Time-course transcriptome of wild-type Arabidopsis leaf
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Hee Jung Koo
PROVIDER: E-GEOD-43616 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac, both associated with actively expressed genes, was monitored in Arabidopsis thaliana leaves at different time points during developmental senescence, along with expression in the form of RNA-seq data. H3K9ac and H3K4me3 marks were highly convergent at all stages of leaf aging, but H3K4me3 marks covered nearly twice the gene area as H3K9ac marks. Genes with the greatest fold-change in expression displayed the largest positively-correlated percent change in coverage for both marks. Most senescence up-regulated genes were pre-marked by H3K4me3 and H3K9ac, but at levels below the whole-genome average, and for these genes, gene expression increased without a significant increase in either histone mark. However, for a subset of genes showing increased or decreased expression, the respective gain or loss of H3K4me3 marks were found to closely match the temporal changes in mRNA abundance. 22% of genes that increased expression during senescence showed accompanying changes in H3K4me3 modification, and they include numerous regulatory genes, which may act as primary response genes. RNA-seq data at different stages of leaf aging.
2015-04-11 | E-GEOD-67777 | biostudies-arrayexpress
Project description:During the senescence stage, leaves undergo degeneration and relocate nutrients accumulated during the growth stage to sink parts such as seeds, critically contributing to plants’ productivity and fitness. Here, we asked how leaf transcriptome is regulated during the senescence stage by performing directional sequencing of total and small RNAs for the entire lifespan of Arabidopsis leaves.
2016-03-16 | GSE43616 | GEO
Project description:The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac, both associated with actively expressed genes, was monitored in Arabidopsis thaliana leaves at different time points during developmental senescence, along with expression in the form of RNA-seq data. H3K9ac and H3K4me3 marks were highly convergent at all stages of leaf aging, but H3K4me3 marks covered nearly twice the gene area as H3K9ac marks. Genes with the greatest fold-change in expression displayed the largest positively-correlated percent change in coverage for both marks. Most senescence up-regulated genes were pre-marked by H3K4me3 and H3K9ac, but at levels below the whole-genome average, and for these genes, gene expression increased without a significant increase in either histone mark. However, for a subset of genes showing increased or decreased expression, the respective gain or loss of H3K4me3 marks were found to closely match the temporal changes in mRNA abundance. 22% of genes that increased expression during senescence showed accompanying changes in H3K4me3 modification, and they include numerous regulatory genes, which may act as primary response genes. H3K4me3 and H3K9ac were measured on a genome-wide scale using ChIP-seq at different stages of leaf aging.
2015-04-11 | E-GEOD-67776 | biostudies-arrayexpress
Project description:We used RNA-Seq to ask whether the transcripts for the proposed BCKDH subunits are upregulated in wild-type plants subjected to prolonged darkness. These experiments were performed using rosette leaves from 5-week-old, short-day-grown (8h light/16h dark) Col-0 wild-type plants moved to constant darkness for 6h, 24h, 48h and 72h, and grown in short day for 72h as control. The transcripts of eight BCAA catabolism genes were increased nine- to 400-fold within the first 6h of prolonged darkness, and remained high until the last time point. These results are consistent with the hypothesis that BCAA catabolic enzymes - including BCKDH subunits E1A1, E1B1, E1B2 and E2 - have one or more physiological roles in the dark. Rosette leaf mRNA profiles of 5-week old Col wild type (WT, CS60000) and BCAA catabolic mutants ivd1-2 and hml1-2 were generated byRNA sequencing, in duplicate, using Illumina HiSeq2500.
2015-04-16 | E-GEOD-67956 | biostudies-arrayexpress
Project description:Enhancing grain production of rice (Oryza sativa L.) is a top priority in ensuring food security for human being. One approach to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. microRNAs (miRNAs) are key regulators for aging and cellular senescence in eukayotes. However, miRNAs and their roles in rice leaf senescence remain unexplored. Here, we report identification of miRNAs and their putative target genes by deep sequencing of six small RNA libraries, six RNA-seq libraries and two degradome libraries from the leaves of two super hybrid rice, Nei-2-You 6 (N2Y6, age-resistant rice) and Liang-You-Pei 9 (LYP9, age-sensitive rice). Totally 372 known miRNAs and 162 miRNA candidates were identified, and 1145 targets were identified. Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively. Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), Auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways. These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding. [miRNA] sample 1:The flag leaves at early stage of grain-filling of N2Y6 rice; sample 2: The flag leaves at middle stage of grain-filling of N2Y6 rice;sample 3:The flag leaves at late stage of grain-filling of N2Y6 rice; sample 4:The flag leaves at early stage of grain-filling of LYP9 rice; sample 5: The flag leaves at middle stage of grain-filling of LYP9 rice;sample 6:The flag leaves at late stage of grain-filling of LYP9 rice. [DGE]: samples 7-12 [degradome (targets)]: samples 13:The flag leaves at mixed stages of grain-filling of N2Y6 rice; sample 14:The flag leaves at mixed stages of grain-filling of LYP9 rice
2015-01-01 | E-GEOD-62200 | biostudies-arrayexpress
Project description:Senescence is the ultimate stage of plant development. Among the different levels of senescence processes, flag leaf senescence plays a crucial role in determining grain quality in rice. In the present study, efforts are made to identify the possible involvement of miRNAs in flag leaf senescence. Four small RNA libraries were generated from different stages of flag leaf senescence and sequenced by Illumina deep sequencing. A total of 29 known miRNA families and 494 novel miRNAs were identified in the senescing flag leaves. 21 known and 116 novel miRNAs exhibited differential expression pattern. Computational prediction and analysis of putative targets of detected miRNAs revealed that miRNAs regulate the flag leaf senescence mainly by regulating transcription factors and hormone metabolism genes. The present study gives a clue about the senescence-associated miRNAs which can be used as a tool for manipulating flag leaf senescence in rice and other crops.
