title: Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response.
abstract: BACKGROUND
  Sensing and responding to ambient temperature is important for controlling growth and development of many organisms, in part by regulating mRNA levels. mRNA abundance can change with temperature, but it is unclear whether this results from changes in transcription or decay rates, and whether passive or active temperature regulation is involved.
  
  
  RESULTS
  Using a base analog labelling method, we directly measured the temperature coefficient, Q10, of mRNA synthesis and degradation rates of the Arabidopsis transcriptome. We show that for most genes, transcript levels are buffered against passive increases in transcription rates by balancing passive increases in the rate of decay. Strikingly, for temperature-responsive transcripts, increasing temperature raises transcript abundance primarily by promoting faster transcription relative to decay and not vice versa, suggesting a global transcriptional process exists that controls mRNA abundance by temperature. This is partly accounted for by gene body H2A.Z which is associated with low transcription rate Q10, but is also influenced by other marks and transcription factor activities.
  
  
  CONCLUSIONS
  Our data show that less frequent chromatin states can produce temperature responses simply by virtue of their rarity and the difference between their thermal properties and those of the most common states, and underline the advantages of directly measuring transcription rate changes in dynamic systems, rather than inferring rates from changes in mRNA abundance.
authors.forename: Kate
authors.initials: K
authors.lastname: Sidaway-Lee
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Costa
authors.forename: David A
authors.initials: DA
authors.lastname: Rand
authors.forename: Bärbel
authors.initials: B
authors.lastname: Finkenstadt
authors.forename: Steven
authors.initials: S
authors.lastname: Penfield
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000502:physiology; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D018869:Heat-Shock Response / Q000235:genetics*; D006657:Histones / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D006657:Histones; C548103:AT1G52740 protein, Arabidopsis