Genome-wide profiling of DNA methylation in two Arabidopsis ecotypes and their reciprocal hybrids
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Hang He
PROVIDER: E-GEOD-34658 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, we found that increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs (sRNAs), implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to remodeling of DNA methylation were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes, CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA, and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA ENHANCER1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in hybrid vigor. Examination of DNA methylation by Bisulfite sequencing in 2 Arabidopsis ecotypes and their reciprocal hybrids.
2011-12-22 | E-GEOD-34657 | biostudies-arrayexpress
Project description:Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, we found that increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs (sRNAs), implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to remodeling of DNA methylation were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes, CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA, and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA ENHANCER1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in hybrid vigor. Examination of mRNA sequencing in 2 Arabidopsis ecotypes and their reciprocal hybrids.
2011-12-22 | E-GEOD-34655 | biostudies-arrayexpress
Project description:Routine methods for assaying steady-state mRNA levels such as RNA-seq and micro-arrays are commonly used as readouts to study the role of transcription factors (TFs) in gene expression regulation. However, cellular RNA levels do not solely depend on activity of TFs and subsequent transcription by RNA polymerase II (Pol II), but are also affected by RNA turnover rate. Here, we demonstrate that integrated analysis of genome-wide TF occupancy, Pol II binding and steady-state RNA levels provide important insights in gene regulatory mechanisms. Pol II occupancy, as detected by Pol II ChIP-seq, was found to correlate better with TF occupancy compared to steady-state RNA levels and is thus a more precise readout for the primary transcriptional mechanisms that are triggered by signal transduction. Furthermore, analysis of differential Pol II occupancy and RNA-seq levels identified genes with high Pol II occupancy and relatively low RNA levels and vice versa. These categories are strongly enriched for genes from different functional classes. Our results demonstrate a complementary value in Pol II chip-seq and RNA-seq approaches for better understanding of gene expression regulation. 3 replicates of RNAPII ChIP-seq and RNA-seq under normal and Wnt suppressed conditions
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Project description:Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid over its parents in many traits, but the underlying molecular basis remains elusive. To investigate whether DNA methylation plays a role in heterosis, we compared at single base-pair resolution the DNA methylomes of Arabidopsis Ler and C24 parental lines and their reciprocal F1 hybrids that exhibited heterosis for many quantitative traits. Both hybrids displayed increased DNA methylation across their entire genomes, especially in transposable elements. Interestingly, we found that increased methylation of the hybrid genomes predominantly occurred in regions that were differentially methylated in the two parents and covered by small RNAs (sRNAs), implying that the RNA-directed DNA methylation (RdDM) pathway may direct DNA methylation in hybrids. In addition, we found that 77 genes sensitive to remodeling of DNA methylation were transcriptionally repressed in both reciprocal hybrids, including genes involved in flavonoid biosynthesis and two circadian oscillator genes, CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL. Moreover, growth vigor of F1 hybrids was compromised by treatment with an agent that demethylates DNA, and by abolishing production of functional small RNAs due to mutations in Arabidopsis RNA methyltransferase HUA ENHANCER1. Together, our data suggest that genome-wide remodeling of DNA methylation directed by the RdDM pathway may play a role in hybrid vigor. Examination of small RNA sequencing in 2 Arabidopsis ecotypes and their reciprocal hybrids.
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2012-09-22 | E-GEOD-38596 | biostudies-arrayexpress
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Project description:modENCODE_submission_2754 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes. These experiments will be conducted in multiple cell types and developmental tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: CHIP-seq EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown; EXPERIMENTAL FACTORS: Antibody dORC2
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