Open Access Research

Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response

Kate Sidaway-Lee1, Maria J Costa2, David A Rand23, Bärbel Finkenstadt4 and Steven Penfield1*

Author Affiliations

1 Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK

2 Systems Biology Centre, University of Warwick, Coventry CV4 7AL, UK

3 Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK

4 Department of Statistics, University of Warwick, Coventry CV4 7AL, UK

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Genome Biology 2014, 15:R45  doi:10.1186/gb-2014-15-3-r45

Published: 3 March 2014

Additional files

Additional file 1:

Plants take up 4SU and incorporate it into RNA. Figure S2. 4SU is not toxic to plants and incorporation rate is temperature-dependent. Figure S3. Scatter plots used in linear regression analysis. Figure S4. Quantitative RT-PCR independently confirms rates calculated from microarray data using an extended time-series analysis. Figure S5. Scatter plots showing a lack of correlation between transcription and decay rates at both 27°C and 17°C and various transcript features: (a,b) 5′ UTR length; (c,d) 3′ UTR length; (e,f) cDNA length; (g,h) uracil content; (i,j) GC content; (k,l) number of introns. Figure S6. No effect of intron number on synthesis and decay rate Q10 distribution in Arabidopsis. Table S2. List of quantitative PCR primers used for rate verification analysis shown in Figure S2 in Additional file 1.

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Additional file 2: Table S1:

Genome-wide data for mRNA synthesis and decay rates and temperature coefficient.

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