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Global transcriptome analysis identifies regulated transcripts and pathways activated during oogenesis and early embryogenesis in Atlantic cod.

Kleppe L, Edvardsen RB, Furmanek T, Taranger GL, Wargelius A - Mol. Reprod. Dev. (2014)

Bottom Line: During early vitellogenesis, several of the most upregulated genes are linked to nervous system signaling, suggesting increasing requirements for ovarian synaptic signaling to stimulate the rapid growth of oocytes.Highly upregulated genes during late vitellogenesis are linked to protein processing, fat metabolism, osmoregulation, and arrested meiosis.One of the genes with the highest upregulation in the ovulated egg is involved in oxidative phosphorylation, reflecting increased energy requirements during fertilization and the first rapid cell divisions of early embryogenesis.

View Article: PubMed Central - PubMed

Affiliation: Institute of Marine Research, Bergen, Norway.

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Related in: MedlinePlus

Heat maps of the expression of the most-regulated (based on fold change) genes from one developmental stage to the next in Atlantic cod, ranging from pre-vitellogenic follicles to gastrulating embryos. The most-up-/downregulated genes are shown for periods between: (A, B) pre- to early-vitellogenic follicles; (C, D) early- to late-vitellogenic follicles; (E, F) late-vitellogenic follicles to ovulated eggs; (G, H) ovulated eggs to blastula embryos; (I, J) blastula to gastrula embryos. 1, pre-vitellogenic follicles; 2, early-vitellogenic follicles; 3, late-vitellogenic follicles; 4, unfertilized eggs; 5, blastula; 6, gastrula. Green and blue colors represent up- and downregulation of genes, respectively. In cases of predicted genes, the Ensembl gene IDs (when possible) or GenBank EST ID's are shown. The predicted genes include: ENSGAUG00000014755, similar to protein tyrosine phosphatase, receptor type, Q isoform 1 precursor; lccot-6j24.fp1_b1.ab1, similar to F57G4.9; ENSGAUG00000013485, hypothetical protein LOC100005938; lccob-6c3.fp0_b1.ab1, similar to predicted protein; lccga-8a16.fp1_b1.ab1, hypothetical protein; and ENSGAUG00000014014, hypothetical protein LOC559540.
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fig04: Heat maps of the expression of the most-regulated (based on fold change) genes from one developmental stage to the next in Atlantic cod, ranging from pre-vitellogenic follicles to gastrulating embryos. The most-up-/downregulated genes are shown for periods between: (A, B) pre- to early-vitellogenic follicles; (C, D) early- to late-vitellogenic follicles; (E, F) late-vitellogenic follicles to ovulated eggs; (G, H) ovulated eggs to blastula embryos; (I, J) blastula to gastrula embryos. 1, pre-vitellogenic follicles; 2, early-vitellogenic follicles; 3, late-vitellogenic follicles; 4, unfertilized eggs; 5, blastula; 6, gastrula. Green and blue colors represent up- and downregulation of genes, respectively. In cases of predicted genes, the Ensembl gene IDs (when possible) or GenBank EST ID's are shown. The predicted genes include: ENSGAUG00000014755, similar to protein tyrosine phosphatase, receptor type, Q isoform 1 precursor; lccot-6j24.fp1_b1.ab1, similar to F57G4.9; ENSGAUG00000013485, hypothetical protein LOC100005938; lccob-6c3.fp0_b1.ab1, similar to predicted protein; lccga-8a16.fp1_b1.ab1, hypothetical protein; and ENSGAUG00000014014, hypothetical protein LOC559540.

Mentions: Differentially expressed genes (DEGs) detected in this study were linked to KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways in order to identify their systems-level function. An overview of the pathways represented by the highest numbers (≥10) of DEGs can be seen in Supplemental material (Additional File 2). “Housekeeping” pathways tend to encompass a large proportion of the DEGs, whereas smaller pathways that might be mainly up- or downregulated will be masked due to their lower contribution of DEGs. As we consider pathways that are clearly activated or silenced, and therefore represented by mostly up- or downregulated genes, respectively, we focused on the ratio between the number of upregulated and downregulated genes within each specific pathway. In addition, we applied a cutoff for this ratio in order to limit the long list of pathways annotated to the DEGs: up/down ≥5 for upregulated pathways, and down/up ≥5 for downregulated pathways. We added “1” to all “numbers of genes” within a pathway to avoid arithmetic errors that would otherwise result from division by pathways with zero genes. Figure 3 shows an overview of the up- and downregulated pathways. As few genes were differentially expressed from ovulated eggs to blastula embryos, this group was not included. The most up- and downregulated (based on fold change (FC)) genes from one stage to the next are shown in Figure 4, and are also presented with associated KEGG pathways in the following sections.


