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Plant organelles modulate nuclear gene expression

ABSTRACT: Maize cytolines provide key nuclear genes that are under the control of retrograde signaling pathways in plants

PROVIDER: PRJEB11473 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1084200_1.fastq.gz	Fastqsanger.gz
	ERR1084200_2.fastq.gz	Fastqsanger.gz
	ERR1084201_1.fastq.gz	Fastqsanger.gz
	ERR1084201_2.fastq.gz	Fastqsanger.gz
	ERR1084202_1.fastq.gz	Fastqsanger.gz

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Zea mays subsp. mays

Project description:Maize cytolines provide key nuclear genes that are under the control of retrograde signaling pathways in plants

| PRJNA298999 | ENA

Maize cytolines provide key nuclear genes that are under the control of retrograde signaling pathways in plants

Project description:By comparing data from the three cytolines (two cytoplsm donors and one nucleus donor) we identified key nuclear genes whose expression is modulated through the retrograde signaling pathways.

2015-10-17 | GSE74096 | GEO

Cytolines as models to study the impact of different cytoplasms on gene expression under heat stress conditions

Project description:Using maize cytolines (same nucleus but different cytoplasms), our research adds a new facet to the paradigm explaining gene expression changes in response to heat stress in an effort to maintain the homeostasis, linking the response to the genetic divergence of the nuclear and organellar genomes.

2021-04-09 | GSE171670 | GEO

Skim sequence data for TC243, T248, and TC221 maize inbred lines

Project description:Skim sequencing of nuclear and organelar genomes in three maize cytolines

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bioadapt2011_cytopheno-CYTOPHENO: Nucleo-cytoplasmic co-adaptation and adaptive plant phenotypes

Project description:The cytopheno project studies cytoplasmic-nucleus interactions by characterizing cytolines (same nucleus but different cytoplasm, and conversely) at several levels (growth, germination, transcriptomic, proteomic, metabolomic) notably in response to nitrogen deficiency. For this project, there are 48 hybridizations performed as following, on leaf samples from hydroponically grown plants. bioadapt2011_cytopheno - bioadapt2011_cytopheno - Evaluation of the impact of nucleo-cytoplasmic co-adaptation disruptions on nuclear genome expression in Arabidopsis - Obtaining samples by hydroponic culture.

2020-06-17 | GSE144597 | GEO

Sigma2 and Sigma6-mediated plastid retrograde signals control nuclear gene expression in Arabidopsis

Project description:Retrograde signaling from the chloroplast to the nucleus is necessary to regulate the chloroplast proteome during development and fluctuating environmental conditions. Although the specific chloroplast process(es) that must occur and the nature of the signal(s) that exits the chloroplast are not well understood, previous studies using drug inhibitors of chloroplast biogenesis have revealed that normal chloroplast development is required to express Photosynthesis Associated Nuclear Genes (PhANGs). In an attempt to determine which specific steps in chloroplast development are involved in retrograde signaling, we analyzed Arabidopsis mutants defective in the six genes encoding sigma factor (Sig) proteins that are utilized by the plastid-encoded RNA polymerase to transcribe specific sets of plastid genes. Here, we demonstrate that both Sig2 and Sig6 have partially redundant roles in not only plastid transcription, but also tetrapyrrole synthesis and retrograde signaling to control PhANG expression. Normal PhANG expression can be partly restored in the sig2 mutant by increasing heme synthesis. Furthermore, there is a genetic interaction between Sig and GUN (genomes uncoupled) genes to generate chloroplast-retrograde signals. These results demonstrate that defective plastid transcription is the source of at least two retrograde signals to the nucleus; one involving tetrapyrrole synthesis and the other involving the accumulation of an unknown plastid transcript. We also propose that the study of sig mutants (with defects in the expression of specific plastid genes) provides a new genetic system, which avoids the use of harsh inhibitors and their potential side effects, to monitor developmental retrograde signaling and to elucidate its mechanisms.

