Figure 4. SE associates with Ser5P and Ser2P pol II complexes.

(A) Summary of mass spectrometry (MS) analysis of immunoprecipitation (IP) reactions using antibodies against RNA polymerase II phosphorylated at Serine 2 (Ser2P) and Serine 5 (Ser5P) of its C-Terminal domain (CTD) from Arabidopsis lysates. Protein coverage and peptide number are represented for known RNA polymerase subunits and SE in three independent biological replicates. (B–E) Co-immunoprecipitation experiments using SE and phosphorylation-specific pol II antibodies. Western blot analysis of pol II Ser5P and IgG (as a negative control) immunoprecipitation experiments from Arabidopsis (B). Immunoprecipitation of SE from B. oleracea using a SE-specific antibody followed by detection of unphosphorylated (D), Ser5P (C) and Ser2P (E) pol II. The images are representative of at least three independent biological replicates. (F–I) Immunolocalization of pol II Ser5P, pol II Ser2P and SE-HA on a 100 nm thin thawed cryosection analyzed by super-resolution microscopy (F,G: Airyscan; H,I: Super-resolution optical fluctuation (SOFI) microscopy). Lines depicte the position for line blot analysis. (J) Proposed mechanism for the function of SE at intronless genes.

Figure 4—figure supplement 1. Analysis of SE and AGO1 targets.

Venn diagram showing the overlap between unique SE- and AGO1-ChIP targets (described in Liu et al., 2018) (hypergeometric test, ****p<0.0001).

Figure 4—figure supplement 2. Analysis of SE target genes down-regulated in se mutants.

Venn diagram showing the overlap between SE-ChIP targets and gene that are up-regulated in se-1 mutants (hypergeometric test, ****p<0.0001).