WAMIDEX: a web atlas of murine genomic imprinting and differential expression

Abstract

The mouse is an established model organism for the study of genomic imprinting. Mice with genetic material originating from only one parent (e.g., mice with uniparental chromosomal duplications) or gene mutations leading to epigenetic deficiencies have proven to be particularly useful tools. In the process of our studies we have accumulated a large set of expression microarray measurements in samples derived from these types of mice. Here, we present the collation of these and third-party microarray data that are relevant to genomic imprinting into a Web Atlas of Murine genomic Imprinting and Differential EXpression (WAMIDEX: https://atlas.genetics.kcl.ac.uk). WAMIDEX integrates the most comprehensive literature-derived catalog of murine imprinted genes to date with a genome browser that makes the microarray data immediately accessible in annotation-rich genomic context. In addition, WAMIDEX exemplifies the use of the self-organizing map method for the discovery of novel imprinted genes from microarray data. The parent-of-origin-specific expression of imprinted genes is frequently limited to specific tissues or developmental stages, a fact that the atlas reflects in its design and data content.

Figure 1

Genome browser output for the imprinted Ddc/Grb10 locus on Chr 11qA1. Because of space limitations, the 5′ part of Ddc and the approximately 70 kb large intergenic region between Ddc and Grb10 was removed from the output (thick green vertical line). The UCSC Known Genes track at the top shows the 3′-most introns and exons of Ddc and Grb10. The subsequent 430v2 and U74Av2 tracks display the target sequence alignments and exact probe matches of the 430v2 and U74Av2 probe sets that represent Ddc and Grb10, respectively. In the following experimental tracks, the measurements displayed for the two replicate Dnmt3l^−/+ experiments were taken by 430v2 probe sets (Ddc: 1426215_at; Grb10: 1425458_a_at and 1425457_a_at), while the measurements in UpDp heart samples were made with U74Av2 probe sets (Ddc: 160074_at; Grb10: 93690_at and 93691_s_at). The color of and the text label with the expression ratios (GCOS/MAS5, PLIER, GC-RMA, RMA) next to the track entries for, for example, Ddc indicate a roughly two-fold upregulation in Dnmt3l^−/+ versus normal 8.5 dpc embryos and four- to six-fold more transcript in paternal UpDp than in maternal UpDp newborn heart samples. These data suggested imprinted paternal-only expression of Ddc in heart, which we recently confirmed. Grb10 is a known imprinted gene that is expressed from the maternal allele and positively regulated by maternal methylation in all tissues except brain, and this was reflected by our

Figure 2

Differential expression measurements for known imprinted genes (blue gene name: expressed from the paternal allele; red: maternally expressed). Gene expression was compared between (A) Dnmt3l^−/+ (average of two independent samples and array hybridizations) versus normal 8.5 dpc embryos, (B) 15.5 dpc embryos with maternal versus paternal Chr 12 UpDp, (C) 15.5 dpc placentae with maternal versus paternal Chr 12 UpDp, and (D) 8.5 dpc embryos with maternal versus paternal Chr 18 UpDp. Genes expressed at low absolute levels in both respective sample types were excluded. The shown expression ratio (log₂ scale) for a gene is the median of four ratios: one for each of the four probe level analysis methods used. The ratios of distinct probe sets representing the same gene and yielding consistent measurements were again summarised by their median. The y-axis has been limited to show ratios up to a 16-fold differential (+/−4), a limit that was exceeded by Cdkn1c in (A) and Gtl2 in (B). (A) genes are ordered by Chr; an uninterrupted block of genes with the same background (white, grey or blue) corresponds to a set of genes belonging to the same coordinately regulated imprinted cluster. A blue background indicates a cluster regulated by a paternally methylated ICR, while white and grey stand for maternally methylated ICRs. For each of Nespas, Ube3a, Gtl2, Rian and Air, multiple representative probe sets exist that gave very different results, shown here side-by-side. For Nesp, GnasXl and Gnas, there is only a single probe set located in the 3′ UTR common to all three genes. (B–D) show only known imprinted genes on the respectively uniparentally duplicated Chr.

Figure 3

The SOM generated from the Dnmt3l^−/+ and UpDp microarray for proximal Chrs 7 and 11. Left and bottom: the map has eight layers, one layer per comparative microarray experiment (2x Dnmt3l^−/+ versus normal 8.5 dpc embryo; maternal versus paternal UpDp in 13.5 dpc embryo and placenta, newborn brain, heart, liver and carcass). Hexagons correspond to SOM elements, i.e., clusters of similar differential expression profiles. The degree of shading of a hexagon in a particular layer indicates the degree (log₂-scale) and direction of differential expression that was observed on average for members of the cluster in the experiment that corresponds to the layer. The superimposed turquoise or magenta hexagons mark clusters containing differential expression profiles of known paternally or maternally expressed imprinted genes, respectively. Top-right: In this universal distance matrix visualisation of the SOM,, hexagons have been labeled with known imprinted gene symbols. Ddc (blue) marks the cluster containing the paternally expressed heart-specifically imprinted Dopa decarboxylase gene. Here, the degree of hexagon shading indicates how dissimilar the neighboring clusters are, which helps to identify particularly distinct “super”-clusters like the region in the top-left corner of the map that contains Ddc and most of the other known paternally expressed imprinted genes.