Reassessment of weak parent-of-origin expression bias shows it rarely exists outside of known imprinted regions
- Department of Genetics, University of Cambridge, United Kingdom
Figures
Figure 1
limited overlap between novel genes identified in the four studies.
(A–B) Euler diagrams showing the overlap of (A) - known imprinted genes and (B) – novel biased genes between the four studies. (C) – overlaps between different classes of novel genes. Class-1 = …
Figure 2 with 2 supplements
Limited overlap between novel genes called by different analysis pipelines.
(A–C) Venn diagrams showing the overlap between allelic biased genes called by our pipeline with the ISoLDE package (gray circles) versus the original studies. A – Dataset A, B - Dataset B, C - …
Figure 2—figure supplement 1
Expression levels of genes called as biased in at least one of the original studies.
Data generated from re-analysis of original RNA-seq datasets. To allow for comparison across the different datasets, expression levels are reported as mean TPM (transcripts per million) from all …
Figure 2—figure supplement 2
Overlapping underdetermined genes called between Dataset B (A) and Dataset C (B) and ISoLDE pipeline.
Number of ISoLDE called genes are in pale gray, and overlaps with original study are in dark gray. Overlapping genes are listed to the right. Genes in red were flagged by ISoLDE and genes in bold …
Figure 3
Weakly biased Class-3 genes are preferentially expressed from the chromosome carrying the germline methylation mark.
(A) Distribution of biased genes by maximum reported bias. Class-1 = novel singletons >1 Mb from another gene identified in any of the studies. Class-2 = novel clusters where two or more novel genes …
Figure 4
Weakly biased Class-3 genes are located at the periphery of known imprinted domains.
(A) – Distribution of Class-3 biased genes in relation to known imprinted genes. Genes flanked by known imprinted genes are shown in turquoise and those peripheral to known imprinted genes are shown …
Figure 5 with 3 supplements
Experimentally validated Class-1 and Class-2 genes.
(A) – Nhlrc1 (Class-1) is paternally biased in all postnatal neuronal tissues tested. (B-C) Bisulfite sequencing analysis in P7 tissues.(B) – Cerebellum, (C)- Liver. Each line represents a different …
Figure 5—figure supplement 1
Coro1c pseudogene is almost exclusively expressed from the castaneus allele.
(A) Nhlrc1 expression bias in P6 cerebellum and liver which were also used for bisulfite sequencing analysis. (B) Allelic balance of expression of Coro1c pseudogene that overlaps the Nhlrc1 DMR. …
Figure 5—figure supplement 2
Allelic bias in Wnk4 novel cluster.
(A) Weak bias in Wnk4 gene. (B) location of genes in the novel cluster, (C) location of gDMRs, and antisense transcript. Graph shows mean expression (%) from the paternal allele (blue) and maternal …
Figure 5—figure supplement 3
Expression levels of genes tested by allele-specific pyrosequencing.
Data are extracted from Supplementary file 1f. Genes that were only validated in the placenta were counted as unvalidated and the two known placental-specific imprinted genes are not included in the …
Figure 6 with 3 supplements
Allele-specific expression analysis of the Dlk1 domain.
(A–F) Allelic bias in Evl (A), Slc25a29 (B), Wars (C) Wdr24 (D) Dlk1 (E), and Dync1h1 (F) Graphs show mean expression (%) from the paternal allele (blue) and maternal allele (red) C57BL/6 × CastEiJ …
Figure 6—figure supplement 1
Allelic bias in the Mcts2 region.
(A) Mcts2 imprinted region. (B–E) Allelic bias (%) in Mcts2 (A), Cox4i2 (B), Bcl2l1 (C) , and Tpx2 (D). Graphs show mean expression (%) from the paternal allele (blue) and maternal allele (red) …
Figure 6—figure supplement 2
Allelic bias (%) in Adam23 (A), Ifitm10 (B), and Ago2 (C).
Graphs show mean expression (%) from the paternal allele (blue) and maternal allele (red) C57BL/6 × CastEiJ (BC) and four CastEiJ × C57BL/6 (CB) crosses. Castaneus allele is denoted by a spotted …
Figure 6—figure supplement 3
Allelic bias in Peg3 region.
