Limits...
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.


Ratio of reads aligned to parental genomes of all SNPs.Points in this figure reflect the ratio of reads aligned to the maternal versus the paternal genomes under the loose standard (SNP sequencing depth greater than 2×). The horizontal axis is log2 (m:f) in cross I, while the vertical axis is log2 (m:f) in cross II. Red points indicate the candidate maternal imprinted SNPs, while the blue points indicate candidate paternal imprinted SNPs.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4498732&req=5

pone.0132345.g002: Ratio of reads aligned to parental genomes of all SNPs.Points in this figure reflect the ratio of reads aligned to the maternal versus the paternal genomes under the loose standard (SNP sequencing depth greater than 2×). The horizontal axis is log2 (m:f) in cross I, while the vertical axis is log2 (m:f) in cross II. Red points indicate the candidate maternal imprinted SNPs, while the blue points indicate candidate paternal imprinted SNPs.

Mentions: Of these SNPs, we found several that potentially exhibited parent-of-origin effects. The proportion of reads aligned to the maternal genome was 0.5 at most SNP loci (chi-square test, p < 0.05. Fig C in S1 File). Under the general standard, we were only able to isolate one SNP in males, located on the autosomes. This SNP was also included under the looser standard, where we were able to select 1,478 SNPs in females (two from autosomes, 1,470 from the Z chromosome, and six unmapped to any chromosome) and 12 SNPs in males (eight from autosomes, one from the Z chromosome, and three unmapped to any chromosome) (Fig 2). Since the female is the heterogametic sex in birds, female Z chromosomes must come from the father, explaining why the 1,470 SNPs on the female Z chromosome exhibited paternal allelic expression. When we merged offspring female and male data, we found that 11 SNPs conformed to the loose standards (eight SNPs from autosomes and three SNPs unmapped to any chromosome).


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)

Ratio of reads aligned to parental genomes of all SNPs.Points in this figure reflect the ratio of reads aligned to the maternal versus the paternal genomes under the loose standard (SNP sequencing depth greater than 2×). The horizontal axis is log2 (m:f) in cross I, while the vertical axis is log2 (m:f) in cross II. Red points indicate the candidate maternal imprinted SNPs, while the blue points indicate candidate paternal imprinted SNPs.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0132345.g002: Ratio of reads aligned to parental genomes of all SNPs.Points in this figure reflect the ratio of reads aligned to the maternal versus the paternal genomes under the loose standard (SNP sequencing depth greater than 2×). The horizontal axis is log2 (m:f) in cross I, while the vertical axis is log2 (m:f) in cross II. Red points indicate the candidate maternal imprinted SNPs, while the blue points indicate candidate paternal imprinted SNPs.
Mentions: Of these SNPs, we found several that potentially exhibited parent-of-origin effects. The proportion of reads aligned to the maternal genome was 0.5 at most SNP loci (chi-square test, p < 0.05. Fig C in S1 File). Under the general standard, we were only able to isolate one SNP in males, located on the autosomes. This SNP was also included under the looser standard, where we were able to select 1,478 SNPs in females (two from autosomes, 1,470 from the Z chromosome, and six unmapped to any chromosome) and 12 SNPs in males (eight from autosomes, one from the Z chromosome, and three unmapped to any chromosome) (Fig 2). Since the female is the heterogametic sex in birds, female Z chromosomes must come from the father, explaining why the 1,470 SNPs on the female Z chromosome exhibited paternal allelic expression. When we merged offspring female and male data, we found that 11 SNPs conformed to the loose standards (eight SNPs from autosomes and three SNPs unmapped to any chromosome).

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.