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Series GSE39232 Query DataSets for GSE39232
Status Public on Jun 03, 2013
Title The maize methylome modulates mRNA splicing and reveals widespread paramutation guided by small RNA.
Organism Zea mays
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Methylation of chromosomal DNA in animals and plants is a fundamental mechanism of epigenetic regulation, and the maize genome, with its diverse complement of transposons and repeats, is a paradigm for transgenerational mechanisms such as paramutation and imprinting. We have determined the genome-wide cytosine methylation map of two maize inbred lines, B73 and Mo17, at high coverage and at single nucleotide resolution. Transposon methylation is highest in CG (65%) and CHG (50%) contexts (where H = A, C or T), while methylation in CHH (5%) contexts is guided by 24nt small interfering RNA (siRNA), and not by 21-22nt siRNA. We have found that CG (8%) methylation seems to deter insertion of Mutator transposons into exons, while CHH and CHG methylation at splice donor and acceptor sites strongly inhibits RNA splicing. Methylation differences between parents are inherited in recombinant inbred lines, but methylation switches, guided by siRNA, are widespread and persist for up to 8 generations. These differences influence splicing, and recurrent switching suggest that paramutation is much more common than previously supposed, and may contribute to heterosis. Our results provide a comprehensive high resolution resource for maize genome methylation, as well as a map of recurrent transgenerational epigenetic shifts (paramutation) in the two most commonly used inbred maize lines.
Overall design Genome-wide cytosine methylation map in 2 maize strains by bisulfite sequencing, and RNA and small RNA profiles in the same tissue using Illumina platform.
Contributor(s) Regulski M, Lu Z, Kendall J, Reinders J, Llaca V, Deschamps S, Smith A, Levy D, McCombie WR, Tingey S, Rafalski A, Hicks J, Ware D, Martienssen R
Citation(s) 23739895
Submission date Jul 10, 2012
Last update date May 15, 2019
Contact name Zhenyuan Lu
Organization name Cold Spring Harbor Laboratory
Lab Doreen Ware
Street address 1 Bungtown Rd
City Cold Spring Harbor
ZIP/Postal code 11724
Country USA
Platforms (1)
GPL9141 Illumina Genome Analyzer (Zea mays)
Samples (35)
GSM958906 B73_RNA_rep1
GSM958907 Mo17_RNA_rep1
GSM958908 B73_RNA_rep2
BioProject PRJNA170520
SRA SRP014211

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Supplementary file Size Download File type/resource
GSE39232_B73_sequence.rmdup.bed.gz 4.0 Gb (ftp)(http) BED
GSE39232_MO17_sequence.rmdup.bed.gz 3.6 Gb (ftp)(http) BED
GSE39232_RAW.tar 31.2 Gb (http)(custom) TAR (of BED, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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