The Composition of the Arabidopsis RNA Polymerase II Transcript Elongation Complex Reveals the Interplay Between Elongation and mRNA Processing Factors

Plant Cell. 2017 Apr;29(4):854-870. doi: 10.1105/tpc.16.00735. Epub 2017 Mar 28.


Transcript elongation factors (TEFs) are a heterogeneous group of proteins that control the efficiency of transcript elongation of subsets of genes by RNA polymerase II (RNAPII) in the chromatin context. Using reciprocal tagging in combination with affinity purification and mass spectrometry, we demonstrate that in Arabidopsis thaliana, the TEFs SPT4/SPT5, SPT6, FACT, PAF1-C, and TFIIS copurified with each other and with elongating RNAPII, while P-TEFb was not among the interactors. Additionally, NAP1 histone chaperones, ATP-dependent chromatin remodeling factors, and some histone-modifying enzymes including Elongator were repeatedly found associated with TEFs. Analysis of double mutant plants defective in different combinations of TEFs revealed genetic interactions between genes encoding subunits of PAF1-C, FACT, and TFIIS, resulting in synergistic/epistatic effects on plant growth/development. Analysis of subnuclear localization, gene expression, and chromatin association did not provide evidence for an involvement of the TEFs in transcription by RNAPI (or RNAPIII). Proteomics analyses also revealed multiple interactions between the transcript elongation complex and factors involved in mRNA splicing and polyadenylation, including an association of PAF1-C with the polyadenylation factor CstF. Therefore, the RNAPII transcript elongation complex represents a platform for interactions among different TEFs, as well as for coordinating ongoing transcription with mRNA processing.

MeSH terms

  • Adenosine Triphosphatases / genetics
  • Adenosine Triphosphatases / metabolism
  • Arabidopsis / genetics
  • Arabidopsis / metabolism*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism*
  • Histone Chaperones / genetics
  • Histone Chaperones / metabolism
  • Proteomics
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • RNA, Plant / genetics
  • RNA, Plant / metabolism*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcription, Genetic / genetics
  • Transcriptional Elongation Factors / genetics
  • Transcriptional Elongation Factors / metabolism


  • Arabidopsis Proteins
  • Histone Chaperones
  • RNA, Messenger
  • RNA, Plant
  • Transcription Factors
  • Transcriptional Elongation Factors
  • transcription factor S-II
  • RNA Polymerase II
  • Adenosine Triphosphatases
  • NAP1 protein, Arabidopsis