High expressed genes enriched with H3K27me3 in maize genome [RNA-seq]
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ABSTRACT:
PROVIDER: PRJNA483942 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7632750_1.fastq.gz | Fastqsanger.gz | |||
| SRR7632750_2.fastq.gz | Fastqsanger.gz | |||
| SRR7632751_1.fastq.gz | Fastqsanger.gz | |||
| SRR7632751_2.fastq.gz | Fastqsanger.gz | |||
| SRR7632752_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:High expressed genes enriched with H3K27me3 in maize genome
| PRJNA483937 | ENA
Project description:H3K27me3 usually enriched with low or no expressed genes in animal or plant genomes. However, some researches indicate that H3K27me3 can be enriched with high expressed genes in human genome. It's still unknown that whether this kind of gene is appeared in plant genomes and the mechanisms are also unclear. In this study we used ChIP-seq to develop high resolution profiles of H3K27me3 distributions in several tissues or cell-types of maize to better understand the role of this mark in an important crop. The integration of ChIP-seq H3K27me3 profiles with RNA-seq and WGBS-seq data sets suggested that H3K27me3 may play diverse roles in regulation chromatin structure and function. We found that subsets of highly expressed genes are significantly enriched with H3K27me3 in maize. The profiles of several maize mutants reveal functional divergence for the control of H3K27me3 among maize genes. The analysis of existing rice and Arabidopsis data finds that a subset of highly expressed genes in these species are also associated with high levels of H3K27me3. Collectively, our analyses demonstrate that H3K27me3 alone or cooperating with DNA methylation and other chromatin features actively regulates subsets of gene expression, thereby providing new insights in diverse functions of H3K27me3 in plants.
2020-07-29 | GSE117982 | GEO
Project description:H3K27me3 usually enriched with low or no expressed genes in animal or plant genomes. However, some researches indicate that H3K27me3 can be enriched with high expressed genes in human genome. It's still unknown that whether this kind of gene is appeared in plant genomes and the mechanisms are also unclear. In this study，we used ChIP-seq to develop high resolution profiles of H3K27me3 distributions in several tissues or cell-types of maize to better understand the role of this mark in an important crop. The integration of ChIP-seq H3K27me3 profiles with RNA-seq and WGBS-seq data sets suggested that H3K27me3 may play diverse roles in regulation chromatin structure and function. We found that subsets of highly expressed genes are significantly enriched with H3K27me3 in maize. The profiles of several maize mutants reveal functional divergence for the control of H3K27me3 among maize genes. The analysis of existing rice and Arabidopsis data finds that a subset of highly expressed genes in these species are also associated with high levels of H3K27me3. Collectively, our analyses demonstrate that H3K27me3 alone or cooperating with DNA methylation and other chromatin features actively regulates subsets of gene expression, thereby providing new insights in diverse functions of H3K27me3 in plants.
2020-07-29 | GSE117964 | GEO
Project description:High expressed genes enriched with H3K27me3 in maize genome [ChIP-seq]
| PRJNA483800 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2020-07-29 | GSE117992 | GEO
Project description:Trimethylation of histone H3 lysine 27 (H3K27me3) plays a critical role in regulating gene expression during plant and animal development. We characterized the genome-wide distribution of H3K27me3 in five developmentally distinct tissues in maize plants of two genetic backgrounds, B73 and Mo17, representatives of two distinct heterotic groups. There are numerous differences in the distribution of H3K27me3 among tissues. In contrast, we found the distribution of H3K27me3 among the two genetic backgrounds to be quite similar. The tissue-specific patterns of H3K27me3 are often associated with differences in gene expression among the tissues and most of the imprinted genes that are expressed solely from the paternal allele in endosperm are targets of H3K27me3. Many maize genes with important developmental roles, including numerous genes encoding putative transcription factors, are modified with H3K27me3 in at least one of the tissues that were profiled. A comparison of the H3K27me3 targets in rice, maize, and Arabidopsis provided evidence for conservation of the H3K27me3 targets among plant species. However, there was limited evidence for conserved targeting of H3K27me3 in the two maize subgenomes derived from whole genome duplication. Genomic profiling of H3K27me3 in loss-of-function mutant stocks for Mez2 and Mez3, two of the three putative H3K27me3 methyltranferases present in the maize genome, suggests partial redundancy of this gene family for maintaining H3K27me3 patterns. Only a portion of the targets of H3K27me3 requires Mez2 and/or Mez3 and there was limited evidence for functional consequences of H3K27me3 at these targets. This study provides a catalogue of 6,337 genes that are marked by H3K27me3 in five maize tissues.
