Figure 5.

RIP-Seq Analysis of Zm-HCF173, Zm-CP33C, and Zm-SRRP1.

Maize chloroplast stroma was used for immunoprecipitations with antibodies to the maize orthologs of HCF173, CP33C, and SRRP1, and the coimmunoprecipitated RNA was analyzed by deep sequencing.

(A) Average sequence coverage in consecutive 10-nucleotide windows along the chloroplast genome, per million reads mapped to the chloroplast genome (NCBI NC_001666).

(B) Ratio of normalized reads/gene in the experimental immunoprecipitations (IP) versus a control using antibody to AtpB (subunit of the chloroplast ATP synthase). Analogous plots for replicate experiments are shown in Supplemental Figure 2B. Read counts are provided in Supplemental Data Set 1, which also includes data for tRNAs. Immunoblots demonstrating immunoprecipitation of each protein are shown in Supplemental Figure 5.