Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci
- Institute for Research on Cancer and Aging of Nice, France
- University of Nice-Sophia Antipolis, France
- Ecole Normale Supérieure, France
- Ecole Normale Supérieure de Lyon, France
Figures
Figure 1 with 1 supplement
Global expression of L1HS elements in a panel of human somatic cell lines.
(a) ORF1p immunoblot analysis of L1 RNP accumulation in the indicated cell lines. Top, ORF1p immunoblot. Bottom, S6 Ribosomal Protein immunoblot as loading control. The quantity of RNP loaded is …
Figure 1—figure supplement 1
Analysis of L1 ORF1p expression in whole cell extracts of various cell lines by immunoblot.
Top, ORF1p immunoblot. Bottom, Tubulin immunoblot as loading control. The quantity of whole cell extracts loaded is indicated at the bottom of the gel.
Figure 2 with 1 supplement
The genetic landscape of L1HS-Ta insertional polymorphisms in 12 human somatic cell lines.
(a) Principle of the ATLAS-seq procedure. The subsequent in silico steps are described in Figure 2—figure supplement 1a. (b–c), Modified IGV genome browser views (Thorvaldsdóttir et al., 2013) of …
Figure 2—figure supplement 1
Fixed and polymorphic L1HS-Ta elements mapped by ATLAS-seq.
(a) A scheme summarizing the principle of ATLAS-seq sequencing data analysis. (b) Barchart showing the discovery rate of fixed L1HS-Ta elements before (empty bars) and after (plain blue bars) …
Figure 3 with 2 supplements
Detection of transcriptionally active L1HS-Ta elements at individual copy resolution in MCF7 cells.
(a) Theoretical scheme representing the outcome of RNA-seq and ChIP-seq read mapping at polymorphic L1 loci. The informative regions are highlighted in beige. (b) Genome browser views of reference …
Figure 3—figure supplement 1
L1HS-Ta loci belongs to low mappability genomic regions.
Genome browser view showing an L1HS-Ta element in the TTC28 locus. This insertion is evolutionary young (human-specific, not present in other Primates). UCSC mappability tracks are shown in black …
Figure 3—figure supplement 2
Impact of shRNA-mediated ORF1 knockdown on RNA levels for each L1HS-Ta genomic instance.
Heat maps showing for each L1HS-Ta instance (row) the Log2 fold change (Log2FC) of RNA-seq signals for each ORF1 shRNA versus a scrambled shRNA control (n=3). (a) MCF7 cells. (b) 2102Ep cells. The …
Figure 4 with 3 supplements
Locus- and cell-type-specific reactivation of individual L1HS-Ta copies in normal and transformed cells.
(a) Heat map displaying expression levels of each L1 instance in each of the analyzed cell lines. Expression level is defined as the number of RNA-seq fragments mapped in a 1 kb-window downstream of …
Figure 4—figure supplement 1
Heat maps for L1HS-Ta loci individual expression in various cell lines.
Legend is identical to Figure 3e. MCF7 RNA-seq data are from the ENCODE Project (MCF7_ENCODE) and from this study (MCF7_Cristofari).
Figure 4—figure supplement 2
RT-PCR validation of individual L1 expression across several cell lines.
PCR primers are anchored in the L1 internal sequence and in the flanking genomic region, respectively. Each RT-PCR included a control reaction without RT (-) to exclude possible genomic DNA …
Figure 4—figure supplement 3
Relationship of expressed L1HS-Ta copies with genes and ploidy.
(a) Distribution of genic L1HS-Ta full-length copies regarding the orientation relative to the overlapping genes. Pie charts indicate the proportion of sense (light blue) and antisense (dark blue) …
Figure 5
Evidence of retrotransposition capability for selected L1HS-Ta copies.
(a) Evidence of retrotransposition competence for the top 20 most expressed L1 copies across all cell lines analyzed. Cellular assays refer to retrotransposition cellular assays of plasmid-borne L1 …
Figure 6
Schematic model showing the highly locus-specific and variable expression of L1HS-Ta elements among different somatic cell types and individuals.
The colored boxes correspond to L1HS-Ta copies, some being polymorphic (pink). The model is developed in the main text.
Additional files
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Supplementary file 1
Description of the cell lines and RNA-seq datasets used in this study.
Note that HEK-293T data were ambiguously named in the original publication, as 'HEK-293' in the main text, but as 'HEK-293T' in the method section (Sultan et al., 2014). We solved this ambiguity by searching for RNA-seq reads matching the SV40 virus and Neomycin-resistance gene sequences, which confirmed the nature of the cells as being 'HEK-293T'.
- https://doi.org/10.7554/eLife.13926.016
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Supplementary file 2
Oligonucleotides used in this study, RNA-seq and ATLAS-seq statistics.
Note that primers used to PCR-validate L1 insertions are described in Supplementary file 3 along with the PCR results.
- https://doi.org/10.7554/eLife.13926.017
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Supplementary file 3
Coordinates of all L1HS-Ta elements mapped in a panel of 12 human cell lines, evidence for 3’ transductions, and correspondence between insertion IDs.
See first sheet for legend.
- https://doi.org/10.7554/eLife.13926.018
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Supplementary file 4
ATLAS-seq PCR validation results obtained in HEK-293T cells.
- https://doi.org/10.7554/eLife.13926.019
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Supplementary file 5
Levels of expression, retrotransposition capability and lineages of the full length L1HS-Ta copies mapped by ATLAS-seq.
- https://doi.org/10.7554/eLife.13926.020