2021-11-30 | GSE123171 | GEO
Project description:Enhancing grain production of rice (Oryza sativa L.) is a top priority in ensuring food security for human being. One approach to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. microRNAs (miRNAs) are key regulators for aging and cellular senescence in eukayotes. However, miRNAs and their roles in rice leaf senescence remain unexplored. Here, we report identification of miRNAs and their putative target genes by deep sequencing of six small RNA libraries, six RNA-seq libraries and two degradome libraries from the leaves of two super hybrid rice, Nei-2-You 6 (N2Y6, age-resistant rice) and Liang-You-Pei 9 (LYP9, age-sensitive rice). Totally 372 known miRNAs and 162 miRNA candidates were identified, and 1145 targets were identified. Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively. Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), Auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways. These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding.
2015-01-01 | GSE62200 | GEO
Project description:Leaf senescence is governed by a complex regulatory network involving dynamic reprogramming of gene expression. Recent evidence indicates that trimethylation of histone H3 at lysine 4 (H3K4me3) alters gene expression during leaf senescence. However, it is largely unknown how histone modification is regulated in an age-dependent manner. We found that JMJ16, an Arabidopsis JmjC-domain containing protein, is a specific H3K4 demethylase that negatively regulates leaf senescence. The histone demethylase activity and the JmjN, JmjC, and FYR domains of JMJ16, but not the zf-C5HC2 domain, are essential for JMJ16 function in the regulation of leaf senescence. Genome-wide analysis revealed a widespread coordinated up-regulation of H3K4me3 and gene expression associated with leaf senescence in the loss-of-function jmj16 mutant compared with the wild type. Genetic analysis indicated that JMJ16 negatively regulates leaf senescence at least partly through repressing the expression of WRKY53 and SAG201, two known positive regulators of leaf senescence. Further analyses demonstrated that JMJ16 associates with WRKY53 and SAG201, and represses precocious expression of WRKY53 and SAG201 in mature leaves by reducing H3K4me3 levels at these loci. Moreover, association of JMJ16 on WRKY53 and SAG201 loci increased at mature stage but decreased at later stage, suggesting that the age-dependent dynamic chromatin association of JMJ16 is required for precise transcriptional activation of SAGs during leaf senescence. Thus, JMJ16 is an important regulator of leaf senescence that demethylates H3K4 at senescence-associated genes in an age-dependent manner.
2019-04-17 | GSE115362 | GEO
Project description:To identify marker genes that are specific for N starvation-induced leaf senescence and suitable to detect cultivar differences at early senescence stages prior to chlorophyll loss, the transcriptomes of leaves of two B. napus cultivars differing in stay-green characteristics and N efficiency were analysed four days after senescence induction by the senescence inducers N starvation, leaf shading and leaf detaching.
2015-01-15 | GSE60108 | GEO
Project description:microRNAs (miRNAs) play important roles in the regulation of gene expression. In Arabidopsis, mature miRNAs are processed from primary miRNA transcripts (pri-miRNAs) by nuclear HYL1/SE/DCL1 complexes that form Dicing bodies (D-bodies). Here we report that a RNA-binding protein MOS2 bound to pri-miRNAs and was required for their efficient processing. MOS2 did not interact with HYL1, SE, and DCL1 and was not localized in D-bodies. Interestingly, in the absence of MOS2, the recruitment of pri-miRNAs by HYL1 was greatly reduced and the localization of HYL1 in D-bodies was compromised. These data suggest that MOS2 facilitates pri-miRNA processing through facilitating the recruitment of pri-miRNAs by the Dicing complexes. Examination of gene expression profiles in Col-0 and mos2-2 plants by deep sequencing
2012-10-27 | E-GEOD-41843 | biostudies-arrayexpress