Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition

Abstract

LINE1s occupy 17% of the human genome and are its only active autonomous mobile DNA. L1s are also responsible for genomic insertion of processed pseudogenes and >1 million non-autonomous retrotransposons (Alus and SVAs). These elements have significant effects on gene organization and expression. Despite the importance of retrotransposons for genome evolution, much about their biology remains unknown, including cellular factors involved in the complex processes of retrotransposition and forming and transporting L1 ribonucleoprotein particles. By co-immunoprecipitation of tagged L1 constructs and mass spectrometry, we identified proteins associated with the L1 ORF1 protein and its ribonucleoprotein. These include RNA transport proteins, gene expression regulators, post-translational modifiers, helicases and splicing factors. Many cellular proteins co-localize with L1 ORF1 protein in cytoplasmic granules. We also assayed the effects of these proteins on cell culture retrotransposition and found strong inhibiting proteins, including some that control HIV and other retroviruses. These data suggest candidate cofactors that interact with the L1 to modulate its activity and increase our understanding of the means by which the cell coexists with these genomic ‘parasites’.

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

“…In the course of their normal cellular lifecycle, TE transcripts interact with a variety of proteins, both self-encoded and host-encoded, to form a ribonucleoprotein complex (RNP) (Goodier et al 2013). RNPs, such as Alu or LINE1, have been shown to interact with a diverse range of host proteins, including chromatin modifiers, transcription factors, DNA repair factors, RNA binding proteins, and RNA Polymerase II (Mariner et al 2008;Blackwell et al 2012;Goodier et al 2013).…”

“…RNPs, such as Alu or LINE1, have been shown to interact with a diverse range of host proteins, including chromatin modifiers, transcription factors, DNA repair factors, RNA binding proteins, and RNA Polymerase II (Mariner et al 2008;Blackwell et al 2012;Goodier et al 2013). It is reasonable to infer that fresh insertion of TE repeats within lncRNA may confer binding to the same complexes, thereby constituting preformed protein-binding domains.…”

“…It is reasonable to infer that fresh insertion of TE repeats within lncRNA may confer binding to the same complexes, thereby constituting preformed protein-binding domains. Among those protein classes recently found to interact with Alu and LINE1 are many, such as chromatin regulatory complexes, that are highly relevant to known functional roles of lncRNA (Blackwell et al 2012;Goodier et al 2013). Thus, there is a relationship, at least at early evolutionary stages, between the TE's activity in the lncRNA context and its role in its original TE context.…”

“…In the case in which this involves the adoption of a structure for protein binding, then we might expect that the TE fragment will confer binding of the host lncRNA to natural partners of the TE, specifically the TE RNP ( Fig. 2; Blackwell et al 2012;Goodier et al 2013). Such RNPs are known to interact with a wide range of proteins, including those with regulatory functions of clear relevance to lncRNA function (Blackwell et al 2012).…”

Phosphorylation of ORF1p is required for L1 retrotransposition

“…Recent studies have shown that phosphorylation-related proteins can be coimmunoprecipitated with ORF1p or L1 RNPs (39,40). In addition, the mitogen-activated protein kinase (MAPK) p38 has been implicated in L1 activation by environmental toxins (41,42), and its expression can be increased by exogenous ORF1p (43).…”