A spontaneous genetically induced epiallele at a retrotransposon shapes host genome function
- Department of Genetics, University of Cambridge, United Kingdom
Figures
Figure 1 with 2 supplements
Intracisternal A-particle (IAP)-Pgm2 methylation is tri-modally distributed and stably inherited in inbred B6 mice.
(A) Map of CpG positions in the IAP-Pgm2 long terminal repeats (LTRs). CpGs assayed in panel B are shown in red. (B) IAP-Pgm2 methylation levels are consistent between the 5′ and 3′ ends. …
Figure 1—figure supplement 1
Genomic structure and coding potential of intracisternal A-particle (IAP)-Pgm2.
Details lifted from the Pfam database (https://pfam.xfam.org). Genomic distances are drawn to scale.
Figure 1—figure supplement 2
The intracisternal A-particle (IAP)-Pgm2 methylation pattern is not sex-linked.
IAP-Pgm2 methylation levels in both B6 males and females segregate into three distinct DNA methylation states: high (blue), intermediate (green), and low (orange).
-
Figure 1—figure supplement 2—source data 1
Numerical data represented in panels B-D, and Figure 1—figure supplement 2.
- https://cdn.elifesciences.org/articles/65233/elife-65233-fig1-figsupp2-data1-v2.xlsx
Figure 2 with 2 supplements
The intracisternal A-particle (IAP)-Pgm2L allele is a solo long terminal repeat (LTR) formed via inter-LTR homologous recombination.
(A) Map of PCR primer pairs P1–P3 and nested PCR primer pairs N1–N3 (not drawn to scale). (B and C) Agarose gel electrophoresis of PCR products amplified from three IAP-Pgm2HH and three IAP-Pgm2LL …
-
Figure 2—source data 1
Numerical data represented in panel F.
- https://cdn.elifesciences.org/articles/65233/elife-65233-fig2-data1-v2.xlsx
Figure 2—figure supplement 1
Possible mechanisms of homologous recombination between intracisternal A-particle (IAP) long terminal repeats (LTRs) leading to the formation of a solo LTR at the Iap5-1 locus.
(A) Intra-chromosomal homologous recombination between the 5′ and 3′ LTRs of the repeat element, giving rise to a solo LTR and a circularised unintegrated viral fragment. (B) Inter-chromosomal …
Figure 2—figure supplement 2
Differential DNA methylation between the Iap5-1full and Iap5-1solo variants extends over the entire long terminal repeat(s) (LTR[s]).
(A and B) Clonal bisulphite sequencing of the 5′ and 3′ ends of Iap5-1full (A) and of the Iap5-1solo LTR (B) in adult liver. Each line represents an individual PCR clone and each circle represents a …
Figure 3
Lack of DNA methylation at Iap5-1solo is accompanied by a loss of H3K9me3 marks.
(A) H3K9me3 ChIP-qPCR on Iap5-1full and Iap5-1solo adult male livers. IAP-Asxl3 and SINE-Rbak are positive control loci, the Gapdh promoter is a negative control locus, and the Rabbit IgG antibody …
-
Figure 3—source data 1
Numerical data represented in panel A.
- https://cdn.elifesciences.org/articles/65233/elife-65233-fig3-data1-v2.xlsx
Figure 4 with 1 supplement
Genetic background influences Iap5-1solo methylation levels.
(A) B6 and CAST sequence alignment of the Iap5-1 insertion site reveals that the Iap5-1 element (purple) and its associated target site duplication (TSD) sequence (red) are not present in the CAST …
Figure 4—figure supplement 1
DNA methylation at Iap5-1solo is unresponsive to maternal dietary methyl supplementation.
Iap5-1solo females were fed a control or methyl supplemented diet 2 weeks prior to mating and for the duration of pregnancy and lactation. DNA methylation levels were quantified in 8-week-old …
-
Figure 4—figure supplement 1—source data 1
Numerical data represented in panels B, C, and Figure 4—figure supplement 1.
- https://cdn.elifesciences.org/articles/65233/elife-65233-fig4-figsupp1-data1-v2.xlsx
Figure 5 with 2 supplements
Functional consequences of the genetically induced epiallele at the Iap5-1 locus.
(A) Scaled map of the genes surrounding Iap5-1. Gene transcripts were extracted from the UCSC Genome Browser (Haeussler et al., 2019). (B) The Iap5-1 polymorphism influences neighbouring gene …
-
Figure 5—source data 1
Numerical gene expression data represented in Figure 5B and Figure 5—figure supplement 1B.
- https://cdn.elifesciences.org/articles/65233/elife-65233-fig5-data1-v2.xlsx
-
Figure 5—source data 2
Numerical data for metabolic experiments shown in Figure 5C and D and Figure 5—figure supplement 2.
- https://cdn.elifesciences.org/articles/65233/elife-65233-fig5-data2-v2.xlsx
Figure 5—figure supplement 1
Bordering genomic regions are transcribed in Iap5-1solo tissues.
(A) Map of RT-qPCR primers (drawn to scale). (B) Transcription of bordering unique DNA was quantified in Iap5-1full and Iap5-1solo thymus and cortex tissues via RT-qPCR. Relative expression was …
Figure 5—figure supplement 2
Metabolic phenotyping of Iap5-1full and Iap5-1solo individuals.
(A) Concentration of metabolic biomarkers in plasma samples collected from Iap5-1full and Iap5-1solo adult males. Box plots show the distribution quartiles and median. Statistics: unpaired t-tests. …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Mus musculus) | C57BL/6J | The Jackson Laboratory via Charles River | 000664 (JAX) 632 (Charles River) | |
| Strain, strain background (Mus musculus) | CAST/EiJ | MRC Harwell Institute | FESA:773 | |
| Cell line (Mus musculus) | C57BL6/J ES cell lines | This paper | See Materials and methods, Generation of ESC lines. | |
| Antibody | Rabbit polyclonal anti-H3K9me3 | Active Motif | RRID:AB_2532132 | ChIP (2.5 µl/30 mg liver tissue) |
Additional files
-
Supplementary file 1
Primer sequences and GEO accession numbers.
- https://cdn.elifesciences.org/articles/65233/elife-65233-supp1-v2.xlsx
-
Transparent reporting form
- https://cdn.elifesciences.org/articles/65233/elife-65233-transrepform-v2.transparentreportingform.docx