2012-09-18 | E-MTAB-4338 | biostudies-arrayexpress

Comparison of transcriptional activity profiling by metabolic labeling or nuclear RNA sequencing

Project description:The application of high-throughput sequencing to cellular transcriptome profiling (RNA-seq) has enabled significant advances in our understanding of gene expression in plants. However, conventional RNA-seq data reports mainly cytoplasmic transcript abundance rather than actual transcription rates. As a result, it is less sensitive to detect unstable and low-abundance nuclear RNA species, such as long non-coding RNAs, and is less directly connected to chromatin features and processes such as DNA replication. To bridge this gap, several protocols have been established to profile newly synthesized RNA in plants and other eukaryotes. These protocols can be technically challenging and present their own difficulties and limitations. Here we analyze newly synthesized nuclear RNA metabolically labeled in vivo with 5-ethynyl uridine (EU-nuclear RNA) in maize (Zea mays L.) root tips and compare it to the entire nuclear RNA population. We also compare both nuclear RNA preparations to conventional RNA-seq analysis of cellular RNA. The transcript abundance profiles of protein coding genes in nuclear RNA and EU-nuclear RNA were tightly correlated with each other (R2=0.767), but quite distinct from that of cellular RNA (R2=0.170 or 0.293). Nuclear and EU-nuclear RNA reads are frequently mapped across entire genes, including introns, while cellular reads are predominantly mapped to mature transcripts. Both nuclear and EU-nuclear RNA exhibited a greater ability to detect both protein coding and non-coding expressed genes.

2025-07-23 | GSE278168 | GEO

Transcriptome response study of arabidopsis wild type (Col6-3), gun1-9 mutant and MORF2 overexpression lines to norflurazon treatment in retrograde signaling

Project description:Analysis of transcriptome response of norflurazon treated or untreated 5-day old whole seedlings with genotypes: Col6-3 (wild type), gun1-9 and MORF2 overexpression lines. GUN1 and MORF2 are involved in chloroplast-to-nucleus retrograde signaling. Results provide insight into the nuclear genes expression profile under control of GUN1 retrograde pathways and the regulation similarity between gun1-9 and MORF2 overexpression lines.

2019-05-02 | GSE110125 | GEO

Expression data from Arabidopsis thaliana accessions Col-0, Ts-1 and Ga-0 in response to high light stress

Project description:Plants have evolved several mechanisms for sensing increased irradiance, involving signal perception by photoreceptors, and subsequent biochemical and metabolic clues to transmit the signals. This retrograde signaling controls nuclear gene expression. We used microarrays to detail the gene expression response to increased irradiance in three photosynthetically diverse accesssions of Arabidopsis thaliana.

2018-07-10 | GSE115051 | GEO

Retrograde signalling during caused by heritable mitochondrial dysfunction is partly mediated by ANAC017 and improves plant performance.

Project description:Mitochondria are crucial for plant viability and are able to communicate information on their functional status to the cellular nucleus via retrograde signalling, thereby affecting gene expression. It is currently unclear if retrograde signalling in response to constitutive mitochondrial biogenesis defects is mediated by the same pathways as those triggered during acute mitochondrial dysfunction. Furthermore, it is unknown if retrograde signalling can effectively improve plant performance when mitochondrial function is constitutively impaired. Here we show that retrograde signalling in mutants defective in mitochondrial proteins RNA polymerase rpotmp or prohibitin atphb3 can be suppressed by knocking out the transcription factor ANAC017. Genome-wide RNA-seq expression analysis revealed that ANAC017 is almost solely responsible for the most dramatic transcriptional changes common to rpotmp and atphb3 mutants, regulating both classical marker genes such as alternative oxidase 1a (AOX1a) and also previously-uncharacterised DUF295 genes that appear to be new retrograde markers. In contrast, ANAC017 does not regulate intra-mitochondrial gene expression or transcriptional changes unique to either rpotmp or atphb3 genotype, suggesting the existence of currently unknown signalling cascades. The data show that the role of ANAC017 extends beyond common retrograde transcriptional responses and affects downstream protein abundance and enzyme activity of alternative oxidase, as well as steady state energy metabolism in atphb3 plants. Furthermore, detailed growth analysis revealed that ANAC017-dependent retrograde signalling provides benefits for growth and productivity in plants with mitochondrial defects. In conclusion, ANAC017 plays a key role in both biogenic and operational mitochondrial retrograde signalling, and improves plant performance when mitochondrial function is constitutively impaired.

2016-07-28 | E-MTAB-4655 | biostudies-arrayexpress

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