Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Epigenetic modifications and their relationships to smRNA and mRNA transcriptomes in maize

ABSTRACT: Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and smRNA transcriptomes in maize We report an integrated genome-wide analysis of DNA methylation, histone modifications, smRNAs and mRNA transcriptional activity, using maize as a model. We surveyed the epigenomes of the maize inbred line B73 in shoot and root tissue by Illumina/Solexa 1G parallel sequencing after digesting genomic DNA with a methylation-sensitive restriction enzyme and after conducting chromatin immunoprecipitations (ChIP) using antibodies that target specific histone modifications (H3K4me3, H3K9ac, H3K27me3, H3K36me3, respectively). Additionally, we profiled RNA pools (micro RNA (miRNA), siRNA and mRNA) using the same sequencing strategy. Keywords: Epigenetics, mRNA transcription and small RNAs H3K4me3, H3K9ac, H3K27me3, H3K36me3, DNA methylation and mRNA, small RNA profiled from shoots and roots of 14 day-old maize B73 seedlings

ORGANISM(S): Zea mays

SUBMITTER: Xiangfeng Wang

PROVIDER: E-GEOD-15286 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize.

Wang Xiangfeng X Elling Axel A AA Li Xueyong X Li Ning N Peng Zhiyu Z He Guangming G Sun Hui H Qi Yijun Y Liu X Shirley XS Deng Xing Wang XW

The Plant cell 20090417 4

Maize (Zea mays) has an exceptionally complex genome with a rich history in both epigenetics and evolution. We report genomic landscapes of representative epigenetic modifications and their relationships to mRNA and small RNA (smRNA) transcriptomes in maize shoots and roots. The epigenetic patterns differed dramatically between genes and transposable elements, and two repressive marks (H3K27me3 and DNA methylation) were usually mutually exclusive. We found an organ-specific distribution of canon ...[more]

PMID: 19376930

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Project description:We tested four gene enrichment and complexity reduction target preparation methods for scoring SFPs on the Affymetrix GeneChip 18k Maize Genome Array (âMaize GeneChipâ). Methylation filtration (MF), Cot filtration (CF), mRNA-derived cRNA, and amplified fragment length polymorphism (AFLP) methods were applied to three diverse maize inbred lines (B73, Mo17, and CML69) with three replications per line (36 Maize GeneChips). Due to large amounts of repetitive, mobile DNA, the maize genome requires a target preparation method that offers both a high level of gene enrichment and accurate scoring of SFPs. The objectives of this research are (i) to determine which target preparation method (CF, MF, mRNA, or AFLP) optimally enriches for gene sequences complementary to probe sequences on the Affymetrix GeneChip Maize Genome Array and (ii) to estimate SFP detection power for each target method. The AFLP technology is covered by patents, and patent applications owned by Keygene N.V. AFLP is a registered trademark of Keygene N.V. GeneChip. This work was supported in part by U.S. National Science Foundation grant DBI-0321467 and USDA-ARS. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Michael Gore. The equivalent experiment is ZM10 at PLEXdb.] Experiment Overall Design: protocol: mRNA - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: mRNA - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: mRNA - genotype: CML69 maize inbred(3-replications) Experiment Overall Design: protocol: Cot filtration (CF) - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: Cot filtration (CF) - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: Cot filtration (CF) - genotype: CML69 maize inbred(3-replications) Experiment Overall Design: protocol: Methylation filtration (MF) - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: Methylation filtration (MF) - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: Methylation filtration (MF) - genotype: CML69 maize inbred(3-replications) Experiment Overall Design: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: B73 maize inbred(3-replications) Experiment Overall Design: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: Mo17 maize inbred(3-replications) Experiment Overall Design: protocol: Amplified fragment restriction polymorphism (AFLP) - genotype: CML69 maize inbred(3-replications)

Project description:Although landscapes of several epigenetic marks are now available for Arabidopsis and rice, such profiles remain static and do not provide information about dynamic changes of plant epigenomes in response to developmental or environmental cues. Here we analyzed the effects of light regulation on four epigenetic histone modifications (H3K9ac, H3K9me3, H3K27ac, H3K27me3). Our genome-wide profiling of H3K9ac and H3K27ac revealed that these modifications are gene-specific. In contrast, we found that H3K9me3 and H3K27me3 target genes, but also intergenic-regions and transposable elements. Specific light conditions affected the number of epigenetically modified regions, as well as the overall correlation strength between the presence of specific epigenetic modifications and transcription. Futhermore, we observed that acetylation is an important contributor to light-regulated genome expression not only through its activating action on HY5 and HYH but also on their downstream targets. We found that dynamic acetylation changes in response to light have a major role in the active regulation of photosynthetic gene expression, while H3K27ac and H3K27me3 are major contributors to light regulation of the gibberellin metabolism. We also identified distinct epigenetic patterns in the epigenome of the photomorphogenic mutant cop1-4, suggesting that COP1 might have a role in the establishment of specific epigenetic modifications. Thus, this work provides a dynamic portrait of the variations in histone modifications in response to the plantM-bM-^@M-^Ys changing light environment and strengthens the concept that epigenetic modifications represent another layer of control for light-regulated genes involved in photomorphogenesis. Arabidopsis ecotype Columbia (Col-0) was the genetic background used for this study. Seeds were stratified for two days at 4M-BM-0C, then germinated and grown for five days at 22M-BM-0C in continuous darkness (D). Six hours before harvest, a number of plates were transferred to continuous white light (D to L). The cop1-4 mutant was also used in this study. Seedlings from the different conditions and genotypes were harvested at the same time of day. Chromatin was immunoprecipitated, washed, reverse crosslinked, amplified and hybridized according to AffymetrixM-bM-^@M-^Y Chromatin Immunoprecipitation Assay Protocol Rev.3. Three M-NM-<l of the following antibodies were used: anti-H3K9ac (Upstate 06-942), anti-H3K9me3 (Upstate 07-442), anti-H3K27ac (Upstate 07-360), anti-H3K27me3 (Upstate 07-449), and anti-H3 (Upstate 07-690). Four biological replicates were hybridized to tiling arrays.

Dataset Information

Epigenetic modifications and their relationships to smRNA and mRNA transcriptomes in maize

Publications

Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize.

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