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

Goodier JL, Cheung LE, Kazazian HH - Nucleic Acids Res. (2013)

Bottom Line: These elements have significant effects on gene organization and expression.By co-immunoprecipitation of tagged L1 constructs and mass spectrometry, we identified proteins associated with the L1 ORF1 protein and its ribonucleoprotein.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.

View Article: PubMed Central - PubMed

Affiliation: McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine.

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'.

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Proteins identified with the L1 form a tight network of interactions dominated by RNA-binding proteins. (A) Pie chart of results of DAVID (Database for Annotation, Visualization and Integrated Discovery) analysis showing selected functional categories for the 96 candidate proteins (42). Protein counts for each category are shown within the slices. Protein names are listed in Supplementary Table S4. (B) STRING (Search tool for the retrieval of interacting genes/proteins)-derived network of known protein–protein interactions among the 96 candidate proteins. The confidence view is shown in Jensen et al. (43).
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gkt512-F2: Proteins identified with the L1 form a tight network of interactions dominated by RNA-binding proteins. (A) Pie chart of results of DAVID (Database for Annotation, Visualization and Integrated Discovery) analysis showing selected functional categories for the 96 candidate proteins (42). Protein counts for each category are shown within the slices. Protein names are listed in Supplementary Table S4. (B) STRING (Search tool for the retrieval of interacting genes/proteins)-derived network of known protein–protein interactions among the 96 candidate proteins. The confidence view is shown in Jensen et al. (43).

Mentions: The list of 96 proteins was used to query the Gene Ontogeny (GO) database (Figure 2A and Supplementary Table S4). A majority of these proteins bind nucleic acids. The L1 ORF1p interactome contains many heterogeneous nuclear ribonucleoproteins (hnRNPs), splicing factors, chaperones, transport and localization proteins, and transcription/translation factors. Querying the STRING database of experimentally confirmed protein–protein interactions returns a tight network of interactions dominated by RNP proteins (Figure 2B).Figure 2.


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

Goodier JL, Cheung LE, Kazazian HH - Nucleic Acids Res. (2013)

Proteins identified with the L1 form a tight network of interactions dominated by RNA-binding proteins. (A) Pie chart of results of DAVID (Database for Annotation, Visualization and Integrated Discovery) analysis showing selected functional categories for the 96 candidate proteins (42). Protein counts for each category are shown within the slices. Protein names are listed in Supplementary Table S4. (B) STRING (Search tool for the retrieval of interacting genes/proteins)-derived network of known protein–protein interactions among the 96 candidate proteins. The confidence view is shown in Jensen et al. (43).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3753637&req=5

gkt512-F2: Proteins identified with the L1 form a tight network of interactions dominated by RNA-binding proteins. (A) Pie chart of results of DAVID (Database for Annotation, Visualization and Integrated Discovery) analysis showing selected functional categories for the 96 candidate proteins (42). Protein counts for each category are shown within the slices. Protein names are listed in Supplementary Table S4. (B) STRING (Search tool for the retrieval of interacting genes/proteins)-derived network of known protein–protein interactions among the 96 candidate proteins. The confidence view is shown in Jensen et al. (43).
Mentions: The list of 96 proteins was used to query the Gene Ontogeny (GO) database (Figure 2A and Supplementary Table S4). A majority of these proteins bind nucleic acids. The L1 ORF1p interactome contains many heterogeneous nuclear ribonucleoproteins (hnRNPs), splicing factors, chaperones, transport and localization proteins, and transcription/translation factors. Querying the STRING database of experimentally confirmed protein–protein interactions returns a tight network of interactions dominated by RNP proteins (Figure 2B).Figure 2.

Bottom Line: These elements have significant effects on gene organization and expression.By co-immunoprecipitation of tagged L1 constructs and mass spectrometry, we identified proteins associated with the L1 ORF1 protein and its ribonucleoprotein.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.

View Article: PubMed Central - PubMed

Affiliation: McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine.

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'.

Show MeSH
Related in: MedlinePlus