Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: The mop1 (mediator of paramutation1) mutation affects the recombination landscape in Zea mays

PROVIDER: PRJNA681556 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13167029_1.fastq.gz	Fastqsanger.gz
	SRR13167029_2.fastq.gz	Fastqsanger.gz
	SRR13167030_1.fastq.gz	Fastqsanger.gz
	SRR13167030_2.fastq.gz	Fastqsanger.gz
	SRR13167031_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

mop1 reshapes maize recombination landscape by modulating DNA methylation at MITEs with open chromatin

Project description:Meiotic recombination ensures genetic diversity and proper chromosome segregation, but its regulation remains not yet completely understood in many species. Here, we investigate the role of Mediator of paramutation1 (Mop1), a key component of the RNA-directed DNA methylation pathway, in reshaping the recombination landscape in maize. Using high-resolution crossover (CO) mapping, we show that mop1 mutants exhibit sex-specific effects on recombination, with CO numbers significantly reduced in male meiosis but unchanged in females. Sequence analysis of CO-associated motifs reveals increased enrichment of A/T polymer motifs in female mop1 and decreased enrichment of C/G motifs in male mop1 mutants, suggesting a transition to open chromatin states at these regions. Furthermore, we demonstrate that mop1 preferentially introduces new CO sites in females within regions of higher genetic diversity, particularly near miniature inverted-repeat transposable elements (MITEs). Epigenomic profiling reveals that mop1 significantly reduces CHH methylation at MITEs near genes. MITEs that overlap with differentially methylated regions (DMRs) and CO sites exhibit higher levels of histone marks associated with open chromatin, such as H2A.Z and histone acetylation, compared to MITEs outside DMRs or COs. However, the removal of CHH methylation in mop1 at MITEs that introduce COs does not alter the expression of flanking genes. Together, these results highlight the critical role of MOP1 in regulating meiotic recombination by modulating DNA methylation and chromatin states at transposable elements, providing new insights into the epigenetic regulation of meiotic recombination.

2025-09-15 | GSE304481 | GEO

Zea mays Epigenomics

Project description:RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2.

2014-12-05 | E-MTAB-4191 | biostudies-arrayexpress

mRNA-seq of Zea mays B73 early-prophase meiocytes, anthers, and seedling control

Project description:A major step in the higher plant life cycle is the decision to leave the mitotic cell cycle and begin the progression through the meiotic cell cycle that leads to the formation of gametes. The molecular mechanisms that regulate this transition and early meiosis remain largely unknown. To gain insight into gene expression features during the initiation of meiotic recombination, we profiled early prophase I meiocytes from maize (Zea mays) using capillary collection to isolate meiocytes, followed by RNA-seq.

2013-07-25 | E-MTAB-4210 | biostudies-arrayexpress

MicroRNAs differential expression under submergence, drought and alternated stress in maize and teosinte

Project description:In this work, we performed high throughput sequencing of small RNA libraries in maize (Zea mays ssp. mays) and teosinte (Zea mays ssp. parviglumis) to investigate the response mediated by miRNAs in these plants under control conditions, submergence, drought and alternated drought-submergence or submergence-drought stress. After Illumina sequencing of 8 small RNA libraries, we obtained from 16,139,354 to 46,522,229 raw reads across the libraries. Bioinformatic analysis identified 88 maize miRNAs and 76 miRNAs from other plants differentially expressed in maize and/or in teosinte in response to at least one of the treatments, and revealed that a larger set of miRNAs were regulated in maize than in teosinte in response to submergence and drought stress.

2020-10-23 | GSE155050 | GEO

Zea mays subsp. mays Transcriptome or Gene expression

Project description:Zea mays subsp. mays Transcriptome or Gene expression Atlas.

2012-09-13 | E-MTAB-4342 | biostudies-arrayexpress

Whole transcriptome analysis of coding and non-coding RNAs associated with Spodoptera frugiperda feeding in Zea mays

Project description:We report the application of whole transcriptome sequencing technology for high-throughput profiling of coding and non-coding RNAs associated with Spodoptera frugiperda feeding in Zea mays. 4,366 mRNAs and 233 lncRNAs were differentially expressed during Spodoptera frugiperda feeding in Zea mays. Our data contribute to the understanding of the function of coding and non-coding RNAs in the regulation of plant-insect interactions.

2023-11-21 | GSE247976 | GEO

Expression data from LCM-captured Zea mays root cells after challenge with Meloidogyne incognita

Project description:The differentiation of specialized feeding sites in Zea mays root cells in response to nematode infestation involves substantial cellular reprogramming of host cells that is not well characterized at the molecular level. Expression data was generated from Zea mays root cells undergoing giant cell formation due to nematode infestation and from non-infested control root cells. Cells were laser captured 14 and 21 days after infestation.

2012-04-28 | GSE37556 | GEO

Transcriptome of 3 developmental stages of Colletotrichum graminicola during infection of Zea mays leaf sheaths

Project description:Transcriptome of 3 developmental stages of Colletotrichum graminicola during infection of Zea mays leaf sheaths

2012-06-04 | GSE34632 | GEO

Maize proteome and transcriptome atlas

Project description:An atlas of RNA and protein expression maps across a diverse set of developmental tissues from Zea mays

2016-08-18 | GSE50191 | GEO

Small RNA SBS signatures identified from maize using Illumina's SBS technology

Project description:Most endogenous siRNAs in Arabidopsis are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. Recent work has demonstrated that the maize MEDIATOR OF PARAMUTATION1 (mop1) gene is a predicted ortholog of the Arabidopsis RDR2 gene. The mop1 gene is required for establishment of paramutation and maintenance of transcriptional silencing of transposons and transgenes, suggesting the potential involvement of small RNAs. We analyzed small RNAs in wildtype maize and in the isogenic mop1-1 loss-of-function mutant using Illumina’s sequencing-by-synthesis (SBS) technology, which allowed us to characterize the complement of maize small RNAs to considerable depth. Similar to rdr2 in Arabidopsis, in mop1-1, the 24 nt (nucleotide) endogenous heterochromatic short-interfering siRNAs were dramatically reduced resulting in an enrichment of miRNAs and trans-acting siRNAs (ta-siRNAs). In contrast to the Arabidopsis rdr2 mutant, the mop1-1 plants retained a highly abundant heterochromatic ~22 nt class of small RNAs. These data suggest that maize, unlike Arabidopsis, has a second mechanism for heterochromatic siRNA production. The enrichment of miRNAs and loss of 24 nt heterochromatic siRNAs in mop1-1 should be advantageous for miRNA discovery as the maize genome becomes more fully sequenced.

2008-10-01 | GSE12173 | GEO

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