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DBTMEE: a database of transcriptome in mouse early embryos.

Park SJ, Shirahige K, Ohsugi M, Nakai K - Nucleic Acids Res. (2014)

Bottom Line: Thereby, users can extensively investigate molecular characteristics among totipotent, pluripotent and differentiated cells while taking genetic and epigenetic characteristics into consideration.We have also designed user friendly web interfaces that enable users to access the data quickly and easily.DBTMEE will help to promote our understanding of the enigmatic fertilization dynamics.

View Article: PubMed Central - PubMed

Affiliation: Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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Working example of the analysis of paternal histone bivalent marks with DBTMEE. 658 genes marked by both H3K4me3 and H3K27me3 in sperm and not expressed in parthenogenesis belong to one of 10 zygotic expression patterns. These genes that particularly exhibit 4-cell transient, maternal RNA and minor ZGA patterns are preferentially up-regulated after fertilization. Asterisks represent the level of statistical significance (P-value of Wilcoxon test): *P < 0.01, **P < 0.001, ***P < 0.0001. Ne, genes marked by neither histones; Bi, genes marked by both histones.
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Figure 4: Working example of the analysis of paternal histone bivalent marks with DBTMEE. 658 genes marked by both H3K4me3 and H3K27me3 in sperm and not expressed in parthenogenesis belong to one of 10 zygotic expression patterns. These genes that particularly exhibit 4-cell transient, maternal RNA and minor ZGA patterns are preferentially up-regulated after fertilization. Asterisks represent the level of statistical significance (P-value of Wilcoxon test): *P < 0.01, **P < 0.001, ***P < 0.0001. Ne, genes marked by neither histones; Bi, genes marked by both histones.

Mentions: Although we have not installed any analytical tools, users can further analyze the downloaded file as desired. For example, after gathering genes that were not expressed at both p1C and p4C (≤1.0 in FPKM) but were expressed at least one stage, we could prepare 658 and 901 genes that were marked by both histones and by neither histones, respectively (Supplementary Tables S1 and S2). These genes belong to one of the zygotic expression patterns shown in Figure 3A-4. To investigate the influence of paternal histone bivalent marks on early development, we plotted FPKM distributions along the stages in each of the zygotic expression patterns (Figure 4). Interestingly, after fertilization, the bivalently marked genes categorized into 4-cell transient, maternal RNA and minor ZGA patterns are likely to be actively transcribed. Although experimental validations are required, this result might be helpful to identify genes that are affected by sperm transmission and to determine the roles of epigenetic inheritance from sperm.


DBTMEE: a database of transcriptome in mouse early embryos.

Park SJ, Shirahige K, Ohsugi M, Nakai K - Nucleic Acids Res. (2014)

Working example of the analysis of paternal histone bivalent marks with DBTMEE. 658 genes marked by both H3K4me3 and H3K27me3 in sperm and not expressed in parthenogenesis belong to one of 10 zygotic expression patterns. These genes that particularly exhibit 4-cell transient, maternal RNA and minor ZGA patterns are preferentially up-regulated after fertilization. Asterisks represent the level of statistical significance (P-value of Wilcoxon test): *P < 0.01, **P < 0.001, ***P < 0.0001. Ne, genes marked by neither histones; Bi, genes marked by both histones.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383872&req=5

Figure 4: Working example of the analysis of paternal histone bivalent marks with DBTMEE. 658 genes marked by both H3K4me3 and H3K27me3 in sperm and not expressed in parthenogenesis belong to one of 10 zygotic expression patterns. These genes that particularly exhibit 4-cell transient, maternal RNA and minor ZGA patterns are preferentially up-regulated after fertilization. Asterisks represent the level of statistical significance (P-value of Wilcoxon test): *P < 0.01, **P < 0.001, ***P < 0.0001. Ne, genes marked by neither histones; Bi, genes marked by both histones.
Mentions: Although we have not installed any analytical tools, users can further analyze the downloaded file as desired. For example, after gathering genes that were not expressed at both p1C and p4C (≤1.0 in FPKM) but were expressed at least one stage, we could prepare 658 and 901 genes that were marked by both histones and by neither histones, respectively (Supplementary Tables S1 and S2). These genes belong to one of the zygotic expression patterns shown in Figure 3A-4. To investigate the influence of paternal histone bivalent marks on early development, we plotted FPKM distributions along the stages in each of the zygotic expression patterns (Figure 4). Interestingly, after fertilization, the bivalently marked genes categorized into 4-cell transient, maternal RNA and minor ZGA patterns are likely to be actively transcribed. Although experimental validations are required, this result might be helpful to identify genes that are affected by sperm transmission and to determine the roles of epigenetic inheritance from sperm.

Bottom Line: Thereby, users can extensively investigate molecular characteristics among totipotent, pluripotent and differentiated cells while taking genetic and epigenetic characteristics into consideration.We have also designed user friendly web interfaces that enable users to access the data quickly and easily.DBTMEE will help to promote our understanding of the enigmatic fertilization dynamics.

View Article: PubMed Central - PubMed

Affiliation: Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

Show MeSH
Related in: MedlinePlus