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The lncRNA DANA2 interacts with the transcription factor ERF84 to regualte drought response in Arabidopsis

ABSTRACT: The lncRNA DANA2 interacts with the transcription factor ERF84 to regualte drought response in Arabidopsis

PROVIDER: PRJNA784258 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17055251_1.fastq.gz	Fastqsanger.gz
	SRR17055251_2.fastq.gz	Fastqsanger.gz
	SRR17055252_1.fastq.gz	Fastqsanger.gz
	SRR17055252_2.fastq.gz	Fastqsanger.gz
	SRR17055253_1.fastq.gz	Fastqsanger.gz

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The lncRNA DANA2 interacts with the transcription factor ERF84 to regualte drought response in Arabidopsis

Project description:DANA2 is a positive regulator of drought response and that DANA2 works jointly with the transcription factor ERF84 to activate the JMJ29 expression during the response to drought.

2022-12-31 | GSE189707 | GEO

The AP2/ERF Transcription Factor TINY Modulates Brassinosteroid-Regulated Plant Growth and Drought Response in Arabidopsis

Project description:The functions of AP2/ERF family transcription factors in stress responses are well documented, but their roles in the brassinosteroid (BR)-regulated growth and stress responses have not been established. Here we show that stress-inducible AP2/ERF family transcription factor TINY inhibits BR-regulated growth while promoting drought response. TINY overexpression plants have stunted growth, increased sensitivity to BR biosynthesis inhibitors and compromised BR-responsive gene expression. In contrast, a tiny tiny2 tiny3 triple mutant has increased BR-regulated growth and BR-responsive gene expression. TINY positively regulates drought response by activating drought responsive genes and promoting abscisic acid-mediated stomatal closure. Global gene expression studies revealed that TINY and BRs oppositely regulate genes involved in plant growth and stress response. TINY interacts with and antagonizes BES1 in the regulation of these genes. The GSK3-like protein kinase BIN2, a negative regulator in the BR pathway, phosphorylates and stabilizes TINY, providing a mechanism for BR-mediated down-regulation of TINY to prevent activation of stress response under optimal growth conditions. Taken together, our results demonstrate that TINY is negatively regulated by BR signaling through BIN2 phosphorylation and positively regulates drought response, as well as inhibits BR-mediated plant growth through TINY-BES1 antagonistic interactions. Our results thus provide insight into the coordination of BR-regulated growth and drought responses.

2019-03-28 | GSE128946 | GEO

NFYA5, a CCAAT binding transcription factor important for drought resistance in Arabidopsis

Project description:NFYA5 is a transcription factor important for drought resistance. Drought stress up-regulates NFYA5 gene expression not only at the transcriptional level but also at the posttranscriptional level by down-regulating the expression of miR169a that targets NFYA5 transcript for cleavage.

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A stress-responsive bZIP transcription factor OsbZIP62 improves drought and oxidative resistance in rice

Project description:Transcription factors play a crucial regulatory role in plant drought stress responses. In this study, a novel drought stress related bZIP transcription factor, OsbZIP62, was identified in rice. This gene was selected from transcriptome analysis of several typical rice varieties with different drought tolerance. The expression of OsbZIP62 was obviously induced by drought, hydrogen peroxide, and abscisic acid (ABA) treatment. Overexpression of OsbZIP62-VP64 (OsbZIP62V) enhanced the drought tolerance and oxidative stress tolerance of transgenic rice, while the osbzip62 mutants showed the opposite phenotype. RNA-seq analysis showed that many stress-related genes (e.g. OsGL1, OsNAC10, and DSM2) were up-regulated in OsbZIP62V plants. OsbZIP62 could bind to the abscisic acid–responsive element (ABRE) and promoters of several putative target genes. Taken together, OsbZIP62 positively regulated rice drought tolerance through regulated the expression of genes associated with stress.

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The 8q24 Enhancer Region including rs6983267 Directly Interacts with Promoter of Oncogenic LncRNA CARLo-5

Project description:The mechanism by which rs6983267 at 8q24.21 increases cancer risk is unclear for the lack of protein?coding genes in the region although the variant is strongly associated with cancer pathogenesis. Here we identify long non-coding RNAs (lncRNAs) near the 8q24 region and show that expression of lncRNA CARLo-5 is significantly correlated with the risk allele of the cancer-associated variant rs6883267. We further report that the 8q24 enhancer region including the variant directly interacts with active regulatory region of the lncRNA CARLo-5 promtoer. Finally, we demonstrate that CARLo-5 has an oncogenic function by regulating cell proliferation and cell-cycle. Our data provide new insight of disease-related variants in a gene desert. Comparison and identification of cell cycle-related genes differentially expressed by CARLo-5 knockdown using Nanostring analysis in HCT116 cells.