(A) Peg3 imprinted region. (B–D) Allelic bias (%) in Smim17 (A), Peg3 (B), and Clcn4 (C). Graphs show mean expression (%) from the paternal allele (blue) and maternal allele (red) C57BL/6 x CastEiJ …
Figure 7
Possible mechanisms behind parent-of-origin expression biases in tissues.
(A-D) Scenarios causing biased expression in heterogenous cell populations: bias occurs in every cell in the tissue (A), random imprinting in the subset of cells (B), cell-type specific imprinting (C…
Tables
Table 1
Table showing the summary of all the allele-specific pyrosequencing performed to validate putative-biased genes.
Values show the mean expression (%) from the paternal allele of both reciprocal crosses to eliminate strain bias. Values above 55% are called as paternally biased (blue) and values below 45% are …
| Genes | Chr. | Dataset | Direction previously reported | Class | e16.5 | e16.5 | e16.5 | P7 | P7 | P7 | P7 | P7 | P60 | P60 | P60 | P60 | P60 | Strain Bias | Validation status |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Plac. | Liver | Brain | Cortex | Hyp. | Cb. | Hipp. | B.S | Cortex | Hyp. | Cb. | Hipp. | B.S | |||||||
| Class-1 (Novel Singletons) | |||||||||||||||||||
| L3mbtl1 | 2 | B | pat | 1 | - | - | - | 48.1 | 53.4 | 53.4 | 46.4 | 50.1 | 49.4 | 49.7 | 46.7 | 51.0 | 49.2 | ✓ | Biallelic |
| Ahi1 | 10 | B,D | pat | 1 | 52.8 | 46.5 | n/a | 47.0 | 51.6 | 50.9 | 52.8 | 46.9 | 48.6 | 49.4 | 50.0 | 52.4 | 51.3 | ✓ | Biallelic |
| Platr20 | 11 | A | pat | 1 | 51.7 | 49.9 | 50.0 | 49.9 | 50.4 | 50.1 | 50.4 | 50.2 | 49.8 | 49.8 | 50.1 | 50.2 | 49.7 | Biallelic | |
| Calm1 | 12 | B,D | pat | 1 | - | - | - | 54.7 | 49.5 | 51.4 | 45.9 | 43.4 | n/a | n/a | n/a | n/a | n/a | ✓ | Biallelic |
| Nhlrc1 | 13 | B, C, D | pat | 1 | - | - | - | 54.8 | ✓ | ||||||||||
| Tnk1 | 11 | A | mat | 1 | - | - | - | - | - | - | - | - | - | - | - | - | - | Low expression | |
| Mlana | 18 | B | mat | 1 | - | - | - | - | - | - | - | - | - | - | - | - | - | Low expression | |
| Gm16299 | 19 | C | pat | 1 | - | - | - | - | - | - | - | - | - | - | - | - | - | Low expression | |
| Class-2 (Novel Clusters) | |||||||||||||||||||
| Stx6 | 1 | C | mat | 2 | - | - | - | 50.7 | 49.2 | 50.3 | 49.8 | 50.1 | n/a | n/a | n/a | n/a | n/a | Biallelic | |
| Gabra5 | 7 | B,D | pat | 2 | - | - | - | 51.5 | 53.2 | 52.5 | 54.8 | 52.6 | 52.3 | 50.7 | 48.6 | 51.5 | 51.5 | Biallelic | |
| Wnk4 | 11 | C | mat | 2 | - | - | - | 50.1 | 52.0 | 45.3 | 50.6 | 48.1 | 50.9 | 45.4 | 48.1 | ✓ | |||
