Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0

The maize methylome modulates mRNA splicing and reveals widespread paramutation guided by small RNA.


ABSTRACT: 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. 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.

ORGANISM(S): Zea mays

SUBMITTER: Zhenyuan Lu 

PROVIDER: E-GEOD-39232 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

altmetric image

Publications


The maize genome, with its large complement of transposons and repeats, is a paradigm for the study of epigenetic mechanisms such as paramutation and imprinting. Here, we present the genome-wide map of cytosine methylation for two maize inbred lines, B73 and Mo17. CG (65%) and CHG (50%) methylation (where H = A, C, or T) is highest in transposons, while CHH (5%) methylation is likely guided by 24-nt, but not 21-nt, small interfering RNAs (siRNAs). Correlations with methylation patterns suggest t  ...[more]

Similar Datasets

2014-10-20 | E-MTAB-3028 | biostudies-arrayexpress
2012-04-16 | E-GEOD-37204 | biostudies-arrayexpress
2014-03-18 | E-GEOD-52346 | biostudies-arrayexpress
2013-01-28 | E-GEOD-16868 | biostudies-arrayexpress
2021-04-22 | GSE172479 | GEO
2009-11-20 | E-GEOD-16789 | biostudies-arrayexpress
2013-06-03 | GSE39232 | GEO
2012-05-26 | E-GEOD-37411 | biostudies-arrayexpress
2023-09-11 | PXD045274 | Pride
2017-08-18 | GSE97206 | GEO