title: Co-ordination and divergence of cell-specific transcription and translation of genes in arabidopsis root cells.
abstract: OBJECTIVE
  A key challenge in biology is to systematically investigate and integrate the different levels of information available at the global and single-cell level. Recent studies have elucidated spatiotemporal expression patterns of root cell types in Arabidopsis thaliana, and genome-wide quantification of polysome-associated mRNA levels, i.e. the translatome, has also been obtained for corresponding cell types. Translational control has been increasingly recognized as an important regulatory step in protein synthesis. The aim of this study was to investigate coupled transcription and translation by use of publicly available root datasets.
  
  
  METHODS
  Using cell-type-specific datasets of the root transcriptome and translatome of arabidopsis, a systematic assessment was made of the degree of co-ordination and divergence between these two levels of cellular organization. The computational analysis considered correlation and variation of expression across cell types at both system levels, and also provided insights into the degree of co-regulatory relationships that are preserved between the two processes.
  
  
  RESULTS
  The overall correlation of expression and translation levels of genes resemble an almost bimodal distribution (mean/median value of 0·08/0·12), with a second, less strongly pronounced 'mode' for negative Pearson's correlation coefficient values. The analysis conducted also confirms that previously identified key transcriptional activators of secondary cell wall development display highly conserved patterns of transcription and translation across the investigated cell types. Moreover, the biological processes that display conserved and divergent patterns based on the cell-type-specific expression and translation levels were identified.
  
  
  CONCLUSIONS
  In agreement with previous studies in animal cells, a large degree of uncoupling was found between the transcriptome and translatome. However, components and processes were also identified that are under co-ordinated transcriptional and translational control in plant root cells.
authors.affiliation: Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, 14476, Germany Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany.
authors.forename: Dhivyaa
authors.initials: D
authors.lastname: Rajasundaram
authors.affiliation: Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, 14476, Germany Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany.
authors.forename: Joachim
authors.initials: J
authors.lastname: Selbig
authors.affiliation: Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany ARC Centre of Excellence in Plant Cell Walls, School of Botany, University of Melbourne, Parkville, VIC 3010, Australia.
authors.forename: Staffan
authors.initials: S
authors.lastname: Persson
authors.affiliation: Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany Targenomix GmbH, Potsdam-Golm, 14476, Germany klie@mpimp-golm.mpg.de.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Klie
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D002473:Cell Wall / Q000378:metabolism*; D019295:Computational Biology; D018506:Gene Expression Regulation, Plant; D009928:Organ Specificity; D018517:Plant Roots / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D020543:Proteome; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D059467:Transcriptome
chemical_list: D029681:Arabidopsis Proteins; D020543:Proteome; D012333:RNA, Messenger; D018749:RNA, Plant
keywords: Arabidopsis thaliana; cell development; data integration; plant cell-wall-related processes; root cells; system-level analysis; transcriptome; translatome