Additional file 1: Table S1. of Maternal vitamin D depletion alters DNA methylation at imprinted loci in multiple generations

(This additional file contains details for all statistical analysis performed, including p values, effect sizes, q values, regression model, and method of statistical test.) (XLSX 45 kb

Phenotype_data_FINAL

see readm

The <i>Xce</i> candidate interval based on historical data.

<p>Panel A is a phylogenetic tree that reflects the sequence divergence within the Chadwick candidate interval for inbred mouse strains with known <i>Xce</i> alleles. Inbred strains with a number one superscript have both MDA and Sanger sequencing information available, while mouse strains with a number two superscript have only MDA genotype data available. Inbred strains with no number are assumed to have identical genotypes to a closely related strain that has been genotyped. Blue and green shading denotes the subspecific origin of the Chadwick interval for each strain (<i>M. m. domesticus</i> and <i>M. m. castaneus</i>, respectively). Panel B is a physical map that shows the locations of the previous <i>Xce</i> candidate intervals <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853-Chadwick1" target="_blank">[26]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853-Cattanach8" target="_blank">[57]</a>. Below the historical candidate intervals are the results of the SDP analyses using inbred strains selected from Panel A (See Methods). Tick marks represent SDPs classified as consistent (black), inconsistent (red), and partially consistent (gray). SNPs that retain consistent SDPs after inclusion of ALS/LtJ, LEWES/EiJ, PERA/EiJ, SJL/J, TIRANO/EiJ, WSB/EiJ, and ZALENDE/EiJ in the analysis are shown as blue tick marks above consistent SDPs. Our new maximum candidate interval is shown in gray below the tick marks. The minimum candidate interval is shown in black, while regions excluded are shown in red.</p

The <i>Xce</i> allelic series.

<p>Panel A shows the order of <i>Xce</i> allele strength. Panel B shows hypothetical distribution and mean XCI ratio skewing in female populations that are either homozygous or heterozygous for <i>Xce</i> alleles.</p

Allelic imbalance in selected female F1 hybrids.

<p>Panel A is a plot of the allele-specific expression data from F1 hybrids, where each colored letter represents an individual gene measurement from brain (“b”), kidney (“k”), and liver (“v”) from an individual female. Panel B is a plot of the posterior mean and confidence intervals for XCI fraction inferred for each genetic cross, based on our statistical model. Throughout, the x-axis reports the fraction of X-linked allele-specific expression from the strain with the unknown <i>Xce</i> allele. The color of each letter (on the right) and each corresponding posterior (on the left) denote the known <i>Xce</i> allele to which it is paired: black <i>Xce^a</i>; blue <i>Xce^b</i> and red <i>Xce^c</i>. Panel C is shows the inbred strains phenotyped for <i>Xce</i>, the strains each were crossed to, the total number of F1 females tested and the <i>Xce</i> alleles excluded and included based on posterior tail probabilities.</p

Maternal inheritance magnifies XCI skewing.

<p>Shown is allele-specific expression from reciprocal F1 <i>Xce</i> heterozygotes. The X-axis is partitioned according to <i>Xce</i> allele pairs. The Y-axis is the ratio of allele-specific expression from the X chromosome harboring the stronger <i>Xce</i> allele. Ratios were determined using either RNAseq or pyrosequencing.</p

Natural history of <i>Xce</i>.

<p>Panel A shows a three-dimensional PCA plot based on hybridization intensity of ten MegaMUGA probes (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen-1003853-g004" target="_blank">Figure 4</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853.s014" target="_blank">Table S10</a>) within the refined <i>Xce</i> candidate interval. Mouse strains with known <i>Xce</i> alleles are shown as large spheres, while predicted mouse strains and wild-mice are shown as smaller spheres. Mouse samples are shaded according to <i>Xce</i> allele or <i>Xce</i> haplotype: Known <i>Xce^a</i> allele, black; predicted <i>Xce^a</i> allele, gray; known <i>Xce^b</i> allele, blue; predicted <i>Xce^b</i> allele, light blue; known <i>Xce^c</i> allele, green; predicted <i>Xce^c</i> allele, light green; known <i>Xce^d</i> allele, orange; predicted <i>Xce^d</i> allele, yellow; known <i>Xce^d</i> allele, orange; predicted <i>Xce^d</i> allele, yellow; known <i>Xce^e</i> allele, red; predicted <i>Xce^e</i> allele, pink; known <i>Xce^f</i> allele, magenta. Panel B shows a phylogenetic tree based on 18 MDA SNP probes within the new <i>Xce</i> candidate interval. The topography of the tree accurately reflects the genetic relationship between the <i>Xce</i> alleles, however because of the limited number of SNP used to generate the tree and the ascertainment bias of the SNPs present on the MDA <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853-Yang1" target="_blank">[40]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853-Keane1" target="_blank">[41]</a>, the tree is misleading with respect to the true genetic distance between <i>Xce</i> haplotypes (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853.s004" target="_blank">Figure S4</a> for a more accurate representation of branch lengths). Open circles represent classical inbred strains with unknown <i>Xce</i> alleles; filled circles represent wild-derived or wild-caught mice with unknown <i>Xce</i> alleles; open squares represent classical inbred strains phenotyped for <i>Xce</i>; filled squares represent wild-derived strains with known <i>Xce</i> alleles. Strains with whole genome sequence data are shown with a star. We color coded the specific or subspecific origin of the candidate interval for the four major branches of the tree: red, <i>M. m. musculus</i>; blue, <i>M. m. domesticus</i>; green, <i>M. m. castaneus</i>, orange, <i>M. spretus</i>, pink, <i>Mus spicilegus </i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853-Yalcin1" target="_blank">[53]</a>.</p

Sequence analysis of the candidate interval.

<p>In panel A, the candidate interval is show as a thick black bar. Below the candidate interval is a dotplot generated from pairwise sequence concordance in the mm9 genome assembly. Diagonal lines slanting down from left to right are duplications, while diagonal lines slanting up from left to right are inversions. Above the dotplot are arrows that show the four duplications (SD1-4) and inversion (I5) identified. Panel B is a phylogenetic tree that depicts the relationship between the duplications. The phylogenetic tree was generated using the CLUSTALW2 alignment software <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853-Larkin1" target="_blank">[71]</a>. Also shown are the ten MegaMUGA markers used for the PCA analysis and their positions in relation to the segmental duplications. Shown in panel C are probe hybridization plots for two of these markers, UNC31159403 and XiD2 (all plots are provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003853#pgen.1003853.s002" target="_blank">Figure S2</a>). The axes represent hybridization intensities for probes tracking alternative alleles at each marker. The colors correspond to the different functional <i>Xce</i> alleles: gray <i>Xce^a</i>; blue <i>Xce^b</i>; red <i>Xce^e</i>; green <i>Xce^c</i>; yellow <i>Xce^d</i>. Note that these plots do not agree with the expectations for standard biallelic variants. Typically biallelic variant plots show three distinct clusters representing homozygous A, homozygous B, or heterozygous A/B.</p

Lung pathology in select preCC mice.

<p>(A). OR63f51—normal parenchyma. (B). OR181f61—airway debris and cuffing and edema surrounding the associated vasculature. (C) OR220f57—denuded airway blocked with debris. (D) OR380f64 –perivascular cuffing including eosinophilia. (E) OR941f69 –alveolitis including hyaline membrane formation, arrows point to hyaline membranes. (F) OR5030f128 –normal airway and associated vasculature.</p

Phenotypic relationships.

<p>Heat map of the relationships between lung pathology, titer and weight loss in the preCC. Yellow indicates positive correlation and blue indicates negative correlation.</p