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Paternally biased X inactivation in mouse neonatal brain.

Wang X, Soloway PD, Clark AG - Genome Biol. (2010)

Bottom Line: X inactivation in female eutherian mammals has long been considered to occur at random in embryonic and postnatal tissues.After RNA-seq data revealed what appeared to be a chromosome-wide bias toward under-expression of paternal alleles in mouse tissue, we applied pyrosequencing to mouse brain cDNA samples from reciprocal cross F1 progeny of divergent strains and found a small but consistent and highly statistically significant excess tendency to under-express the paternal X chromosome.In addition, we propose an efficient method to identify and confirm genes that escape X inactivation in normal mice by directly comparing the allele-specific expression ratio profile of multiple X-linked genes in multiple individuals.

View Article: PubMed Central - HTML - PubMed

Affiliation: Deptartment of Molecular Biology and Genetics, Cornell University, 227 Biotechnology Building, Ithaca, NY 14853, USA.

ABSTRACT

Background: X inactivation in female eutherian mammals has long been considered to occur at random in embryonic and postnatal tissues. Methods for scoring allele-specific differential expression with a high degree of accuracy have recently motivated a quantitative reassessment of the randomness of X inactivation.

Results: After RNA-seq data revealed what appeared to be a chromosome-wide bias toward under-expression of paternal alleles in mouse tissue, we applied pyrosequencing to mouse brain cDNA samples from reciprocal cross F1 progeny of divergent strains and found a small but consistent and highly statistically significant excess tendency to under-express the paternal X chromosome.

Conclusions: The bias toward paternal X inactivation is reminiscent of marsupials (and extraembryonic tissues in eutherians), suggesting that there may be retained an evolutionarily conserved epigenetic mark driving the bias. Allelic bias in expression is also influenced by the sampling effect of X inactivation and by cis-acting regulatory variation (eQTL), and for each gene we quantify the contributions of these effects in two different mouse strain combinations while controlling for variability in Xce alleles. In addition, we propose an efficient method to identify and confirm genes that escape X inactivation in normal mice by directly comparing the allele-specific expression ratio profile of multiple X-linked genes in multiple individuals.

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Chromosomal scans of imprinting status. (a) Imprinting status for chromosome 11. (b) Imprinting status for chromosome X. Each plot contains unique Entrez genes covered by SNP-containing Illumina reads with counts no less than 4 in each reciprocal cross. The height of each bar is the difference of the AKR percentage in the two reciprocal crosses (p1-p2), representing the intensity of imprinting. The color indicates the direction of expression bias: blue for paternal over-expression and red for maternal over-expression. The intensity of the color represents the significance: grey for not significant (q-value ≥ 0.10), lighter blue and pink for marginally significant (0.05 ≤ q-value < 0.10), darker blue and red for significant (q-value < 0.05). The gene name is indicated for the instances where/ p1-p2/ ≥ 0.3. Data are from [29].
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Figure 1: Chromosomal scans of imprinting status. (a) Imprinting status for chromosome 11. (b) Imprinting status for chromosome X. Each plot contains unique Entrez genes covered by SNP-containing Illumina reads with counts no less than 4 in each reciprocal cross. The height of each bar is the difference of the AKR percentage in the two reciprocal crosses (p1-p2), representing the intensity of imprinting. The color indicates the direction of expression bias: blue for paternal over-expression and red for maternal over-expression. The intensity of the color represents the significance: grey for not significant (q-value ≥ 0.10), lighter blue and pink for marginally significant (0.05 ≤ q-value < 0.10), darker blue and red for significant (q-value < 0.05). The gene name is indicated for the instances where/ p1-p2/ ≥ 0.3. Data are from [29].

Mentions: In our previous effort to identify novel imprinted genes in mouse [29], we performed an 'RNA-seq' study in which more than 69 million sequence reads were sampled from the transcriptomes of reciprocal F1 female P2 neonatal brains (AKR/J and PWD/PhJ strains) by Illumina short-read sequencing. Relative expression ratios of the two parental alleles were obtained by directly counting the allele-specific sequence reads at the SNP positions within the transcripts [29]; 5,076 unique Entrez genes had a coverage of four or more sequence reads overlapping each SNP position in both reciprocal crosses across the mouse genome. The imprinting status was quantified as the difference between the AKR percentages in the F1 progeny derived from the two reciprocal crosses. For most genes this difference in expression was close to zero, indicating a lack of significant imprinting [29]. The known imprinted genes and novel imprinted gene candidates had an obvious and highly statistically significant bias in allelic expression. When we compared the pattern of skewed allelic expression of autosomes with the X chromosome, we noted that for every autosome, there was approximately the same number of preferentially paternally and maternally expressed genes. However, X chromosomal genes showed consistently elevated maternal expression, and there was not a single significant paternally over-expressed gene (Figure 1a,b). Because we saw exclusively maternal over-expression in progeny of both reciprocal crosses of PWD and AKR strains, the results cannot be explained by differences in alleles at Xce, a locus that influences in an allele-specific manner the probability of X inactivation [30].


