Fig 1.
Maternal gene expression in zebrafish eggs.
(A) Experiment design: the transcriptomes of 24 individual zebrafish eggs was determined in five clutches. (B) Gene-expression distribution of the 11,118 expressed (red) and 11,353 non-expressed (green) unique Ensembl-defined genes. (C) Top 15 over-represented KEGG pathways associated with the maternally non-expressed genes. (D) Top 15 over-represented KEGG pathways associated with the maternally-expressed genes.
Fig 2.
Differential gene expression in the maternal transcriptome.
Variability of the maternal transcriptome. (A) Distribution of maximum fold changes (mFCs) in gene expression per gene between individual eggs (black, B left panel) and per gene within clutches (grey, B right panel). (B) Left panel, the maximum fold change (mFC) in gene expression between individual eggs, calculated as the difference per gene of the log intensity of the highest gene expression in any egg and the lowest log intensity of any other egg; Right panel, the maximum fold change within clutches was calculated per gene as the largest of the differences of the highest log intensity in any clutch (≈ mother) and the lowest log intensity in the same clutch (≈ mother). The red dashed line represents an absolute gene-expression mFC of 2. (C) Four illustrative examples of similar gene-expression in clutches from different mothers (color code see Fig 1A). Labels on the X-axes represent ‘Mother (clutch)’.
Fig 3.
Obvious mother-specific maternal gene-expression.
Maternal genes expressed at mother-specific distinct levels. (A) Heatmap showing 17 clusters of genes containing at least 25 genes that are expressed at a mother-specific or group-of-mothers specific level (see main text paragraph 3.4). The first 10 clusters are numbered by their relative gene-expression level between mothers as indicated by a 5-digit code (1 = high; 2 = low). In these 17 clusters only two levels were present because clusters with more than two levels contain less than 25 genes (S6 File) (B) Raw intensity data of three probes that query the transcript (ENSDART00000132835, pax1b-001) at positions: 985, 1268 and 1472 (color code: see Fig 1A). Labels on the X-axes represent ‘Mother (clutch)’, labels on the Y-axes represent log2 Intensity. (C) Illustrative examples of genes with mother-specific gene expression of the 16 clusters from A that have an inverse counterpart (color code see Fig 1A). Labels on the X-axes represent ‘Mother (clutch)’, labels on the Y-axes represent log2 Intensity.
Fig 4.
Subtle mother-specific maternal gene-expression.
Overall low-variable maternal genes are almost all mother-specific differentially expressed. (A) Representation of the first four principal components of a PCA on the 11,118 expressed genes. (color code see Fig 1A). The contribution to the total variability is given as a percentage at the axes. (B) Scatterplots of the per gene average clutch expression value of the first clutch against the four other clutches. Red dots represent the 2,224 genes that show an absolute distinct mother-specific expression level; green dots represent all other expressed genes. Dashed lines represent a fold change of 2 between the two clutches (also S14 File). Labels on the Y-axes represent ‘Clutch 1’. (C) Illustrative examples of four mother-specific differentially-expressed genes that do not have an absolute distinct mother-specific expression. Labels on the X-axes represent ‘Mother (clutch)’, labels on the Y-axes represent log2 Intensity.
Fig 5.
Characteristics of mother-specific maternal gene expression.
Characteristics of the 17 mother-specific gene clusters defined by relative gene-expression differences (see Fig 3A). (A) Clusterogram of chromosome location of the genes per cluster. Indicated is the relative occurrence of genes on a chromosome: dark blue, low; bright yellow, high. (B) Schematic representation of the overrepresented, TRANSFAC-defined transcription-factor binding sites (TFBS) in the upstream regions of the genes per cluster. Each horizontal line denotes a specific TFBS (specified in the same order from top to bottom in S13 File). A bar indicates that a specific TFBS is found overrepresented in the specified mother-specific gene cluster. Red bars indicate that a specific TFBS is found overrepresented in both related, inversed gene clusters. (C) Representation of the overrepresented miRNA target sequences in the transcript sequences of the genes per cluster, as well as for the expressed and non-expressed genes. The targets for miRNAs reported in the following references were tested: a Abramov et al. [51], b: Juanchich et al. [52], c: Yao et al. [53], d: Wei et al. [54], b* whereas in [52] the minor form of miR-181 was reported, here the targets for the major form of miR-181 were tested, because in TargetScanFish 6.2 no targets for miR-181* are available.