Eukaryotic genomes encode hundreds of RNA-binding proteins, yet the functions of most of these proteins are unknown. In a genetic study of stress signal transduction in Arabidopsis, we identified a K homology (KH)-domain RNA-binding protein, HOS5 (High Osmotic Stress Gene Expression 5), as required for stress gene regulation and stress tolerance. HOS5 was found to interact with FIERY2/RNA polymerase II (RNAP II) carboxyl terminal domain (CTD) phosphatase-like 1 (FRY2/CPL1) both in vitro and in v ...[more]
Project description:Although Sm-like proteins (LSMs) form the core of U6 RNPs and function in pre-mRNA splicing, little is known regarding their regulatory role in selection of splice sites, alternative splicing (AS) and splicing efficiency in eukaryotes. The Arabidopsis SAD1 locus encodes the LSM5 protein and was defined in a genetic screen for components that regulate the expression of stress-responsive gene. To further investigate regulatory role of the protein SAD1 in pre-mRNA splicing, we performed RNA sequencing (RNA-seq) to examine the changes of the global alternative splicing (AS) among the wildtype Arabidopsis plant (C24), the mutant plant (sad1) and the sad1-overexpressed plant (SAD1-OE). Our work not only provided novel insights into the regulatory role of SAD1 or LSM proteins in splicing, but also provided new cues to improving splicing efficiency and optimizing biological functions and screening the stress-resistant plant.
Project description:Phosphate (Pi) deficiency alters root hair length and frequency as a means of increasing the absorptive surface area of roots. Three partly redundant single R3 MYB proteins, CAPRICE (CPC), ENHANCER OF TRY AND CPC1 (ETC1) and TRIPTYCHON (TRY), positively regulate the root hair cell fate by participating in a lateral inhibition mechanism. To identify putative targets and processes that are controlled by these three transcription factors (TFs), we conducted transcriptional profiling of roots from Arabidopsis thaliana wild-type plants, and cpc, etc1 and try mutants grown under Pi-replete and Pi-deficient conditions using RNA-seq.
Project description:Arabidopsis thaliana infiltrated with different strains of DC3000 were used to elicit PTI, ETI, or a disease response compared to a mock control. This experiment was carried out in both Col-0 wild-type plants as well as mutants deficient in non-sense mediated decay via disruption of the promoter of upf1 (genotype background upf1-5). To identify differentially expressed and alternatively spliced transcripts elicited by bacterial infection, the NMD-impaired and wild-type host transcriptomes were profiled using RNA-seq. Wild-type and upf1-5 mutant plants were independently challenged with pathogenic (DC3000 COR-) or non-pathogenic P. syringae strains (DC3000 COR- ΔhrpS and DC3000 COR- avrPphB).
Project description:We performed RNA-Seq of P. trichocarpa calluses that were firstly induced from roots. Then the total RNAs were isolated from the control and salt-stressed calluses (200 mM NaCl for 6, 12, 24, and 48 h) using a CTAB procedure. Note: All samples in SRA were assigned the same sample accession (SRS938530). This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
Project description:Kharchia local is an Indian tall landrace wheat cultivar. It is native to sodic-saline soils of Kharchia tehsil of the Pali district of Rajasthan, and is a line developed from selections from farmer's fields. It is the most salt tolerant wheat genotype found in India. No systematic study has been carried out in this direction so far. The gaps in understanding of the mechanism underlying salt tolerance limit our ability to improve the salt tolerance in other crop plants. Transcriptome analysis of Kharchia Local under salt stress will provide the insight into the genes involved in salinity tolerance.
Project description:To analyze global changes in AS under salt stress, we obtained high-coverage (~200 times) RNA sequencing data from Arabidopsis thaliana seedlings that were treated with different concentrations of NaCl. Our study provided a comprehensive view of AS under salt stress and revealed novel insights into the potential roles of AS in plant response to salt stress.
Project description:DNA methylation is an important epigenetic modification involved in many biological processes, and active DNA demethylation plays critical roles in regulating expression of genes and anti-silencing of transgenes. In this study, we isolated mutations in one arabidopsis gene, ROS5, which causes the silencing of transgenic 35S-NPTII because of DNA hypermethylation, but no effect on transgenic RD29A-LUC. ROS5 encodes an atypical small heat shock protein. ROS5 can physically interact with IDM1 and is required for preventing DNA hypermethylation of some endogenous genes that are also regualated by IDM1 and ROS1. We propose that ROS5 may regulate active DNA demethylation by interacting with IDM1, thereby creating a friendly chromatin environment that facilitates the binding of ROS1 to erase DNA methylation.
Project description:Members of the ARGONAUTE gene family are known to have roles in RNA-mediated silencing during development. One of these, MEL1, was shown to be germ-cell specific and essential for progression through sporogenesis at both premeiotic mitosis and meiosis. To understand how the MEL1 gene product is responsible for these effects requires analysis of the changes of the transcriptome. The mel1 gene was identified by TOS 17 insertion mutagenesis of Oryza sativa Japonica, cultivar Nipponbare. The TOS 17 insertion line of mel1 and the wild-type parent were the sources of RNA. RNA was extracted from rice panicle (3 cM) of rice grown under natural conditions in rice fields. Small RNAs associated with MEL1 and small RNAs in total RNA were sequenced by Illumina GAII.
Project description:Multiple RNA-sequencing datasets were generated from wild-type Col-0 and hda6, pol IV or pol V null mutant samples to dissect genetic requirements for the maintenance of epigenetic memory and silent locus identity in Arabidopsis thaliana.
Project description:To better understand the complex mechanisms regulating Pi homeostasis in rice (Oryza sativa L. cv. Nipponbare), a time course experiment was performed, where pre-germinated seedlings were grown hydroponically for two weeks on Pi-sufficient medium (0.32 mM Pi), before transferring half of the plants to Pi-deficient solution (0 mM Pi) for 21 days (d). After three weeks of Pi-starvation treatment, half of these plants where then re-supplied with Pi sufficient media for up to 24 hours (h). In total, nine time points were selected in order to cover short and long term responses to Pi starvation as well as the effects of Pi re-supply on Pi starved plants.