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Next-Generation Sequencing Techniques Reveal that Genomic Imprinting Is Absent in Day-Old Gallus gallus domesticus Brains.

Wang Q, Li K, Zhang D, Li J, Xu G, Zheng J, Yang N, Qu L - PLoS ONE (2015)

Bottom Line: Attempts to find evidence of genomic imprinting from long non-coding RNAs yielded negative results.We therefore conclude that genomic imprinting is absent in the brains of 1-day-old chickens.However, due to the temporal and tissue specificity of imprinting, our results cannot be extended to all growth stages and tissue types.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.

ABSTRACT
Genomic imprinting is a phenomenon characterized by parent-of-origin-specific gene expression. While widely documented in viviparous mammals and plants, imprinting in oviparous birds remains controversial. Because genomic imprinting is temporal- and tissue-specific, we investigated this phenomenon only in the brain tissues of 1-day-old chickens (Gallus gallus). We used next-generation sequencing technology to compare four transcriptomes pooled from 11 chickens, generated from reciprocally crossed families, to the DNA sequences of their parents. Candidate imprinted genes were then selected from these sequence alignments and subjected to verification experiments that excluded all but one SNP. Subsequent experiments performed with two new sets of reciprocally crossed families resulted in the exclusion of that candidate SNP as well. Attempts to find evidence of genomic imprinting from long non-coding RNAs yielded negative results. We therefore conclude that genomic imprinting is absent in the brains of 1-day-old chickens. However, due to the temporal and tissue specificity of imprinting, our results cannot be extended to all growth stages and tissue types.

No MeSH data available.


Results of further verification experiments on the SNP most likely to exhibit imprinting.The sequence near the SNP is CTCCCA/GAACGC. (A) This gene appeared to be expressed in a way indicative of genomic imprinting when examined with direct Sanger sequencing. However, the parent-of-origin characteristics were exhibited only in females. The relevant SNP is the third base. Differences between parent and offspring sequences in the first base are due to the introduction of mismatch bases in the offspring for dCAPS assays. (B) Pyrosequencing results are consistent with direct Sanger sequencing results. (C) Cross III and Cross IV, two different reciprocally crossed families, had parents homozygous at that SNP locus. This is in accordance with data from the previous four parents and was confirmed by Sanger sequencing. We detected the brain cDNA of offspring individually, using pyrosequencing. Neither males nor females in crosses III and IV exhibited parent-origin-specific gene expression patterns.
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pone.0132345.g004: Results of further verification experiments on the SNP most likely to exhibit imprinting.The sequence near the SNP is CTCCCA/GAACGC. (A) This gene appeared to be expressed in a way indicative of genomic imprinting when examined with direct Sanger sequencing. However, the parent-of-origin characteristics were exhibited only in females. The relevant SNP is the third base. Differences between parent and offspring sequences in the first base are due to the introduction of mismatch bases in the offspring for dCAPS assays. (B) Pyrosequencing results are consistent with direct Sanger sequencing results. (C) Cross III and Cross IV, two different reciprocally crossed families, had parents homozygous at that SNP locus. This is in accordance with data from the previous four parents and was confirmed by Sanger sequencing. We detected the brain cDNA of offspring individually, using pyrosequencing. Neither males nor females in crosses III and IV exhibited parent-origin-specific gene expression patterns.

Mentions: Finally, the results of our pyrosequencing revealed that the expression patterns of most candidate genes were not in accord with the characteristics of genomic imprinting (Fig 3E and Table 2). One gene (No. 6, gene ENSGALG00000000194) did appear to show expression patterns indicative of imprinting, but as it only exhibited parent-of-origin effects in females (Fig 4A and 4B), we believe it is more likely to be a sex-specific imprinted gene.


Next-Generation Sequencing Techniques Reveal that Genomic Imprinting Is Absent in Day-Old Gallus gallus domesticus Brains.

Wang Q, Li K, Zhang D, Li J, Xu G, Zheng J, Yang N, Qu L - PLoS ONE (2015)

Results of further verification experiments on the SNP most likely to exhibit imprinting.The sequence near the SNP is CTCCCA/GAACGC. (A) This gene appeared to be expressed in a way indicative of genomic imprinting when examined with direct Sanger sequencing. However, the parent-of-origin characteristics were exhibited only in females. The relevant SNP is the third base. Differences between parent and offspring sequences in the first base are due to the introduction of mismatch bases in the offspring for dCAPS assays. (B) Pyrosequencing results are consistent with direct Sanger sequencing results. (C) Cross III and Cross IV, two different reciprocally crossed families, had parents homozygous at that SNP locus. This is in accordance with data from the previous four parents and was confirmed by Sanger sequencing. We detected the brain cDNA of offspring individually, using pyrosequencing. Neither males nor females in crosses III and IV exhibited parent-origin-specific gene expression patterns.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4498732&req=5

pone.0132345.g004: Results of further verification experiments on the SNP most likely to exhibit imprinting.The sequence near the SNP is CTCCCA/GAACGC. (A) This gene appeared to be expressed in a way indicative of genomic imprinting when examined with direct Sanger sequencing. However, the parent-of-origin characteristics were exhibited only in females. The relevant SNP is the third base. Differences between parent and offspring sequences in the first base are due to the introduction of mismatch bases in the offspring for dCAPS assays. (B) Pyrosequencing results are consistent with direct Sanger sequencing results. (C) Cross III and Cross IV, two different reciprocally crossed families, had parents homozygous at that SNP locus. This is in accordance with data from the previous four parents and was confirmed by Sanger sequencing. We detected the brain cDNA of offspring individually, using pyrosequencing. Neither males nor females in crosses III and IV exhibited parent-origin-specific gene expression patterns.
Mentions: Finally, the results of our pyrosequencing revealed that the expression patterns of most candidate genes were not in accord with the characteristics of genomic imprinting (Fig 3E and Table 2). One gene (No. 6, gene ENSGALG00000000194) did appear to show expression patterns indicative of imprinting, but as it only exhibited parent-of-origin effects in females (Fig 4A and 4B), we believe it is more likely to be a sex-specific imprinted gene.

Bottom Line: Attempts to find evidence of genomic imprinting from long non-coding RNAs yielded negative results.We therefore conclude that genomic imprinting is absent in the brains of 1-day-old chickens.However, due to the temporal and tissue specificity of imprinting, our results cannot be extended to all growth stages and tissue types.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.

ABSTRACT
Genomic imprinting is a phenomenon characterized by parent-of-origin-specific gene expression. While widely documented in viviparous mammals and plants, imprinting in oviparous birds remains controversial. Because genomic imprinting is temporal- and tissue-specific, we investigated this phenomenon only in the brain tissues of 1-day-old chickens (Gallus gallus). We used next-generation sequencing technology to compare four transcriptomes pooled from 11 chickens, generated from reciprocally crossed families, to the DNA sequences of their parents. Candidate imprinted genes were then selected from these sequence alignments and subjected to verification experiments that excluded all but one SNP. Subsequent experiments performed with two new sets of reciprocally crossed families resulted in the exclusion of that candidate SNP as well. Attempts to find evidence of genomic imprinting from long non-coding RNAs yielded negative results. We therefore conclude that genomic imprinting is absent in the brains of 1-day-old chickens. However, due to the temporal and tissue specificity of imprinting, our results cannot be extended to all growth stages and tissue types.

No MeSH data available.