Global transcriptome analysis identifies regulated transcripts and pathways activated during oogenesis and early embryogenesis in Atlantic cod.

Kleppe L, Edvardsen RB, Furmanek T, Taranger GL, Wargelius A - Mol. Reprod. Dev. (2014)

Heat maps of the expression of the most-regulated (based on fold change) genes from one developmental stage to the next in Atlantic cod, ranging from pre-vitellogenic follicles to gastrulating embryos. The most-up-/downregulated genes are shown for periods between: (A, B) pre- to early-vitellogenic follicles; (C, D) early- to late-vitellogenic follicles; (E, F) late-vitellogenic follicles to ovulated eggs; (G, H) ovulated eggs to blastula embryos; (I, J) blastula to gastrula embryos. 1, pre-vitellogenic follicles; 2, early-vitellogenic follicles; 3, late-vitellogenic follicles; 4, unfertilized eggs; 5, blastula; 6, gastrula. Green and blue colors represent up- and downregulation of genes, respectively. In cases of predicted genes, the Ensembl gene IDs (when possible) or GenBank EST ID's are shown. The predicted genes include: ENSGAUG00000014755, similar to protein tyrosine phosphatase, receptor type, Q isoform 1 precursor; lccot-6j24.fp1_b1.ab1, similar to F57G4.9; ENSGAUG00000013485, hypothetical protein LOC100005938; lccob-6c3.fp0_b1.ab1, similar to predicted protein; lccga-8a16.fp1_b1.ab1, hypothetical protein; and ENSGAUG00000014014, hypothetical protein LOC559540.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4265210&req=5

fig04: Heat maps of the expression of the most-regulated (based on fold change) genes from one developmental stage to the next in Atlantic cod, ranging from pre-vitellogenic follicles to gastrulating embryos. The most-up-/downregulated genes are shown for periods between: (A, B) pre- to early-vitellogenic follicles; (C, D) early- to late-vitellogenic follicles; (E, F) late-vitellogenic follicles to ovulated eggs; (G, H) ovulated eggs to blastula embryos; (I, J) blastula to gastrula embryos. 1, pre-vitellogenic follicles; 2, early-vitellogenic follicles; 3, late-vitellogenic follicles; 4, unfertilized eggs; 5, blastula; 6, gastrula. Green and blue colors represent up- and downregulation of genes, respectively. In cases of predicted genes, the Ensembl gene IDs (when possible) or GenBank EST ID's are shown. The predicted genes include: ENSGAUG00000014755, similar to protein tyrosine phosphatase, receptor type, Q isoform 1 precursor; lccot-6j24.fp1_b1.ab1, similar to F57G4.9; ENSGAUG00000013485, hypothetical protein LOC100005938; lccob-6c3.fp0_b1.ab1, similar to predicted protein; lccga-8a16.fp1_b1.ab1, hypothetical protein; and ENSGAUG00000014014, hypothetical protein LOC559540.
Mentions: Differentially expressed genes (DEGs) detected in this study were linked to KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways in order to identify their systems-level function. An overview of the pathways represented by the highest numbers (≥10) of DEGs can be seen in Supplemental material (Additional File 2). “Housekeeping” pathways tend to encompass a large proportion of the DEGs, whereas smaller pathways that might be mainly up- or downregulated will be masked due to their lower contribution of DEGs. As we consider pathways that are clearly activated or silenced, and therefore represented by mostly up- or downregulated genes, respectively, we focused on the ratio between the number of upregulated and downregulated genes within each specific pathway. In addition, we applied a cutoff for this ratio in order to limit the long list of pathways annotated to the DEGs: up/down ≥5 for upregulated pathways, and down/up ≥5 for downregulated pathways. We added “1” to all “numbers of genes” within a pathway to avoid arithmetic errors that would otherwise result from division by pathways with zero genes. Figure 3 shows an overview of the up- and downregulated pathways. As few genes were differentially expressed from ovulated eggs to blastula embryos, this group was not included. The most up- and downregulated (based on fold change (FC)) genes from one stage to the next are shown in Figure 4, and are also presented with associated KEGG pathways in the following sections.

Bottom Line: During early vitellogenesis, several of the most upregulated genes are linked to nervous system signaling, suggesting increasing requirements for ovarian synaptic signaling to stimulate the rapid growth of oocytes.Highly upregulated genes during late vitellogenesis are linked to protein processing, fat metabolism, osmoregulation, and arrested meiosis.One of the genes with the highest upregulation in the ovulated egg is involved in oxidative phosphorylation, reflecting increased energy requirements during fertilization and the first rapid cell divisions of early embryogenesis.

View Article: PubMed Central - PubMed

Affiliation: Institute of Marine Research, Bergen, Norway.

Show MeSH
Related in: MedlinePlus