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| Status |
Public on Dec 16, 2011 |
| Title |
Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm |
| Organism |
Zea mays |
| Experiment type |
Methylation profiling by genome tiling array
|
| Summary |
Imprinting describes the differential expression of alleles based upon their parent of origin. Deep sequencing of RNAs from maize endosperm and embryo tissue 14 days after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm including 54 maternally expressed genes (MEGs) and 46 paternally expressed genes (PEGs). Three of these genes have been previously identified as imprinted while the remaining 97 genes represent novel imprinted maize genes. A genome-wide analysis of DNA methylation identified regions with reduced endosperm DNA methylation in, or near, 19 of the 100 imprinted genes. The reduced levels of DNA methylation in endosperm are caused by hypomethylation of the maternal allele for both MEGs and PEGs in all cases tested. Many of the imprinted genes with reduced DNA methylation levels also show endosperm-specific expression patterns. The imprinted maize genes were compared with imprinted genes identified in genome-wide screens of rice and Arabidopsis and at least 10 examples of conserved imprinting between maize and each of the other species were identified.
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| |
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| Overall design |
Methylation profiles across endosperm tissue in B73 and Mo17 were assayed for three biological replications using a custom 2.1M gene-focused NimbleGen array.
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| |
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| Contributor(s) |
Waters AJ, Swanson-Wagner RA, Eichten SR, Vaughn MW, Springer NM |
| Citation(s) |
22198147 |
| |
| Submission date |
Nov 16, 2011 |
| Last update date |
Jul 29, 2013 |
| Contact name |
Steve R Eichten |
| E-mail(s) |
eicht021@umn.edu
|
| Organization name |
University of Minnesota
|
| Department |
Plant Biology
|
| Lab |
Springer Lab
|
| Street address |
1445 Gortner Ave
|
| City |
St. Paul |
| State/province |
MN |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13499 |
NimbleGen 2.1M Maize Methylation Array |
|
| Samples (6)
|
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| Relations |
| BioProject |
PRJNA148441 |
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