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Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean.

Xu W, Dai M, Li F, Liu A - Nucleic Acids Res. (2014)

Bottom Line: Genomic imprinting often results in parent-of-origin specific differential expression of maternally and paternally inherited alleles.In total, 57 of the imprinted genes were validated via reverse transcriptase-polymerase chain reaction sequencing, and analysis of the genomic DNA methylation distribution between embryo and endosperm tissues showed significant hypomethylation in the endosperm and an enrichment of differentially methylated regions around the identified genes.These results largely extended gene imprinting information existing in plants, providing potential directions for further research in gene imprinting.

View Article: PubMed Central - PubMed

Affiliation: Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China Graduate University of the Chinese Academy of Sciences, Beijing, China.

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Allele-specific expression analysis detected in castor bean seed. (A) Validation of imprinted genes (MEGs: 30128.m008741, 30190.m010937; PEGs: 28629.m000565, 30005.m001245) by RT-PCR sequencing. (B) Confirmation of genes with non-imprinted allele-specific expression pattern (ZB107: 28597.m000122, 28492.m000467, 30114.m000526; ZB306: 29726.m004084).
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Figure 3: Allele-specific expression analysis detected in castor bean seed. (A) Validation of imprinted genes (MEGs: 30128.m008741, 30190.m010937; PEGs: 28629.m000565, 30005.m001245) by RT-PCR sequencing. (B) Confirmation of genes with non-imprinted allele-specific expression pattern (ZB107: 28597.m000122, 28492.m000467, 30114.m000526; ZB306: 29726.m004084).

Mentions: For experimental confirmation, we tested the allelic-specific expression patterns observed among the mRNA-seq analysis for a subset of MEGs with 95% or greater bias, and more than 100 reads abundance (see Supplementary Table S5) and all the PEGs. Using reverse transcriptase-PCR (RT-PCR) sequencing analysis of an independent sample of hybrid 35-DAF endosperm tissue, we found 51 of the 58 tested MEGs were predominantly expressed from maternal alleles in reciprocal crosses, whereas 6 of all 9 PEGs tested were preferentially paternally expressed from the maternal alleles in reciprocal crosses (see Figure 3A and Supplementary Figure S2), consistent with mRNA-seq data. Five genes (30174.m008685, 30170.m014148, 29279.m000134, 29816.m000679, 29827.m002618), however, exhibited a significant accession dependency in 35 DAF hybrid endosperm tissue, in which they were exclusively maternally or paternally expressed in one direction of cross but biallelically expressed in the other reciprocal cross (Supplementary Figure S2).


Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean.

Xu W, Dai M, Li F, Liu A - Nucleic Acids Res. (2014)

Allele-specific expression analysis detected in castor bean seed. (A) Validation of imprinted genes (MEGs: 30128.m008741, 30190.m010937; PEGs: 28629.m000565, 30005.m001245) by RT-PCR sequencing. (B) Confirmation of genes with non-imprinted allele-specific expression pattern (ZB107: 28597.m000122, 28492.m000467, 30114.m000526; ZB306: 29726.m004084).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4066788&req=5

Figure 3: Allele-specific expression analysis detected in castor bean seed. (A) Validation of imprinted genes (MEGs: 30128.m008741, 30190.m010937; PEGs: 28629.m000565, 30005.m001245) by RT-PCR sequencing. (B) Confirmation of genes with non-imprinted allele-specific expression pattern (ZB107: 28597.m000122, 28492.m000467, 30114.m000526; ZB306: 29726.m004084).
Mentions: For experimental confirmation, we tested the allelic-specific expression patterns observed among the mRNA-seq analysis for a subset of MEGs with 95% or greater bias, and more than 100 reads abundance (see Supplementary Table S5) and all the PEGs. Using reverse transcriptase-PCR (RT-PCR) sequencing analysis of an independent sample of hybrid 35-DAF endosperm tissue, we found 51 of the 58 tested MEGs were predominantly expressed from maternal alleles in reciprocal crosses, whereas 6 of all 9 PEGs tested were preferentially paternally expressed from the maternal alleles in reciprocal crosses (see Figure 3A and Supplementary Figure S2), consistent with mRNA-seq data. Five genes (30174.m008685, 30170.m014148, 29279.m000134, 29816.m000679, 29827.m002618), however, exhibited a significant accession dependency in 35 DAF hybrid endosperm tissue, in which they were exclusively maternally or paternally expressed in one direction of cross but biallelically expressed in the other reciprocal cross (Supplementary Figure S2).

Bottom Line: Genomic imprinting often results in parent-of-origin specific differential expression of maternally and paternally inherited alleles.In total, 57 of the imprinted genes were validated via reverse transcriptase-polymerase chain reaction sequencing, and analysis of the genomic DNA methylation distribution between embryo and endosperm tissues showed significant hypomethylation in the endosperm and an enrichment of differentially methylated regions around the identified genes.These results largely extended gene imprinting information existing in plants, providing potential directions for further research in gene imprinting.

View Article: PubMed Central - PubMed

Affiliation: Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China Graduate University of the Chinese Academy of Sciences, Beijing, China.

Show MeSH