Paternally biased X inactivation in mouse neonatal brain.

Wang X, Soloway PD, Clark AG - Genome Biol. (2010)

Chromosomal scans of imprinting status. (a) Imprinting status for chromosome 11. (b) Imprinting status for chromosome X. Each plot contains unique Entrez genes covered by SNP-containing Illumina reads with counts no less than 4 in each reciprocal cross. The height of each bar is the difference of the AKR percentage in the two reciprocal crosses (p1-p2), representing the intensity of imprinting. The color indicates the direction of expression bias: blue for paternal over-expression and red for maternal over-expression. The intensity of the color represents the significance: grey for not significant (q-value ≥ 0.10), lighter blue and pink for marginally significant (0.05 ≤ q-value < 0.10), darker blue and red for significant (q-value < 0.05). The gene name is indicated for the instances where/ p1-p2/ ≥ 0.3. Data are from [29].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2926790&req=5

Figure 1: Chromosomal scans of imprinting status. (a) Imprinting status for chromosome 11. (b) Imprinting status for chromosome X. Each plot contains unique Entrez genes covered by SNP-containing Illumina reads with counts no less than 4 in each reciprocal cross. The height of each bar is the difference of the AKR percentage in the two reciprocal crosses (p1-p2), representing the intensity of imprinting. The color indicates the direction of expression bias: blue for paternal over-expression and red for maternal over-expression. The intensity of the color represents the significance: grey for not significant (q-value ≥ 0.10), lighter blue and pink for marginally significant (0.05 ≤ q-value < 0.10), darker blue and red for significant (q-value < 0.05). The gene name is indicated for the instances where/ p1-p2/ ≥ 0.3. Data are from [29].
Mentions: In our previous effort to identify novel imprinted genes in mouse [29], we performed an 'RNA-seq' study in which more than 69 million sequence reads were sampled from the transcriptomes of reciprocal F1 female P2 neonatal brains (AKR/J and PWD/PhJ strains) by Illumina short-read sequencing. Relative expression ratios of the two parental alleles were obtained by directly counting the allele-specific sequence reads at the SNP positions within the transcripts [29]; 5,076 unique Entrez genes had a coverage of four or more sequence reads overlapping each SNP position in both reciprocal crosses across the mouse genome. The imprinting status was quantified as the difference between the AKR percentages in the F1 progeny derived from the two reciprocal crosses. For most genes this difference in expression was close to zero, indicating a lack of significant imprinting [29]. The known imprinted genes and novel imprinted gene candidates had an obvious and highly statistically significant bias in allelic expression. When we compared the pattern of skewed allelic expression of autosomes with the X chromosome, we noted that for every autosome, there was approximately the same number of preferentially paternally and maternally expressed genes. However, X chromosomal genes showed consistently elevated maternal expression, and there was not a single significant paternally over-expressed gene (Figure 1a,b). Because we saw exclusively maternal over-expression in progeny of both reciprocal crosses of PWD and AKR strains, the results cannot be explained by differences in alleles at Xce, a locus that influences in an allele-specific manner the probability of X inactivation [30].

Bottom Line: X inactivation in female eutherian mammals has long been considered to occur at random in embryonic and postnatal tissues.After RNA-seq data revealed what appeared to be a chromosome-wide bias toward under-expression of paternal alleles in mouse tissue, we applied pyrosequencing to mouse brain cDNA samples from reciprocal cross F1 progeny of divergent strains and found a small but consistent and highly statistically significant excess tendency to under-express the paternal X chromosome.In addition, we propose an efficient method to identify and confirm genes that escape X inactivation in normal mice by directly comparing the allele-specific expression ratio profile of multiple X-linked genes in multiple individuals.

View Article: PubMed Central - HTML - PubMed

Affiliation: Deptartment of Molecular Biology and Genetics, Cornell University, 227 Biotechnology Building, Ithaca, NY 14853, USA.

ABSTRACT

Background: X inactivation in female eutherian mammals has long been considered to occur at random in embryonic and postnatal tissues. Methods for scoring allele-specific differential expression with a high degree of accuracy have recently motivated a quantitative reassessment of the randomness of X inactivation.

Results: After RNA-seq data revealed what appeared to be a chromosome-wide bias toward under-expression of paternal alleles in mouse tissue, we applied pyrosequencing to mouse brain cDNA samples from reciprocal cross F1 progeny of divergent strains and found a small but consistent and highly statistically significant excess tendency to under-express the paternal X chromosome.

Conclusions: The bias toward paternal X inactivation is reminiscent of marsupials (and extraembryonic tissues in eutherians), suggesting that there may be retained an evolutionarily conserved epigenetic mark driving the bias. Allelic bias in expression is also influenced by the sampling effect of X inactivation and by cis-acting regulatory variation (eQTL), and for each gene we quantify the contributions of these effects in two different mouse strain combinations while controlling for variability in Xce alleles. In addition, we propose an efficient method to identify and confirm genes that escape X inactivation in normal mice by directly comparing the allele-specific expression ratio profile of multiple X-linked genes in multiple individuals.

Show MeSH
Related in: MedlinePlus