Quantitative regulation of FLC via coordinated transcriptional initiation and elongation

Zhe Wu, Robert Ietswaart, Fuquan Liu, Hongchun Yang, Martin Howard, Caroline Dean

Research output: Contribution to journalArticlepeer-review

65 Citations (Scopus)
168 Downloads (Pure)


The basis of quantitative regulation of gene expression is still poorly understood. In Arabidopsis thaliana, quantitative variation in expression of FLOWERING LOCUS C (FLC) influences the timing of flowering. In ambient temperatures, FLC expression is quantitatively modulated by a chromatin silencing mechanism involving alternative polyadenylation of antisense transcripts. Investigation of this mechanism unexpectedly showed that RNA polymerase II (Pol II) occupancy changes at FLC did not reflect RNA fold changes. Mathematical modeling of these transcriptional dynamics predicted a tight coordination of transcriptional initiation and elongation. This prediction was validated by detailed measurements of total and chromatin-bound FLC intronic RNA, a methodology appropriate for analyzing elongation rate changes in a range of organisms. Transcription initiation was found to vary ∼ 25-fold with elongation rate varying ∼ 8- to 12-fold. Premature sense transcript termination contributed very little to expression differences. This quantitative variation in transcription was coincident with variation in H3K36me3 and H3K4me2 over the FLC gene body. We propose different chromatin states coordinately influence transcriptional initiation and elongation rates and that this coordination is likely to be a general feature of quantitative gene regulation in a chromatin context.
Original languageEnglish
Pages (from-to)218-223
Number of pages6
JournalProceedings of the National Academy of Sciences
Issue number1
Publication statusPublished - 05 Jan 2016


  • chromatin
  • alternative polyadenylation
  • flowering

ASJC Scopus subject areas

  • General Agricultural and Biological Sciences
  • General Biochemistry,Genetics and Molecular Biology


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