (25). Addi- tionally, there are exonic and intronic splice enhancers (ESE and ISE) and silencers (ESS and ISS) that can modulate splice site usage. A consensus sequence for the most often occurring 50and 30 ESE is G/AAAGAA (26). Deviation from the canon- ical SD or SA sequences may either lead to exon skipping, or it may result in the usage of cryptic splice sites in the vicinity. Both constitutive and alternative splicing are responsible for the 3-fold increase in protein diversity compared with the number of protein-encoding genes in humans (27,28) with *To whom correspondence should be addressed. 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