Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Variation in DNA methylation patterns more common among maize inbreds than among tissues

ABSTRACT: Transposable elements (TEs) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence the chromatin state of neighboring low-copy sequences. This would allow TEs to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I TEs (retrotransposons) that are present in moderate to high copy numbers, and many are found in regions near genes, which provides an opportunity to test whether the spreading of heterochromatin from retrotransposons is prevalent. We have investigated the extent of heterochromatin spreading into DNA flanking each family of retrotransposons by profiling DNA methylation and di-methylation of lysine 9 of histone 3 (H3K9me2) in low-copy regions of the maize genome. RNA–seq was performed on three biological replicates of four tissues: 3rd leaf, immature ear (SRP013432), embryo and endosperm(SRP009313) for both B73 and Mo17.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Zea mays

SUBMITTER: Nathan Springer

PROVIDER: E-MTAB-4318 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Spreading of heterochromatin is limited to specific families of maize retrotransposons.

Eichten Steven R SR Ellis Nathanael A NA Makarevitch Irina I Yeh Cheng-Ting CT Gent Jonathan I JI Guo Lin L McGinnis Karen M KM Zhang Xiaoyu X Schnable Patrick S PS Vaughn Matthew W MW Dawe R Kelly RK Springer Nathan M NM

PLoS genetics 20121213 12

Transposable elements (TEs) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence the chromatin state of neighboring low-copy sequences. This would allow TEs to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I TEs (re ...[more]

PMID: 23271981

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Project description:This study focuses on epigenetic reprogramming in the mouse germ line: DNA methylation marks, including those of imprinted genes, are thought to be erased between E11.5 and E13.5 in primordial germ cells (PGCs), which are the direct progenitors of sperm or oocyte. DNA methylation patterns are then re-established during the de novo methylation phase in the male germ line several days later (around E15.5) and in the female germ line after birth during adult life. Epigenetic reprogramming in PGCs is poorly understood mainly because of the technical challenges that arise from very low cell numbers in the embryo. The aim of this study is to create genome-wide maps of DNA methylation patterns of male and female PGCs at crucial time points during epigenetic reprogramming and to investigate the changes in those profiles on a single-gene level. We have already successfully prepared and sequenced the first set of BS-Seq libraries of PGCs with Illumina's GAIIx platform. From this, we gained significant insight into the global DNA methylation levels and methylation patterns over multy-copy-loci such as repeat elements. In order further enhance our analysis and finish this project for publication, it is crucial to increase the genomic coverage of our datasets. This will also allow us to link the BS-Seq data with other MeDIP-Seq and RNA-Seq datasets that have already been created in this study.Protocol: Input DNA was sonicated using a Bioruptor UCD-200 (Diagenode) to a final size distribution of 300bp 1000bp. End-repair and A-tailing were performed with the NEBNext DNA Sample Prep Master Mix Set 1. Illuminas Early Access Methylation Adaptor Oligo Kit was used for the adapter ligation. The adapter-ligated DNA was treated with sodium-bisulfite using the Imprint DNA Modification Kit from Sigma-Aldrich according to the manufacturers instructions for the two-step protocol. After the clean up, the bisulfite-treated DNA was amplified using PfuTurbo Cx Hotstart DNA Polymerase from Agilent with 18 cycles of amplification. The entire PCR reaction was run on a 1.5% agarose TBE gel and size selection was performed for DNA fragments between 200bp 250bp. DNA from the excised gel piece was purified with the Qiagen Gel Extraction Kit.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

Dataset Information

Variation in DNA methylation patterns more common among maize inbreds than among tissues

Publications

Spreading of heterochromatin is limited to specific families of maize retrotransposons.

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