| Vat1 | 11 | B | mat | 2 | 50.9 | 52.6 | 49.6 | 48.8 | 50.4 | 51.0 | 49.9 | 46.4 | 51.3 | 50.8 | 49.8 | 50.4 | ✓ | ||
| Rdm1 | 11 | A | mat | 2 | 49.4 | - | - | 48.8 | 48.8 | 50.1 | 50.2 | 50.7 | 46.9 | 49.5 | 50.5 | 50.1 | 48.7 | ✓ | Biallelic |
| Gaa | 11 | B,D | pat | 2 | 48.9 | 52.3 | 53.6 | 51.3 | 47.1 | 51.7 | 53.1 | 51.8 | 51.8 | 51.6 | 47.9 | 51.9 | 50.8 | ✓ | Biallelic |
| Pcdhb10 | 18 | D | mat | 2 | - | - | - | - | - | - | - | - | - | - | - | - | - | Low expression | |
| Pcdhb12 | 18 | B,C | mat | 2 | - | - | - | ||||||||||||
| Pcdhb20 | 18 | B,C | pat | 2 | - | - | 52.7 | 51.5 | 51.6 | 52.0 | 52.6 | 53.1 | 51.5 | 52.3 | 51.6 | 51.6 | 50.1 | ✓ | Biallelic |
| Prdx5 | 19 | B | pat | 2 | 46.9 | 51.1 | 49.4 | 49.0 | 50.4 | 48.8 | 49.4 | 49.9 | 49.2 | 50.2 | 50.0 | 48.3 | 49.2 | ✓ | Biallelic |
| Rtn3 | 19 | D | pat | 2 | 49.9 | 50.7 | 49.4 | 47.3 | 49.5 | 49.5 | 49.2 | 49.1 | 50.9 | 49.7 | 50.4 | 50.4 | |||
| Pla2g16 | 19 | B | mat | 2 | 51.6 | 50.6 | 51.7 | 49.7 | 48.9 | 48.5 | 50.7 | 51.5 | 51.2 | 49.2 | 46.8 | 48.3 | ✓ | ||
| Mr1 | 1 | C | mat | 2 | - | - | - | - | - | - | - | - | - | - | - | - | - | Low expression | |
| BC034090 | 1 | C | mat | 2 | - | - | - | - | - | - | - | - | - | - | - | - | - | Low expression | |
| Tmem106a | 11 | A | mat | 2 | - | - | - | - | - | - | - | - | - | - | - | - | - | Low expression | |
| Class-3 (Close to known imprinted genes) | |||||||||||||||||||
| Adam23 | 1 | A,B,C,D | pat | 3 | 48.0 | 52.0 | 53.7 | 53.5 | 54.1 | ||||||||||
| Mcts2 | 2 | A,B,C | pat | K | |||||||||||||||
| Cox4i2 | 2 | C | pat | 3 | 49.3 | - | - | 51.0 | 52.8 | 54.9 | |||||||||
| Bcl2l1 | 2 | A,B,C,D | pat | 3 | 49.5 | 50.2 | |||||||||||||
| Tpx2 | 2 | C | pat | 3 | - | 49.7 | 49.1 | 53.4 | 52.6 | 50.7 | 53.6 | 51.4 | ✓ | ||||||
| Herc3 | 6 | A,B,C,D | mat | K | 47.0 | 45.8 | 45.7 | 49.9 | ✓ | ||||||||||
| Fam13a | 6 | B,D | mat | 3 | - | 46.1 | 53.2 | 47.9 | 47.1 | 51.3 | 49.4 | 48.4 | n/a | n/a | n/a | n/a | n/a | ✓ | Biallelic |
| Zfp78 | 7 | B | both | 3 | - | - | - | - | - | - | - | - | - | - | - | - | - | Low expression | |
| Smim17 | 7 | B,D | mat | 3 | - | - | 48.8 | 50.9 | 45.2 | 52.1 | 50.8 | 49.3 | |||||||
| Peg3 | 7 | A,B,C,D | pat | K | ✓ | ||||||||||||||
| Zfp954 | 7 | B | mat | 3 | - | - | - | - | - | - | - | - | - | - | - | - | - | Low expression | |
| Zfp773 | 7 | B | mat | 3 | - | - | - | - | - | - | - | - | - | - | - | - | - | Low expression | |
| Zfp772 | 7 | B | mat | 3 | - | - | - | - | - | - | - | - | - | - | - | - | - | Low expression | |
| Clcn4-2 | 7 | B | mat | 3 | 54.5 | 48.5 | 48.9 | 48.8 | 49.9 | 49.1 | 48.0 | 49.5 | 50.7 | 51.0 | 49.6 | 50.7 | ✓ | ||
