+ Site Statistics
References:
54,258,434
Abstracts:
29,560,870
PMIDs:
28,072,757
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species



Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species



Proceedings of the National Academy of Sciences of the United States of America 110(48): 19639-19644



In plants, a subset of genes exhibit imprinting in endosperm tissue such that expression is primarily from the maternal or paternal allele. Imprinting may arise as a consequence of mechanisms for silencing of transposons during reproduction, and in some cases imprinted expression of particular genes may provide a selective advantage such that it is conserved across species. Separate mechanisms for the origin of imprinted expression patterns and maintenance of these patterns may result in substantial variation in the targets of imprinting in different species. Here we present deep sequencing of RNAs isolated from reciprocal crosses of four diverse maize genotypes, providing a comprehensive analysis that allows evaluation of imprinting at more than 95% of endosperm-expressed genes. We find that over 500 genes exhibit statistically significant parent-of-origin effects in maize endosperm tissue, but focused our analyses on a subset of these genes that had >90% expression from the maternal allele (69 genes) or from the paternal allele (108 genes) in at least one reciprocal cross. Over 10% of imprinted genes show evidence of allelic variation for imprinting. A comparison of imprinting in maize and rice reveals that 13% of genes with syntenic orthologs in both species exhibit conserved imprinting. Genes that exhibit conserved imprinting between maize and rice have elevated nonsynonymous to synonymous substitution ratios compared with other imprinted genes, suggesting a history of more rapid evolution. Together, these data suggest that imprinting only has functional relevance at a subset of loci that currently exhibit imprinting in maize.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 052269805

Download citation: RISBibTeXText

PMID: 24218619

DOI: 10.1073/pnas.1309182110


Related references

Characterization of Imprinted Genes in Rice Reveals Conservation of Regulation and Imprinting with Other Plant Species. Plant Physiology 177(4): 1754-1771, 2018

Genome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm. Plant journal 36(1): 30-44, 2003

Trait to gene analysis reveals that allelic variation in three genes determines seed vigour. New Phytologist 212(4): 964-976, 2016

A genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm. Plos Genetics 7(6): E1002125-E1002125, 2011

Imprinting the genome: imprinted genes, imprinting genes, and a hypothesis for their interaction. Annual Review of Genetics 27: 7-31, 1993

Study of DNA methylation patterns of imprinted genes in children born after assisted reproductive technologies reveals no imprinting errors: A pilot study. Experimental and Therapeutic Medicine 2(4): 751-755, 2011

The regulatory complex of HLA class I promoters exhibits locus-specific conservation with limited allelic variation. Journal of Immunology 152(8): 3873-3883, 1994

Comparative sequence analysis of imprinted genes between human and mouse to reveal imprinting signatures. Genomics 83(3): 395-401, 2004

Allelic variation in candidate genes associated with QTL for the maize anther culture response. Maydica 45(4): 267-276, 2000

Phylogenetic analysis reveals conservation and diversification of micro RNA166 genes among diverse plant species. Genomics 103(1): 114-121, 2014

Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria. Bmc Genomics 14: 112-112, 2013

Comprehensive meta-analysis reveals association between multiple imprinting disorders and conception by assisted reproductive technology. Journal of Assisted Reproduction and Genetics: -, 2018

Allelic variation in the effector genes of the tomato pathogen Cladosporium fulvum reveals different modes of adaptive evolution. Molecular Plant-Microbe Interactions 20(10): 1271-1283, 2007

Genome-wide allelic methylation analysis reveals disease-specific susceptibility to multiple methylation defects in imprinting syndromes. Human Mutation 34(4): 595-602, 2013

Genome-wide DNA methylation analysis of patients with imprinting disorders identifies differentially methylated regions associated with novel candidate imprinted genes. Journal of Medical Genetics 51(4): 229-238, 2014