Dual Roles for CND1 in Maintenances of Nuclear and Chloroplast Genome Stability in Plants [ChIP-seq]
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE220489 | GEO | 2022/12/13
REPOSITORIES: GEO
Similar Datasets
Project description:The coordination of chloroplast and nuclear genome status are critical for plant cell function, but the mechanism remain largely unclear. In this study, we report that Arabidopsis thaliana CHLOROPLAST AND NUCLEUS DUAL-LOCALIZED PROTEIN 1 (CND1) maintains genome stability in both the chloroplast and the nucleus.
2022-12-13 | GSE220490 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-12-13 | GSE220491 | GEO
Project description:Chloroplast biogenesis represents a crucial step in seedling development, and is essential for the transition to autotrophic growth in plants. This light-controlled process relies on the transcription of nuclear and plastid genomes that drives the effective assembly and regulation of the photosynthetic machinery. Here we reveal a novel regulation level for this process by showing the involvement of chromatin remodelling in the coordination of nuclear and plastid gene expression for proper chloroplast biogenesis and function. The two Arabidopsis homologs of the yeast EPL1 proteins, core components of the NuA4 histone acetyl-transferase complex, are essential for the correct assembly and performance of chloroplasts. EPL1 proteins are necessary for the coordinated expression of nuclear genes encoding most of the components of chloroplast transcriptional machinery, specifically promoting H4K5Ac deposition in these loci. These data unveil a key participation of epigenetic regulatory mechanisms in the coordinated expression of the nuclear and plastid genomes.
2022-07-26 | GSE180614 | GEO
Project description:The aim of this investigation is to analyse the effect on nuclear gene expression of inhibition of chloroplast division. Transgenic Arabidopsis lines (Ler) were generated that contained a chemically inducible promoter (XVE) upstream of AtMinD1. AtMinD1 encodes a product involved in chloroplast division; overexpression of AtMinD1 leads to chloroplast division inhibition.
2010-04-20 | GSE20228 | GEO
Project description:The aim of this investigation is to analyse the effect on nuclear gene expression of inhibition of chloroplast division. Transgenic Arabidopsis lines (Ler) were generated that contained a chemically inducible promoter (XVE) upstream of AtMinD1. AtMinD1 encodes a product involved in chloroplast division; overexpression of AtMinD1 leads to chloroplast division inhibition. 6 samples were used in this experiment. Three treatments were performed: Treatment 1: Empty vector control seedlings (transformed with PER-10 only) were sown onto lehle, sprayed at 13 days old with 2uM 17-B-estradiol (inducer) and harvested 24 hours later. Treatment 2: Seeds were sown on lehle containing inducer and sprayed every 24 hours with 2uM inducer until harvested at 14 days old. Treatment 3: Seeds were sown on lehle plates, sprayed at 13 days old with 2uM inducer and harvested 24 hours later. For all three treatments, seedlings were grown in constant light conditions, and tissue was harvested from 14-day-old seedlings (4 rosette leaves) and snap frozen in liquid nitrogen before RNA preparation.
2010-04-28 | E-GEOD-20228 | biostudies-arrayexpress
Project description:The regulator for chloroplast biogenesis (rcb) mutant was identified as a mutant defective in phytochrome-mediated chloroplast biogenesis. The rcb mutant has long hypocotyl and albino phenotypes. RCB initiates chloroplast biogenesis in the nucleus by promoting the degradation of the master repressors for chloroplast biogenesis, the PIFs (Phytochrome Interacting Factors). To understand how RCB regulates the expression of PIF-regulated genes, we performed genome-wide expression analysis of RCB-dependent genes using a rcb-10 null allele.
2019-06-20 | GSE122351 | GEO
Project description:Introduction: The Plant Organelle RNA Recognition (PORR) domain proteins are nucleus-encoded RNA-binding proteins that have acquired specific roles in organelle RNA metabolism as splicing factors of chloroplast group II introns. LEFKOTHEA (At5g62990) is a nuclear gene encoding a PORR domain protein that carries a transit peptide (TP) and monopartite or bipartite nuclear localization signals (NLS). These motifs result in dual-targeting of LEFKOTHEA to the nucleus and chloroplasts implying a role in the splicing of chloroplast group II introns and nuclear pre-mRNA introns. Therefore, we examined the splicing efficiency of plastid and nuclear genes in lefko2 mutant. Methods: The lefko2 mutant is represented by the Salk T-DNA collection unicode SALK_044699/emb1692 and was obtained from the Nottingham Arabidopsis Stock Centre (NASC, Nottingham, UK). Embryo development in homozygous lefko2 plants is ceased abruptly arresting embryogenesis upon globular-to-heart stage transition. Total RNA was extracted using plant RNA kit spin columns with an on-column DNase treatment from heart-stage lefko2 mutant and wild-type Arabidopsis embryos. The quantity and integrity of the RNA was assessed using a NanoDrop 1000 spectrophotometer and agarose gel electrophoresis. RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina). Sequencing was performed on an Illumina HiSeq 2000 instrument at BGI (Beijing Genomics Institute). Raw reads were filtered into clean reads and aligned to the Arabidopsis genome (TAIR10). RNA-seq data were analyzed using the SOAPnuke (version v.1.5.2) with parameters “-l 15 -q 0.2 -n 0.05” and the HISAT2 pipeline (version 2.0.4) with parameters “--phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000”. Differential alternative splicing events were detected for lefko1 and wild-type using rMATS and visualized using the Integrative Genomics Viewer (IGV) tool. Results: RNA-seq uncovered an outstanding number of coding or non-coding novel transcripts in lefko2 mutant embryos. Splicing defects were observed in numerous nuclear and plastid genes of lefko2 embryos compared to wild type. Among them, intron retention (IR) events were the most prominent. Further, the fidelity of 5’ splice site (5’SS) donor and 3’SS acceptor splicing was highly disturbed in lefko2 embryos. To less extend, exon skipping (ES) defects were also detected. Conclusions: Detailed nuclear and chloroplast splicing events were widely observed in lefko2 aborted mutant embryos demonstrating a prevalent role of LEFKOTHEA in the splicing of nuclear pre-mRNA introns and chloroplast group II introns.
2017-09-01 | GSE94576 | GEO
Project description:The experiment was conducted to examine the influence of non-chloroplast genomes rearangements on chloroplast transcription in cucumber
2011-09-10 | E-MEXP-3233 | biostudies-arrayexpress
Project description:In this study we analyzed the effects of CRY2 over-expression on chloroplast genome transcription of tomato, by developing and using a tiling array. This array containing about 90,000 overlapping probes (5-nt resolution) is a versatile tool for global functional studies of tomato cp genome. We profiled transcription in leaves of wild-type (WT) and CRY2-overexpressing (CRY2-OX) plants grown in a diurnal cycle, to generate a comprehensive map of plastid transcription and to monitor potential specific modulations of chloroplast transcriptome induced by the overexpression of CRY2.
2016-06-24 | E-MTAB-1757 | biostudies-arrayexpress
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