High expressed genes enriched with H3K27me3 in maize genome [RNA-seq]
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE117982 | GEO | 2020/07/29
REPOSITORIES: GEO
Similar Datasets
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 [RNA-seq]
| PRJNA483942 | ENA
Project description:High expressed genes enriched with H3K27me3 in maize genome [ChIP-seq]
| PRJNA483800 | ENA
Project description:High expressed genes enriched with H3K27me3 in maize genome
| PRJNA483937 | ENA
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:Saha2011- Genome-scale metabolic network of
Zea mays (iRS1563)
This model is described in the article:
Zea mays iRS1563: a
comprehensive genome-scale metabolic reconstruction of maize
metabolism.
Saha R, Suthers PF, Maranas
CD.
PLoS ONE 2011; 6(7): e21784
Abstract:
The scope and breadth of genome-scale metabolic
reconstructions have continued to expand over the last decade.
Herein, we introduce a genome-scale model for a plant with
direct applications to food and bioenergy production (i.e.,
maize). Maize annotation is still underway, which introduces
significant challenges in the association of metabolic
functions to genes. The developed model is designed to meet
rigorous standards on gene-protein-reaction (GPR) associations,
elementally and charged balanced reactions and a biomass
reaction abstracting the relative contribution of all biomass
constituents. The metabolic network contains 1,563 genes and
1,825 metabolites involved in 1,985 reactions from primary and
secondary maize metabolism. For approximately 42% of the
reactions direct literature evidence for the participation of
the reaction in maize was found. As many as 445 reactions and
369 metabolites are unique to the maize model compared to the
AraGEM model for A. thaliana. 674 metabolites and 893 reactions
are present in Zea mays iRS1563 that are not accounted for in
maize C4GEM. All reactions are elementally and charged balanced
and localized into six different compartments (i.e., cytoplasm,
mitochondrion, plastid, peroxisome, vacuole and extracellular).
GPR associations are also established based on the functional
annotation information and homology prediction accounting for
monofunctional, multifunctional and multimeric proteins,
isozymes and protein complexes. We describe results from
performing flux balance analysis under different physiological
conditions, (i.e., photosynthesis, photorespiration and
respiration) of a C4 plant and also explore model predictions
against experimental observations for two naturally occurring
mutants (i.e., bm1 and bm3). The developed model corresponds to
the largest and more complete to-date effort at cataloguing
metabolism for a plant species.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180064.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180064 | BioModels
Project description:Saha2011 - Genome-scale metabolic network of
Arabidopsis thaliana (iRS1597)
This model is described in the article:
Zea mays iRS1563: a
comprehensive genome-scale metabolic reconstruction of maize
metabolism.
Saha R, Suthers PF, Maranas
CD.
PLoS ONE 2011; 6(7): e21784
Abstract:
The scope and breadth of genome-scale metabolic
reconstructions have continued to expand over the last decade.
Herein, we introduce a genome-scale model for a plant with
direct applications to food and bioenergy production (i.e.,
maize). Maize annotation is still underway, which introduces
significant challenges in the association of metabolic
functions to genes. The developed model is designed to meet
rigorous standards on gene-protein-reaction (GPR) associations,
elementally and charged balanced reactions and a biomass
reaction abstracting the relative contribution of all biomass
constituents. The metabolic network contains 1,563 genes and
1,825 metabolites involved in 1,985 reactions from primary and
secondary maize metabolism. For approximately 42% of the
reactions direct literature evidence for the participation of
the reaction in maize was found. As many as 445 reactions and
369 metabolites are unique to the maize model compared to the
AraGEM model for A. thaliana. 674 metabolites and 893 reactions
are present in Zea mays iRS1563 that are not accounted for in
maize C4GEM. All reactions are elementally and charged balanced
and localized into six different compartments (i.e., cytoplasm,
mitochondrion, plastid, peroxisome, vacuole and extracellular).
GPR associations are also established based on the functional
annotation information and homology prediction accounting for
monofunctional, multifunctional and multimeric proteins,
isozymes and protein complexes. We describe results from
performing flux balance analysis under different physiological
conditions, (i.e., photosynthesis, photorespiration and
respiration) of a C4 plant and also explore model predictions
against experimental observations for two naturally occurring
mutants (i.e., bm1 and bm3). The developed model corresponds to
the largest and more complete to-date effort at cataloguing
metabolism for a plant species.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180011.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180011 | BioModels
Project description:we determine genome-wide binding profiles of a maize CCA1 homolog, ZmCCA1b, in maize inbreds and F1 hybrids at different times of the day. ZmCCA1b is characterized as a central clock regulator gene with evolutionarily conserved molecular and circadian functions and nonadditively expressed in F1 hybrid seedlings. ZmCCA1b binds to over 4,300 target genes in the maize genomes, of which annotation confirms energy metabolic pathways as the main output. We report that an altered temporal binding activity of ZmCCA1b in the hybrid seedlings, which increases expression of carbon fixation genes, increases carbon fixation rates and biomass, demonstrating a novel example of how circadian-regulatory networks directly contribute to growth vigor in maize hybrids. These results collectively offer new insights into clock-mediated regulation of growth vigor in hybrid plants and crops. Profiling genome-wide binding events of ZmCCA1b in the maize inbreds and F1 hybrids at ZT3, ZT9 and ZT15 using chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). 2 biological replicates for each sample were used. Input DNA sample corresponding to each ChIP sample was also sequenced in parallel. We have developed a native antibody for the protein (GRMZM2G014902; epitope: residues 11-77) for the ChIP-seq study.
2016-06-30 | E-GEOD-67655 | biostudies-arrayexpress
Project description:Drought is a major abiotic stress that threatens global food security. Circular RNAs (circRNAs) are endogenous RNAs. How these molecules influence plant stress responses remains elusive. Here, a large scale circRNA profiling identified 2174 and 1354 high-confidence circRNAs in maize and Arabidopsis, respectively, and most were differentially expressed in response to drought. A substantial number of drought-associated circRNA hosting genes were involved in conserved or species-specific pathways in drought responses. Comparative analysis revealed that circRNA biogenesis was more complex in maize than in Arabidopsis. In most cases, maize circRNAs were negatively correlated with sRNA accumulation. In 368 maize inbred lines, the circRNA-hosting genes were enriched for SNPs associated with circRNA expression and drought tolerance, implying either important roles of circRNAs in maize drought responses or their potential use as biomarkers for breeding drought-tolerant maize. Additionally, the expression levels of circRNAs derived from drought-responsible genes encoding calcium-dependent protein kinase and cytokinin oxidase/dehydrogenase were significantly associated with drought tolerance of maize seedlings. Specifically, Arabidopsis plants overexpressing circGORK (Guard cell outward-rectifying K+-channel) were hypersensitive to ABA, but insensitive to drought, suggesting a positive role of circGORK in drought tolerance. We report the transcriptomic profiling and transgenic studies of circRNAs in plant drought responses, and provide evidences highlighting the universal molecular mechanisms involved in plant drought tolerance.
2018-12-25 | GSE124340 | GEO