Dual Roles for CND1 in Maintenances of Nuclear and Chloroplast Genome Stability in Plants [ChIP-seq]
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PROVIDER: PRJNA910067 | ENA |
REPOSITORIES: ENA
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: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 | GSE220489 | GEO
Project description:Dual Roles for CND1 in Maintenances of Nuclear and Chloroplast Genome Stability in Plants
| PRJNA909997 | ENA
Project description:Dual Roles for CND1 in Maintenances of Nuclear and Chloroplast Genome Stability in Plants [RNA-seq]
| PRJNA910068 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-12-13 | GSE220491 | 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: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:Protein N-termini are prone to post translational modification and are major determinants of protein stability in bacteria, eukaryotes, and perhaps also in chloroplasts. Most chloroplast proteins undergo N-terminal maturation, but this is poorly understood due to insufficient experimental information and the N-termini of mature chloroplast proteins cannot be accurately predicted. This motivated an extensive characterization of chloroplast protein N-termini using terminal amine isotopic labeling of substrates (TAILS). Many nuclear-encoded plastid proteins accumulated with two or three different N-termini; we evaluated the significance of these different proteoforms. Ala, Val, Thr (often in N-Î? acetylated form) and Ser were the most frequently observed N-terminal residues, even after normalization for their frequency in the plastid proteome, while other residues were absent or highly under-represented. Plastid-encoded proteins showed a similar distribution of N-terminal residues, but with a higher frequency of Met. Infrequent residues such as Ile, Arg, Cys, Pro, Asp and Glu were observed for several abundant proteins likely reflecting functional regulation through their N-termini. In contrast, the thylakoid lumenal proteome showed a wide diversity of N-terminal residues, including those typically associated with instability (Asp, Glu, Leu, Phe). We propose that after cleavage of the chloroplast transit peptide by stromal processing peptidase, additional processing by unidentified peptidases occurs to avoid unstable or otherwise unfavorable N-terminal residues. The possibility of a chloroplast N-end rule is discussed. This work provides a baseline for understanding N-terminal processing and maturation of chloroplast proteins.
2017-11-14 | MSV000081716 | MassIVE