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Transcription profiling of Arabidopsissiz1-3 response to drought stress

Project description:Post-translational modifications of proteins by Small Ubiquitin-like Modifiers (SUMOs) regulate protein degradation and localization, protein-protein interaction, and transcriptional activity. SUMO E3 ligase functions are executed by SIZ1/SIZ2 in yeast and PIAS family members in human. The Arabidopsis genome contains only one gene, SIZ1, that is orthologous to yeast SIZ1/SIZ2. Here, we show that the Arabidopsis SIZ1 interacts with SUM1 and SCE1a, the SUMO E2 conjugating enzyme. Compared to WT, the null mutant siz-1-3 is smaller in statue because of reduced expression of gene involved in brassinosteroid biosynthesis and signalling. Drought stress induces the accumulation of SUMO-protein conjugates, which is in part dependent on SIZ1 but not on ABA. Mutant plants of siz1-3 have significant lower tolerance to drought stress. Genome wide expression analysis identified about 2,000 Arabidopsis genes that are responsive to drought, and SIZ1 mediates the induction of 600 of these genes by a pathway independent of DREB2A and ABA. SIZ1-dependent, drought-responsive genes include those encoding enzymes of the anthocyanin synthesis pathway and jasmonate response. From these results, we conclude that SIZ1 regulates Arabidopsis development and plays a role in drought stress response probably through the control of gene expression. Experiment Overall Design: 12 samples that includes 3 replicates of Col 0 under control conditions, 3 replicates of Col 0 expossed to 2 hr of dehydration, 3 replicates of siz1-3 under control conditions and 3 replicates of siz1-3 expossed to 2 hr of dehydration.

2008-06-15 | E-GEOD-6583 | biostudies-arrayexpress

Overexpression of OsERF71, an AP2/ERF Transcription Factor, Alters Rice Root Structure That Confers Drought Resistance

Project description:Plant responses to drought stress require the regulation of transcriptional networks via drought responsive transcription factors, which mediate a range of morphological and physiological changes. AP2/ERF transcription factors are known to act as key regulators of drought resistance transcriptional networks; however, little is known about the associated molecular mechanisms that give rise to specific morphological and physiological adaptations. In this study, we functionally characterized the rice (Oryza sativa) drought responsive AP2/ERF transcription factor, OsERF71, which is predominantly expressed in the root meristem, pericycle, and endodermis. Overexpression of OsERF71 either throughout the entire plant or specifically in roots, resulted in a drought resistance phenotype at the vegetative growth stage, indicating that overexpression in roots was sufficient to confer drought resistance. The root specific overexpression was more effective in conferring drought resistance at the reproductive stage, such that grain yield was increased by 23-42% over wild type plants or whole-body overexpressing transgenic lines under drought conditions. OsERF71 overexpression in roots elevated the expression levels of genes related to cell wall loosening and lignin biosynthetic genes, which correlated with changes in root structure, the formation of enlarged aerenchyma and high lignification levels. Furthermore, OsERF71 was found to directly bind to the promoter of OsCCR1, a key gene in lignin biosynthesis. These results indicate that the OsERF71-mediated drought resistance pathway recruits factors involved in cell wall modification to enable root morphological adaptations, thereby providing a mechanism for enhancing drought resistance.

2016-09-30 | GSE81325 | GEO

Identification of drought stress-responsive transcription factor in ramie (Boehmeria nivea L．Gaud)

Project description:Drought is a main environment stress which severely inhibits the stem growth of ramie and lead to a decrease of the fiber yield. The mechanisms of ramie responding to drought stress are poorly understood. Using Illumina sequencing, approximately 4.8 million (M) 21-nt cDNA tags were sequenced in the cDNA library derived from the drought-stressed ramie (DS), and about 4.7 M were sequenced in the cDNA library constructed from the control ramie under well water condition (CO). The tags generated from two libraries were aligned with ramie transcriptome to annotate their function and a total of 23,912 and 22,826 ramie genes were matched by these tags of DS and CO library, respectively. Comparison of gene expression level between CO and DS ramie based on the differences of tag frequencies appearing in two libraries revealed that 1101 and 505 genes were respectively up- and down- regulated under drought stress. Pathway enrichment analysis identified a set of significantly enriched pathways of DEGs. A series of candidate genes and pathways that may contribute to drought tolerance in ramie will be helpful for further improving ramie drought tolerance ability.

2013-04-23 | GSE46253 | GEO

RUNX1 interacts with lncRNA SMANTIS to regulate monocytic cell functions [RNA_THP1_SMANTIS_RUNX1_KO]

Project description:RUNX1 interacts with lncRNA SMANTIS to regulate monocytic cell functions [RNA_THP1_SMANTIS_RUNX1_KO]

| PRJNA1071501 | ENA

RUNX1 interacts with lncRNA SMANTIS to regulate monocytic cell functions [RNA_iPSC_diff_Mono]

Project description:RUNX1 interacts with lncRNA SMANTIS to regulate monocytic cell functions [RNA_iPSC_diff_Mono]

| PRJNA1071500 | ENA