Dragon TIS Spotter: An Arabidopsis-derived predictor of translation initiation sites in plants
Jankovic, Boris R.
Archer, John A.C.
Bajic, Vladimir B.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Computer Science Program
Applied Mathematics and Computational Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Online Publication Date2012-10-30
Print Publication Date2013-01
Permanent link to this recordhttp://hdl.handle.net/10754/325435
MetadataShow full item record
AbstractIn higher eukaryotes, the identification of translation initiation sites (TISs) has been focused on finding these signals in cDNA or mRNA sequences. Using Arabidopsis thaliana (A.t.) information, we developed a prediction tool for signals within genomic sequences of plants that correspond to TISs. Our tool requires only genome sequence, not expressed sequences. Its sensitivity/specificity is for A.t. (90.75%/92.2%), for Vitis vinifera (66.8%/94.4%) and for Populus trichocarpa (81.6%/94.4%), which suggests that our tool can be used in annotation of different plant genomes. We provide a list of features used in our model. Further study of these features may improve our understanding of mechanisms of the translation initiation. The Author(s) 2012. Published by Oxford University Press.
CitationMagana-Mora A, Ashoor H, Jankovic BR, Kamau A, Awara K, et al. (2012) Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants. Bioinformatics 29: 117-118. doi:10.1093/bioinformatics/bts638.
PublisherOxford University Press (OUP)
PubMed Central IDPMC3530916
The following license files are associated with this item:
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/3.0
- Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences.
- Authors: Kalkatawi M, Rangkuti F, Schramm M, Jankovic BR, Kamau A, Chowdhary R, Archer JA, Bajic VB
- Issue date: 2012 Jan 1
- TITER: predicting translation initiation sites by deep learning.
- Authors: Zhang S, Hu H, Jiang T, Zhang L, Zeng J
- Issue date: 2017 Jul 15
- MetaTISA: Metagenomic Translation Initiation Site Annotator for improving gene start prediction.
- Authors: Hu GQ, Guo JT, Liu YC, Zhu H
- Issue date: 2009 Jul 15
- Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids.
- Authors: Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H, Wang X, Bowers J, Paterson A, Lisch D, Freeling M
- Issue date: 2008 Dec
- ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes.
- Authors: Hu GQ, Zheng X, Yang YF, Ortet P, She ZS, Zhu H
- Issue date: 2008 Jan
Showing items related by title, author, creator and subject.
An Arabidopsis SUMO E3 Ligase, SIZ1, Negatively Regulates Photomorphogenesis by Promoting COP1 ActivityLin, Xiao-Li; Niu, De; Hu, Zi-Liang; Kim, Dae Heon; Jin, Yin Hua; Cai, Bin; Liu, Peng; Miura, Kenji; Yun, Dae-Jin; Kim, Woe-Yeon; Lin, Rongcheng; Jin, Jing Bo (PLOS Genetics, Public Library of Science (PLoS), 2016-04-29) [Article]COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1), a ubiquitin E3 ligase, is a central negative regulator of photomorphogenesis. However, how COP1 activity is regulated by post-translational modifications remains largely unknown. Here we show that SUMO (small ubiquitin-like modifier) modification enhances COP1 activity. Loss-of-function siz1 mutant seedlings exhibit a weak constitutive photomorphogenic phenotype. SIZ1 physically interacts with COP1 and mediates the sumoylation of COP1. A K193R substitution in COP1 blocks its SUMO modification and reduces COP1 activity in vitro and in planta. Consistently, COP1 activity is reduced in siz1 and the level of HY5, a COP1 target protein, is increased in siz1. Sumoylated COP1 may exhibits higher transubiquitination activity than does non-sumoylated COP1, but SIZ1-mediated SUMO modification does not affect COP1 dimerization, COP1-HY5 interaction, and nuclear accumulation of COP1. Interestingly, prolonged light exposure reduces the sumoylation level of COP1, and COP1 mediates the ubiquitination and degradation of SIZ1. These regulatory mechanisms may maintain the homeostasis of COP1 activity, ensuing proper photomorphogenic development in changing light environment. Our genetic and biochemical studies identify a function for SIZ1 in photomorphogenesis and reveal a novel SUMO-regulated ubiquitin ligase, COP1, in plants.
The role of auxin and cytokinin signalling in specifying the root architecture of Arabidopsis thalianaMuraro, Daniele; Byrne, Helen M.; King, John; Bennett, Malcolm (Journal of Theoretical Biology, Elsevier BV, 2013-01) [Article]Auxin and cytokinin are key hormonal signals that control the cellular architecture of the primary root and the initiation of new lateral root organs in the plant Arabidopsis thaliana. Both developmental processes are regulated by cross-talk between these hormones and their signalling pathways. In this paper, sub-cellular and multi-cellular mathematical models are developed to investigate how interactions between auxin and cytokinin influence the size and location of regions of division and differentiation within the primary root, and describe how their cross-regulation may cause periodic branching of lateral roots. We show how their joint activity may influence tissue-specific oscillations in gene expression, as shown in Moreno-Risueno et al. (2010) and commented upon in Traas and Vernoux (2010), and we propose mechanisms that may generate synchronisation of such periodic behaviours inside a cell and with its neighbours. Using a multi-cellular model, we also analyse the roles of cytokinin and auxin in specifying the three main regions of the primary root (elongation, transition and division zones), our simulation results being in good agreement with independent experimental observations. We then use our model to generate testable predictions concerning the effect of varying the concentrations of the auxin efflux transporters on the sizes of the different root regions. In particular, we predict that over-expression of the transporters will generate a longer root with a longer elongation zone and a smaller division zone than that of a wild type root. This root will contain fewer cells than its wild type counterpart. We conclude that our model can provide a useful tool for investigating the response of cell division and elongation to perturbations in hormonal signalling. © 2012 Elsevier Ltd.
Role of the plant-specific endoplasmic reticulum stress-inducible gene TIN1 in the formation of pollen surface structure in Arabidopsis thalianaIwata, Yuji; Nishino, Tsuneyo; Iwano, Megumi; Takayama, Seiji; Koizumi, Nozomu (Plant Biotechnology, Japanese Society for Plant Cell and Molecular Biology, 2012) [Article]Accumulation of unfolded proteins in the endoplasmic reticulum (ER) of eukaryotic cells triggers the transcriptional activation of ER-resident molecular chaperones and folding enzymes to maintain cellular homeostasis. This process is known as the ER stress response or the unfolded protein response. We have identified tunicamycin induced 1 (TIN1), a plant-specific ER stress-inducible Arabidopsis thaliana gene. The TIN1 protein is localized in the ER; however, its molecular function has yet to be clarified. In this study, we performed functional analysis of TIN1 in planta. RT-PCR analysis showed that TIN1 is highly expressed in pollen. Analysis using the β-glucuronidase reporter gene demonstrated that the TIN1 promoter is active throughout pollen development, peaking at the time of flowering and in an ovule of an open flower. Although a T-DNA insertion mutant of TIN1 grows normally under ambient laboratory conditions, abnormal pollen surface morphology was observed under a scanning electron microscope. Based on the current and previous observations, a possible physiological function of TIN1 during pollen development is discussed. © 2012 The Japanese Society for Plant Cell and Molecular Biology.