Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Reprograming of gene expression and DNA methylation during first initiation stages of the different roots in rice

ABSTRACT: Rice has a fibrous root system with a primary root, lateral roots and crown roots. The cellular origins and early morphologies of the three root types vary greatly, but the adult structures are remarkably similar. Previous studies have highlighted diverse mechanisms involved in rice roots formation However, the gene expression reprograming and the underling epigenetic mechanisms of cell differentiation and initiation of the different roots are not studied. Here, we analyzed spatiotemporally resolved transcriptomes and DNA methylomes during the initiation processes of the three root types using a precise laser microdissection (LM) coupled with RNA-Seq and BS-seq. The analysis reveals distinct gene expression programs during the first stages during the initiation of the three root types. DNA methylome analysis uncovers a dynamic but distinct CHH methylation reprogramming during initiation of the three roots, with a genome-wide decrease of CHH methylation in crown and lateral root initials, but an increase in embryonic root primordium. In addition, a more drastic reprogramming of CHH methylation was observed in lateral root initials. Together, the results provide stage-specific gene expression signatures of the rice roots initiation and show distinct epigenetic and gene expression reprograming during the formation of the three different root types in rice.

ORGANISM(S): Oryza sativa Japonica Group

PROVIDER: GSE136767 | GEO | 2020/02/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Histone acetyltransferase OsGCN5 palys an important role in establishing programs of cell proliferation of crown root meristem

Project description:Shoot-borne crown roots are the major root system in cereals. Previous work has shown that the Wuschel-related homeobox gene WOX11 is necessary and sufficient to promote rice crown root emergence and elongation. Here, we show that WOX11 recruits the ADA2-GCN5 histone acetyltransferase (HAT) module to activate downstream target genes in crown root meristem. OsGCN5 and OsADA2 are highly expressed in root meristem. Knockdown of OsGCN5 and OsADA2 affects crown root initiation and elongation. Here we sought to find the downstream genes of OsGCN5 in rice crown root tip.

2017-03-28 | GSE95481 | GEO

Genome-wide transcriptome of rice laser-microdissected crown root primordia reveals genes expressed specifically during the early differentiation stages of crown roots

Project description:Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by genetics and functional genomics approaches. Nevertheless these approaches are impaired by gene function redundancy and mutant lethality. To overcome these limitations, genome-wide transcriptome analysis can help to identify genes involved in crown root formation and early development. In this study we aimed to identify the genes speciffically expressed in developing crown root primordia in comparison with adjacent cortex tissue of stem at three different developmental stages before emergence from the stem. For this, we used Laser Capture Microdissection to collect crown root primordia in the stem base of 8-day-old rice seedlings. Affymetrix microarrays were processed in the Microarray Core Facility “Transcriptome“ of the Institute in Regenerative Medicine and Biotherapy, CHU de Montpellier-INSERM-UM Montpellier, http://irmb.chu-montpellier.fr/ .

2020-08-26 | GSE133593 | GEO

Overexpression of OsbHLH044 transcription factor controls a negative regulatory module associated with plant cell death and stress inhibition in rice crown root development

Project description:Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by genetics and functional genomics approaches. The CROWN ROOTLESS1 (CRL1) transcription factor is necessary for crown root initiation in rice. The basic helix-loop-helix 044 (OsbHLH044) transcription factor was identified as a CRL1-regulated gene. In this study, we aimed to determine OsbHLH044-regulated genes, with transcriptome analysis of OsbHLH44 overexpressing plants in crl1 mutant background. We analysed the transcriptional profile of overexpressing lines stem bases in comparison with corresponding null segregant sister control lines. Affymetrix microarrays were processed in the Microarray Core Facility “Transcriptome“ of the Institute in Regenerative Medicine and Biotherapy, CHU de Montpellier-INSERM-UM Montpellier, http://irmb.chu-montpellier.fr/ .

2020-03-20 | GSE147200 | GEO

Time-series transcript profiling analysis in stem base of rice crown rootless 1 mutant after ectopic expression induction by dexamethasone of the CRL1 gene

Project description:Lateral Organ Boundary Domain (LBD) transcription factors are specific of plants and are involved in the control of development. One LBD clade is related to the control of root development (Coudert et al., 2013, Mol. Biol. Evol. 30, 569-572). Belonging to this clade, CROWN ROOTLESS 1 controls the initiation of crown roots in rice (Inukai Plant Cell, 17, 1387-1396, Liu et al., 2005, Plant J., 43, 47-56). The aim of this study was to identify the genes that are regulated by CRL1 in a time-dependant manner after its induction. A total of 1748 differentially expressed genes (DEG) were identified, 1034 of them upregulated, and 706 downregulated, and 14 both upregulated and downregulated at some point during the time series. Data analysis revealed three distinct phases in the time series that can represent three developemntal stage during crown root primordia formation. Affymetrix microarrays were processed in the Microarray Core Facility “Transcriptome“ of the Institute in Regenerative Medicine and Biotherapy, CHU de Montpellier-INSERM-UM Montpellier, http://irmb.chu-montpellier.fr/ .