| Ifitm10 | 7 | C,D | mat | 3 | 46.9 | 52.3 | 48.7 | 47.5 | 53.0 | 49.4 | 49.0 | 50.7 | 47.0 | ✓ | |||||
| Ctsd | 7 | B,D | mat | 3 | 46.8 | 47.8 | 50.1 | 50.0 | 49.0 | 48.4 | 48.9 | 49.8 | 49.3 | 50.2 | 49.0 | 50.5 | 49.5 | Biallelic | |
| Evl | 12 | B | pat | 3 | 46.2 | 48.3 | 50.2 | 48.7 | 51.3 | 51.1 | 50.2 | 49.5 | 50.9 | 50.9 | 52.6 | 50.8 | 50.6 | ✓ | Biallelic |
| Slc25a29 | 12 | B | pat | 3 | 45.5 | 52.3 | 53.9 | 56.2 | 54.5 | 53.3 | 54.2 | 52.8 | 53.8 | 50.6 | 53.6 | 53.2 | ✓ | ||
| Wars | 12 | C | pat | 3 | 45.2 | 52.5 | 53.9 | 54.5 | 53.3 | 54.2 | 52.8 | 53.9 | 50.6 | 53.6 | 53.2 | ||||
| Wdr25 | 12 | B,D | pat | 3 | - | - | - | 50.7 | 52.9 | 52.0 | 50.6 | 48.7 | 51.8 | 49.9 | 51.7 | - | ✓ | ||
| Dlk1 | 12 | A,B,C,D | pat | K | |||||||||||||||
| Ppp2r5c | 12 | B,C | pat | 3 | 52.4 | 51.3 | 48.5 | 48.6 | 49.3 | 54.0 | 50.6 | 48.2 | 50.6 | 48.7 | 45.2 | 51.0 | 49.3 | ✓ | Biallelic |
| Dync1h1 | 12 | B,C | pat | 3 | 46.9 | 49.8 | 50.4 | 50.7 | 50.7 | 51.1 | 49.9 | 50.4 | 51.0 | 50.4 | 50.1 | 50.1 | 49.8 | Biallelic | |
| Ago2 | 15 | A,B,C,D | mat | 3 | 47.7 | 50.7 | |||||||||||||
| Ampd3 | 7 | B | mat | K | 47.5 | 51.4 | 48.6 | 48.5 | 48.3 | 51.8 | 50.9 | 50.1 | 46.7 | 50.9 | 49.4 | 51.5 | ✓ | ||
| Gab1 | 8 | A | pat | K | 50.4 | 49.8 | 52.7 | 49.6 | 48.6 | 49.4 | 51.0 | 47.1 | 49.6 | 48.8 | 50.1 | 50.2 | |||
Additional files
-
Supplementary file 1
Data generated in this study.
(a) Study information for Dataset A (Babak et al., 2008), Dataset B (Bonthuis et al., 2015), Dataset C (Perez et al., 2015), Dataset D (Crowley et al., 2015) and Dataset E (Andergassen et al., 2017). (b) All genes called in original studies. (c) Overlapping Novel genes called in original studies. (d) All genes called in this study using ISoLDE. (e) Number of genes called in individual tissues in the original study and this study. (f) Expression levels of genes in RNA-seq data used for ISoLDE and called as biased in original study - Figure 2—figure supplement 1. (g) Strain biased genes called in Dataset B and Dataset C in this study. (h) CpG Methylation and H3K27me3 over promoter regions of imprinted and Class-3 genes - Figure 3D. (i) Overlapping genes called in this study and the original one. This list includes genes generated in the undetermined list by the ISoLDE pipeline. (j) List of primers used in the study.
- https://cdn.elifesciences.org/articles/83364/elife-83364-supp1-v2.xlsx
-
MDAR checklist
- https://cdn.elifesciences.org/articles/83364/elife-83364-mdarchecklist1-v2.docx
