Rht in wheat
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB76483 | ENA |
REPOSITORIES: ENA
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Project description:Common wheat is one of the most widely cultivated staple crops worldwide. Elucidating the gene regulatory network will provide essential information for mechanism studies and targeted manipulation of gene activity for breeding. However, detecting cis-regulatory elements and transcription factor (TF) bindings in the extremely large intergenic regions of the wheat genome is challenging. Linking cis-regulatory elements and TF binding to target genes is even more difficult given that enhancers can function irrespective of the strand and distance from target genes. Combining genome-wide TF binding profiles, epigenomic patterns, and transcriptome analysis is a compelling approach to detect the hierarchical regulatory network. We generated and collected 189 TF binding profiles, 90 epigenomic datasets, and 2,356 transcriptomic datasets in common wheat, which were further integrated using machine learning approach to infer direct target genes and the hierarchical regulatory network. We developed a web-based platform, Wheat-RegNet, that provides four major functions: (i) to identify regulatory elements regulating input gene(s), and to infer the tissue and environmental response specificity; (ii) to identify the TFs responsible for regulating input gene(s) or locus/loci; (iii) to construct the hierarchical regulatory network regulating input gene(s); and (iv) to browse hundreds of TF binding, epigenomic, and transcriptomic profiles of an input region or gene(s). Well-organized results and multiple tools for interactive visualization are available through a user-friendly web interface, making Wheat-RegNet a highly useful resource for exploring gene regulatory information for hypothesis-driven studies and for targeted manipulation for breeding research in common wheat. Wheat-RegNet is freely available at http://bioinfo.sibs.ac.cn/Wheat-RegNet
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Project description:The economic importance of wheat and its contribution to human and livestock diets has been already demonstrated. However, wheat production is impacted by pests that induce yield reductions. Among these pests, wheat curl mite (WCM, Aceria tosichella Keifer) impacts wheat all around the world. WCM are tiny pests that feed within the whorl of developing leaves and prevent the leaves from unfurling by causing leaves curling. The curling of the leaves provides a protective niche for the WCM. Additionally, WCM are also the vector of serious viruses in wheat. Little is known regarding the impact of the WCM on wheat transcriptome, and to date, only one article has been published describing the wheat transcriptomic changes after 1 day of WCM feeding. To better understand the wheat transcriptome variation after long-term feeding by WCM (10 days post infestation (dpi)), we used an RNA-seq approach. We collected leaves uninfested and infested with WCR from two wheat cultivars: Byrd (WCM resistant) and Settler CL (WCM susceptible) at 10 dpi. Our transcriptomic analysis revealed the common and specific transcriptomic variations in WCM resistant and susceptible wheat cultivars, chromosome specific location of the differentially expressed genes, and also identified the gene functions and pathways involved in WCM resistance. Collectively, our study provides important insights on wheat defense mechanisms against WCM after long-term feeding.
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Project description:The DELLA genes encode conserved master growth repressors in plants, and they are also known as ‘Green Revolution’ genes because of their pivotal role in modulating stature of the high-yielding wheat varieties, which were crucial for the success of the ‘Green Revolution’ in the 1960s. At the cellular level, DELLA proteins are nuclear-localized transcription regulators, which play a central role in controlling plant development in response to internal and environmental cues. Recent studies indicate that DELLAs regulate expression of target genes via direct protein-protein interaction of their C-terminal GRAS domain with hundreds of key transcription factors (TFs) and epigenetic regulators. However, the molecular mechanism of DELLA-mediated transcription reprogramming remains unclear. Here, by characterizing missense alleles of an Arabidopsis DELLA, REPRESSOR OF ga1-3 (RGA), we unveil a novel function of the PFYRE subdomain within its GRAS domain for binding to histone H2A via pulldown and co-IP assays. ChIP-Seq analysis further show that this activity is essential for RGA association with its target chromatin globally. Our results indicate that although DELLAs are recruited to target gene promoters by binding to TFs via its LHR1 subdomain, DELLA-H2A interaction via its PFYRE subdomain is necessary to stabilize the TF-DELLA-H2A complex at the target chromatin. This study provides new insight into the two distinct key modular functions in DELLA for its genome-wide transcription regulation in plants. The assay for transposase-accessible chromatin using sequencing (ATAC-seq) for RGA vs rga-11 and RGA treated with GA or mock.
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Project description:The DELLA genes encode conserved master growth repressors in plants, and they are also known as ‘Green Revolution’ genes because of their pivotal role in modulating stature of the high-yielding wheat varieties, which were crucial for the success of the ‘Green Revolution’ in the 1960s. At the cellular level, DELLA proteins are nuclear-localized transcription regulators, which play a central role in controlling plant development in response to internal and environmental cues. Recent studies indicate that DELLAs regulate expression of target genes via direct protein-protein interaction of their C-terminal GRAS domain with hundreds of key transcription factors (TFs) and epigenetic regulators. However, the molecular mechanism of DELLA-mediated transcription reprogramming remains unclear. Here, by characterizing missense alleles of an Arabidopsis DELLA, REPRESSOR OF ga1-3 (RGA), we unveil a novel function of the PFYRE subdomain within its GRAS domain for binding to histone H2A via pulldown and co-IP assays. ChIP-Seq analysis further show that this activity is essential for RGA association with its target chromatin globally. Our results indicate that although DELLAs are recruited to target gene promoters by binding to TFs via its LHR1 subdomain, DELLA-H2A interaction via its PFYRE subdomain is necessary to stabilize the TF-DELLA-H2A complex at the target chromatin. This study provides new insight into the two distinct key modular functions in DELLA for its genome-wide transcription regulation in plants. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RGA, rga-11 as well as the negative control sly1 dP and sly1 dQ.
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