2020-08-27 | GSE123819 | GEO

Transcript profiling in rice stem base of wild type and crown root less 1 mutant after auxin treatment

Project description:Lateral Organ Boundary Domain (LBD) transcription factors are specific of plants and are involved in the control of development. One LBD clade is related to the control of root development (Coudert et al., 2013, Mol. Biol. Evol. 30, 569-572). Belonging to this clade, CROWN ROOT LESS 1 controls the initiation of crown roots in rice and its expression is induced by auxin (Inukai Plant Cell, 17, 1387-1396, Liu et al., 2005, Plant J., 43, 47-56). The aim of this study was to identify CRL1-dependant auxin responsive genes. Transcriptome analysis in wild-type and crl1 mutant stem bases after exogenous auxin treatment of plantlets revealed 126 CRL1-dependant auxin responsive genes including a large part of genes encoding proteins involved in signal transduction pathways that may be related to cell division, expansion and differentiation, and root development.

2017-11-30 | GSE53689 | GEO

Transcript profiling in stem base of crown root less 1 mutant after ectopic expression induction by dexamethasome of CRL1

Project description:Lateral Organ Boundary Domain (LBD) transcription factors are specific of plants and are involved in the control of development. One LBD clade is related to the control of root development (Coudert et al., 2013, Mol. Biol. Evol. 30, 569-572). Belonging to this clade, CROWN ROOT LESS 1 controls the initiation of crown roots in rice (Inukai Plant Cell, 17, 1387-1396, Liu et al., 2005, Plant J., 43, 47-56). The aim of this study was to identify the genes that are regulated by CRL1. Transcriptome analysis in crl1 mutant plants where the CRL1 gene expression was ectopically induced revealed a set of 277 up regulated genes including a large part of genes encoding transcription factors and genes encoding proteins associated to hormone homeostasis, to cell division, expansion and differentiation.

2015-01-01 | GSE53272 | GEO

Expression data from rice stem bases in two different genotypes

Project description:Crown roots differentiate from stem base in rice. In this study, we followed gene expression in stem base of two Vietnamese indica rice varieties that belong to two haplotypes defining a QTL associated with crown root number. We used microarrays to look for the gene differentially expressed in stem base of two varieties.

2018-01-31 | GSE77130 | GEO

The distinct transcription patterns correlate with the differential growth responses to salt stress in maize roots

Project description:We found that primary root (PR) is more resistant to salt stress compared with crown roots (CR) and seminal roots (SR). To understand better salt stress responses in maize roots, six RNA libraries were generated and sequenced from primary root (PR), primary roots under salt stress (PR-salt) , seminal roots (SR), seminal roots under salt stress (SR-salt), crown roots (CR), and crown roots under salt stress (CR-salt). Through integrative analysis, we identified 444 genes regulated by salt stress in maize roots, and found that the expression patterns of some genes and enzymes involved in important pathway under salt stress, such as reactive oxygen species scavenging, plant hormone signal perception and transduction, and compatible solutes synthesis differed dramatically in different maize roots. 16 of differentially expressed genes were selected for further validation with quantitative real time RT-PCR (qRT-PCR).We demonstrate that the expression patterns of differentially expressed genes are highly diversified in different maize roots. The differentially expressed genes are correlated with the differential growth responses to salt stress in maize roots. Our studies provide deeper insight into the molecular mechanisms about the differential growth responses of different root types in response to environmental stimuli in planta. Examination of three root types of maize under salt treatment for understanding the different responding mechenism to salt stress.

2014-03-01 | E-GEOD-53995 | biostudies-arrayexpress

MERISTEM ACTIVITYLESS1 (MAL1) is involved in crown root development through the maintenance of meristem size in rice

Project description:Rice MERISTEM ACTIVITYLESS1 (MAL1) is an RING-H2 finger domain (RFD) contained gene. To elucidate the molecular functions of MAL1 during crown root development, we generated MAL1 knock-down transgenic plants. MAL1 RNA interfering (RNAi) transgenic plants exhibited shorter crown root length and less crown root number phenotype accompanied by low cell division rate.Here we sought to find the downstream genes of OsMAL1 in rice crown root tip

2020-10-09 | GSE141854 | GEO

A Redox-Dependent Pathway for Regulating Reversible HDACs Synchronizes Crown Root Development in Rice

Project description:As a signal molecular in aerobic organism, how reactive oxygen species (ROS) regulates normal life is a fundamental biological question. Locally accumulated ROS have been reported to balance cell division and differentiation in root apical meristem. However, the underlying molecular mechanism is unclear. Here, we reveal that developmentally produced H2O2 in plant root apical meristem (RAM) triggers reversible acetylation modification of proteins which involved in protein synthesis and cell proliferation. WOX11, an essential transcription factor for crown roots (CRs) formation, modulates ROS homeostasis by directly regulating class III peroxidases. HDACs (histone deacetylases) sense cellular redox status to enhance their enzyme activities, which drives protein acetylation level alterations in rice roots. Oxidation-dependent on WOX11 triggered protein acetylation modification leads to a robust root system in rice. Our study revealed a novel regulatory mechanism which cellular redox status via a WOX11-dependent manner regulates protein acetylation during rice crown root development. The molecular link between the redox status and HDACs activities through WOX11-dependent pathway may provide new insight into which plants exploit developmentally produced ROS to direct organogenesis. Additionally, HDACs reversible enzyme activity via redox-regulated endows with the flexibility of protein modification control in dealing with developmental and changing environmental cues.

2022-08-10 | PXD029260 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data