Supplemental Table S6 (original) (raw)
Related papers
Trends in plant science, 2005
Arabidopsis proteins related to FCP (C-terminal domain phosphatase-like). CBC: nuclear cap-binding complex, composed of CBP80 and CBP20 subunits. CF1, CF2: cleavage factors 1 and 2, parts of the mRNA 3 0 end processing machinery. CPSF: cleavage and polyadenylation specificity factor. CStF: mammalian cleavage stimulation factor. CTD: C-terminal domain of RNAP II. eIF4F, eIFiso4F: cytoplasmic cap binding complexes (heterodimers of eIF4E/eIF4G and eIFiso4E/eIFiso4G, respectively). EJC: exon junction complex, deposited as a consequence of splicing. FCP: TFIIF-associating component of CTD phosphatase. Dephosphorylates Serine 2 of the CTD. GT: guanylyltransferase component of the capping enzyme. GUS: b-glucuronidase. hnRNP: heterogeneous nuclear ribonucleoprotein. mRNP: messenger ribonucleoprotein. MT: N 7 G methyltransferase component of the capping enzyme. NMD: nonsense-mediated decay, a specialized mRNA degradation pathway. Targets mRNAs containing premature stop codons. PABP: major poly(A) binding protein, predominantly cytoplasmic at steady state but has an important role in nuclear 3 end processing as well. PABPN: nuclear-specific poly(A) binding protein, regulates PAP. PAP: poly(A) polymerase. P-TEFb: transcription elongation factor composed of cyclin T and CDK9 kinase. RNAP II: RNA polymerase II. RT: RNA triphosphatase component of the capping enzyme. SCP: small CTD phosphatase, dephosphorylates Serine 5 of CTD. snRNA: small nuclear RNAs, key constituents of the spliceosome. SR proteins: Ser/Arg-rich proteins participating in many aspects of splicing. TAR: trans-activating response region. TBRP: trans-activation response RNA-binding protein. TFIIH: transcription initiation factor that contains CDK7 kinase and cyclin H.
Geneexpress: A Computer System for Description, Analysis, and Recognition of Regulatory Sequences in
2014
via the particular signal transduction pathway to GeneExpress system has been designed to integrate description, analysis, and recognition of eukaryotic regulatory sequences. The system includes 5 basic units: (1) GeneNet contains an object-oriented database for accumulation of data on gene networks and signal transduction pathways and a Java-based viewer that allows an exploration and visualization of the GeneNet information; (2) Transcription Regulation combines the database on transcription regulatory regions of eukaryotic genes (TRRD) and TRRD Viewer; (3) Transcription Factor Binding Site Recognition contains a compilation of transcription factor binding sites (TFBSC) and programs for their analysis and recognition; (4) mRNA Translation is designed for analysis of structural and contextual features of mRNA 5’UTRs and prediction of their translation efficiency; and (5) ACTIVITY is the module for analysis and site activity prediction of a given nucleotide sequence. Integration of ...
Molecular Plant
The activities of transcription factors (TFs) require interactions with specific DNA sequences and other reg-ulatory proteins. To detect such interactions in Arabidopsis, we developed a high-throughput screening system with a Gateway-compatible Gal4-AD–TF library of 1589 Arabidopsis TFs, which can be easily screened by mating-based yeast-one-hybrid (Y1H) and yeast-two-hybrid (Y2H) methods. The efficiency of the system was validated by examining two well-characterized TF–DNA and TF–protein interactions: the CHE–CCA1 promoter interaction by Y1H and NPR1–TGAs interactions by Y2H. We used this system to identify eight TFs that interact with a Mediator subunit, Med25, a key reg-ulator in JA signaling. We identified five TFs that interacted with the GCC-box cis-element in the promoter of PDF1.2, a downstream gene of Med25. We found that three of these TFs, all from the AP2-EREBP family, interact directly both with Med25 and the GCC-box of PDF1.2, suggesting that Med25 regulates PDF1.2 exp...
2003b-BMC Evol Bio-Lijavetzky et al.pdf
Background: Dof proteins are a family of plant-specific transcription factors that contain a particular class of zinc-finger DNA-binding domain. Members of this family have been found to play diverse roles in gene regulation of processes restricted to the plants. The completed genome sequences of rice and Arabidopsis constitute a valuable resource for comparative genomic analyses, since they are representatives of the two major evolutionary lineages within the angiosperms. In this framework, the identification of phylogenetic relationships among Dof proteins in these species is a fundamental step to unravel functionality of new and yet uncharacterised genes belonging to this group.
Genes Genom DOI 10.1007/s13258-013-0138-9 RESEARCH ARTICLE
Superoxide dismutase (SOD) isoenzymes are essential for scavenging excess reactive oxygen species in living organisms. So far, expression pattern of SOD isoenzymes genes along leaf development plus their sub-cellular localization and physical interaction network have not yet been clearly elucidated. Using multiple bioinformatics tools, we predicted the sub-cellular localizations of SOD isoforms and described their physical interactions in rice. Using in silico approaches, we obtained several evidences for existence of seven SOD genes and a SOD copper chaperone gene. Their transcripts were differentially expressed along with different developmental stage of rice leaf. Finally, we performed quantitative real time-polymerase chain reaction (qRT-PCR) to validate in silico differential expression pattern of SOD genes experimentally. Expression of two cytosolic cCuZn-SODs was high during the whole vegetative stage. Two plastidic Fe-SODs were found and their expression levels were very low and started to increase from the late vegetative stage. Their expression patterns were very similar to each other, indicating the formation of heterodimer. However, their expression patterns are different from those for Arabidopsis Fe-SODs. The expression of pCuZn-SOD was very high in the early developmental stage, but qRT-PCR results were different, which remains for further study. From the results on the differential expression of SOD genes, we can understand the role of each SOD gene and even predict their role under certain circumstances based on in silico analysis.
Nucleic Acids Research, 2002
PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Links to the EMBL, TRANSFAC and MEDLINE databases are provided when available. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data. Apart from a general description for specific transcription factor sites, levels of confidence for the experimental evidence, functional information and the position on the promoter are given as well. New features have been implemented to search for plant cis-acting regulatory elements in a query sequence. Furthermore, links are now provided to a new clustering and motif search method to investigate clusters of co-expressed genes. New regulatory elements can be sent automatically and will be added to the database after curation. The PlantCARE relational database is available via the World Wide Web at http://sphinx.rug.ac.be:8080/PlantCARE/.
A gene expression map of Arabidopsis thaliana development
Nature …, 2005
Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in those of animals 1 . Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.