Regulatory evolution of innate immunity through co-option of endogenous retroviruses

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Science  04 Mar 2016:
Vol. 351, Issue 6277, pp. 1083-1087
DOI: 10.1126/science.aad5497
  • Fig. 1 Dispersion of IFNG-inducible regulatory elements by ERVs.

    (A) Age distribution (left) and enrichment within ChIP-seq data sets (right) of 27 TE families that were enriched within binding sites for IFNG-stimulated cells (18). Estimated primate/rodent divergence time (82 million years ago) is from (34). (B) Frequency histogram of absolute distances from each ERV to the nearest ISG, for CD14+ cells. The background expectation is from the genome-wide ERV distribution (18). Statistical significance of the observed enrichment within the first 10 kb of the nearest ISG was assessed by binomial test. (C) Heat map of CD14+ ChIP-seq signals centered across STAT1 peak summits within MER41B elements. Bottom metaprofiles represent average normalized ChIP signal across bound elements. (D) Schematic of the MER41B LTR consensus sequence. Triangles indicate gamma activated site (GAS; TTCNNNGAA, where N = any nucleotide) motifs predicted to bind STAT1 in response to IFNG (13). Heat map depicts the presence of GAS motifs across 728 extant STAT1-bound MER41B copies in HeLa cells (18). Bottom metaprofile represents average presence of STAT1 motifs relative to the MER41 consensus sequence, overlain with normalized STAT1 ChIP-seq density across the same elements.

  • Fig. 2 A MER41 element is essential for AIM2 inflammasome activation.

    (A) Genome browser view of AIM2. ChIP-seq tracks are normalized per million reads. The “uniqueness” track displays genome-wide short-read alignability. (B) Quantitative polymerase chain reaction (qPCR) of AIM2 levels in wild-type and ΔMER41.AIM2 HeLa cells after 24 hours of IFNG treatment. (C) Western blot of AIM2 in wild-type and ΔMER41.AIM2 cells after IFNG treatment. (D) Luciferase reporter assays of MER41.AIM2, MER41.AIM2 with mutations in the predicted STAT1 sites, and primate orthologs of MER41.AIM2 (see fig. S7A). (E) Western blot of caspase-1 from supernatants of wild-type and ΔMER41.AIM2 cells infected with vaccinia virus (18). *P < 0.05, Student’s t test. Error bars denote SD.

  • Fig. 3 Multiple MER41 elements have been co-opted to regulate the IFNG response.

    (A) Genome browser views of MER41 elements located near APOL1, IFI6, and SECTM1. ChIP-seq data are depicted as normalized signal per million reads. (B) qPCR of each gene comparing IFNG-inducible levels in wild-type HeLa cells and MER41 deletion mutants. *P < 0.05, Student’s t test. Error bars denote SD.

  • Fig. 4 IFNG-inducible ERVs are pervasive in mammalian genomes.

    (A) A consensus mammalian species phylogeny overlain with boxplots (median and 25th/75th percentiles) depicting the estimated age of MER41-like amplifications (18). My, million years ago; triangles depict conserved GAS motifs. (B) Luciferase reporter assays of MER41-like LTR consensus sequences from cow and dog (18). (C) Heat map of ChIP-seq signals centered on STAT1 peak summits within muroid-specific RLTR30B elements. Columns depict STAT1 ChIP-seq data from mouse bone marrow–derived macrophages (BMM) that were either untreated or treated with IFNB or IFNG. Only RLTR30B elements that are bound by STAT1 upon IFNG treatment are shown. Bottom metaprofiles represent average normalized ChIP signal across bound elements. (D) Rodent phylogeny overlain with a boxplot depicting the amplification of RLTR30B, as in (A). ISRE denotes interferon-stimulated response element motif (TTTCNNTTTC) predicted to bind STAT1 in response to IFNB (13). (E) Luciferase reporter assay of RLTR30B consensus sequence, as in (B). [Time-calibrated phylogenies in (A) and (D) are from (34).] *P < 0.05, Student’s t test. Error bars denote SD.

Supplementary Materials

  • Regulatory evolution of innate immunity through co-option of endogenous retroviruses

    Edward B. Chuong, Nels C. Elde, Cédric Feschotte

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S11
    • Captions for tables S1 to S6
    • References
    Table S1
    TE enrichment analyses for human and mouse ChIP-Seq datasets.
    Table S2
    Analysis of STAT1/IRF1-bound ERVs and IFNG-stimulated genes in primary CD14+ macrophages.
    Table S3
    List of MER41 and RLTR30B repeats bound by TFs and their closest gene.
    Table S4
    BLAST analysis of presence/absence of MER41-like elements across mammalian species representative of each major eutherian lineage.
    Table S5
    Uniformly analyzed ChIP-Seq peaks used in this study.
    Table S6
    Sequences used in this study (CRISPR-Cas9 gRNAs, qPCR and genotyping primers, synthesized LTR promoters).

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