2013-02-20 | GSE39456 | GEO
Project description:Trimethylation of histone H3 lysine 27 (H3K27me3) plays a critical role in regulating gene expression during plant and animal development. We characterized the genome-wide distribution of H3K27me3 in five developmentally distinct tissues in maize plants of two genetic backgrounds, B73 and Mo17, representatives of two distinct heterotic groups. There are numerous differences in the distribution of H3K27me3 among tissues. In contrast, we found the distribution of H3K27me3 among the two genetic backgrounds to be quite similar. The tissue-specific patterns of H3K27me3 are often associated with differences in gene expression among the tissues and most of the imprinted genes that are expressed solely from the paternal allele in endosperm are targets of H3K27me3. Many maize genes with important developmental roles, including numerous genes encoding putative transcription factors, are modified with H3K27me3 in at least one of the tissues that were profiled. A comparison of the H3K27me3 targets in rice, maize, and Arabidopsis provided evidence for conservation of the H3K27me3 targets among plant species. However, there was limited evidence for conserved targeting of H3K27me3 in the two maize subgenomes derived from whole genome duplication. Genomic profiling of H3K27me3 in loss-of-function mutant stocks for Mez2 and Mez3, two of the three putative H3K27me3 methyltranferases present in the maize genome, suggests partial redundancy of this gene family for maintaining H3K27me3 patterns. Only a portion of the targets of H3K27me3 requires Mez2 and/or Mez3 and there was limited evidence for functional consequences of H3K27me3 at these targets. This study provides a catalogue of 6,337 genes that are marked by H3K27me3 in five maize tissues. B73 tissues for h3k27 analysis: Samples are replicated in triplicate with antibody pulldown (IP) and control genomic DNA (input) channels. histone modification mutants for h3k27 analysis: Samples are replicated in triplicate with antibody pulldown (IP) and control genomic DNA (input) channels. Mo17 tissues for h3k27 analysis: Samples contain antibody pulldown (IP) and control genomic DNA (input) channels.
2013-02-20 | E-GEOD-39456 | biostudies-arrayexpress
Project description:Several signaling pathways require JMJD3 binding to promoters to activate the expression of target genes. Despite the known H3K27me3 demethylase activity of JMJD3 the transcriptional coactivator mechanism remains unclear. Here we reveal that JMJD3 promotes transcription of TGFb responsive genes through regulation of RNAPII progression on gene bodies. ChIPseq experiments demonstrate that upon TGFb treatment, JMJD3 and RNAPII.ser2P colocalyze extensively along intragenic regions of TGF target genes. M-BM- According to these data, genome wide analysis shows that JMJD3 dependent TGF target genes are enriched in H3K27me3 prior to TGF signaling pathway activation. M-BM- Further molecular analysis indicate that JMJD3 removes H3K27me3 and pave the way for the RNAPII.Overall, these findingsM-BM- uncover the mechanism ofM-BM- JMJD3 function in transcriptional activation We performed chromatin immunoprecipitation followed by sequencing (ChIPseq) of H3K27me3 mark in mouse neural stem cells growing under standard conditions. We also performed ChIPseq of elongating RNAPII (Ser2P) and JMJD3 in neural stem cells stimulated with TGFb cytokine.
2012-12-31 | E-GEOD-38269 | biostudies-arrayexpress
Project description:Purpose: To identify the potential genes that regulate seed germination speed in maize, we performed a time-series transcriptome analysis with two inbred maize lines (72-3 fast germination, F9721 slow germination) during the seed germination and compared the differentially expressed genes (DEGs) in transcriptome with genes identified by GWAS Methods: Methods: mRNA profiles of two maize inbred lines 72-3 and F9721 showing divergent seed germination at six stages during germination were generated by deep sequencing, in triplicate, using Illumina Hiseq2500. The sequence reads that passed quality filters were analyzed at the gene level. Hisat2 was used to align clean reads to maize B73 reference genome, and HTSeq was used to count transcript abundance. DESeq2 models were used to compare DEGs at each germination stage within or between samples Results: Comparative transcriptome study identified 12 hours after imbibition (HAI) as the critical stage responsible for the variation of germination speed. The DEGs between 72-3 and F9721 were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, oxidoreductase activity pathways, hormone signal transduction, and amino acid transporter activity pathways Conclusions: Combined with evidence from gene expression data, GWAS, and gene synteny with other model species, we finally anchored three genes as the likely candidate genes regulating germination speed in maize
2022-03-02 | GSE193292 | GEO
Project description:Several signaling pathways require JMJD3 binding to promoters to activate the expression of target genes. Despite the known H3K27me3 demethylase activity of JMJD3 the transcriptional coactivator mechanism remains unclear. Here we reveal that JMJD3 promotes transcription of TGFb responsive genes through regulation of RNAPII progression on gene bodies. ChIPseq experiments demonstrate that upon TGFb treatment, JMJD3 and RNAPII.ser2P colocalyze extensively along intragenic regions of TGF target genes. According to these data, genome wide analysis shows that JMJD3 dependent TGF target genes are enriched in H3K27me3 prior to TGF signaling pathway activation. Further molecular analysis indicate that JMJD3 removes H3K27me3 and pave the way for the RNAPII.Overall, these findings uncover the mechanism of JMJD3 function in transcriptional activation
2012-12-31 | GSE38269 | GEO