Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus

Abstract

Posttranscriptional regulation in eukaryotes requires cis- and trans-acting features and factors including RNA secondary structure and RNA-binding proteins (RBPs). However, a comprehensive view of the structural and RBP interaction landscape of nuclear RNAs has yet to be compiled for any organism. Here, we use our ribonuclease-mediated structure and RBP-binding site mapping approaches to globally profile these features in Arabidopsis seedling nuclei in vivo. We reveal anticorrelated patterns of secondary structure and RBP binding throughout nuclear mRNAs that demarcate sites of alternative splicing and polyadenylation. We also uncover a collection of protein-bound sequence motifs, and identify their structural contexts, co-occurrences in transcripts encoding functionally related proteins, and interactions with putative RBPs. Finally, using these motifs, we find that the chloroplast RBP CP29A also interacts with nuclear mRNAs. In total, we provide a simultaneous view of the RNA secondary structure and RBP interaction landscapes in a eukaryotic nucleus.

Figure 1. Overview of PIP-seq in Arabidopsis Nuclei

(A) The PIP-seq approach in the Arabidopsis nucleus. Nuclei were purified from 10-day-old Arabidopsis seedlings that were crosslinked using a 1% formaldehyde solution. Nuclei were lysed and separated into footprinting and structure-only samples. Four total sequencing libraries were then prepared for each replicate experiment as previously described (Silverman et al., 2014). (B) An example of PPS identification (dsRNase #28) in exon 13 of DCL1. (C) Read coverage across the DCL1 transcript for the ds- (top, green line) and ssRNA-seq (bottom, purple line) structure-only samples. (D) Structure scores for the DCL1 transcript based on read coverage seen in (C). (E) mRNA secondary structure model for DCL1 determined using our methodology. See also Figures S1–S3.

Figure 2. Characterization of Arabidopsis Nuclear PPSs

(A) Overlap between PPSs identified from two replicate nuclear PIP-seq experiments. (B) Comparison of average PhastCons scores between PPSs (green bars) and equal-sized flanking regions (orange bars) for various genomic regions. *** denotes p value < 1×10⁻¹⁰, Kolmogorov-Smirnov test. Error bars, ± SEM. (C) Analysis of the total number of SNPs identified by the 1001 Genomes Project (Cao et al., 2011) in PPSs compared to a shuffled background control. *** denotes p value < 1×10⁻¹⁰, χ² test. Error bars, ± SD. (D) Absolute distribution of PPSs throughout various RNA species and transcript regions. (E) Average PPS count per pre-mRNA transcript region. Percentages indicate the fraction of annotated RNAs that contain sequencing information for that region. (F) Genomic enrichment of PPS density, measured as log₂ enrichment of the fraction of PPS base coverage normalized to the fraction of genomic bases covered by indicated nuclear mRNA regions for the dsRNase (yellow bars) and ssRNase (red bars) libraries. (G) Breakdown of bound compared to unbound nuclear lincRNAs that are conserved between Arabidopsis thaliana and Brassica rapa. See also Figure S4 and Table S1.

Figure 3. Patterns of Protein Occupancy and Secondary Structure in Specific Nuclear mRNA Regions

(A and B) PPS density and structure score profiles for nuclear mRNAs based on our PIP-seq experiments. Average PPS density (blue lines) and structure scores (red lines) at each position ± 100 nt from canonical (A) start and (B) stop codons for Arabidopsis nuclear mRNAs. (C) PPS density and structure score profiles for exon/intron boundaries of nuclear mRNAs. Average PPS density (blue lines) and structure scores (red lines) at each position ± 30 nt from splice donor and acceptor sites. (D) Model depicting the canonical protein and RNA interactions of the U2-type spliceosome at the splice donor and acceptor sites depicted in (C). See also Figure S5.

Figure 4. Protein Occupancy and Secondary Structure Landscapes at Alternative Splicing and Polyadenylation Sites

(A) Diagram of constitutive introns (blue), cassette exons (turquoise), intron retention events (green), and U12-type introns (red). Large boxes represent exons, lines represent constitutive introns, and small boxes represent alternatively spliced sequences, with the black brackets indicating the regions graphed in (B) and (C) for reference. (B) PPS density profiles for constitutive and alternative splicing events in Arabidopsis. Average PPS density at each position −50 to +30 nt at the donor splice site, and −30 to +50 nt at the acceptor splice site. Line colors correspond to examples shown in (A). (C) Structure score profiles for constitutive and alternative splicing events in Arabidopsis covering the same regions as (B). Line colors correspond to examples shown in (A). (D) PPS density profiles for constitutive and alternative poly(A) sites of nuclear mRNAs. Average PPS density at each position ± 30 nt from constitutive (light-green line) and alternative (dark-green line) cleavage and polyadenylation sites. (E) Average structure score profiles for constitutive and APA sites covering the same regions as (D). See also Figure S6.

Figure 5. The Landscape of Protein-Bound RNA Motifs

(A–E) Overrepresented sequence motifs identified by MEME (A) or HOMER (B–E) analysis of PPS sequences. (F–J) The relative distribution of protein-bound and unbound motifs from (A) to (E) throughout specific pre-mRNA regions, including the CDS (blue), 5′ UTR (purple), 3′ UTR (green), and intron (orange). (K–O) Structure score profiles at RBP-binding motifs from (A) to (E). Average structure score at each position ± 50 nt up- and downstream of bound (red lines) and unbound (orange lines) motif occurrences from (A) to (E).

Figure 6. Clusters of Motifs Are Present in Functionally Related Genes

(A) Multidimensional scaling analysis of RBP-bound motif co-occurrence in Arabidopsis transcripts. The motifs used for this analysis were identified by HOMER- and MEME-based analyses of PPS sequences. Sequences for all of the motifs used in this analysis can be seen in the figure and found in Table S2. Colored dots indicate cluster membership as defined by k-means clustering (k = 3). (B) The most significantly enriched biological processes (and corresponding p value) for target transcripts of the specified clusters of motifs identified in (A) where three or more of the motifs are protein-bound and co-occurring. See also Table S2.

Figure 7. Identification of Arabidopsis RNA-Interacting Proteins

(A and B) Identification of proteins that interact with specific overrepresented sequence motifs. (A) The fold enrichment over negative control of peptides from each designated protein identified by mass spectrometry analysis of eluates after RNA-affinity chromatography with each specified motif. (B) The fold enrichment of peptides from proteins identified by mass spectrometry analysis after RNA-affinity chromatography with the GAN repeat motif (Figure 5A). The top candidate identified by this analysis, CP29A, is annotated and denoted with a red circle. Dotted line indicates cutoff of 6-fold enrichment. (C) Western blot analysis of INTACT-purified nuclei and Arabidopsis 10-day-old seedling lysates using an antibody to CP29A. (D) RT-qPCR analysis of three nuclear GAN motif-containing genes (AT1G70290, AT1G29690, and AT2G26300), two positive control chloroplast transcripts (ATCG00680 and ATCG00490 [also with motif]), and an ACTIN negative control following RIP with an α-CP29A or α-His antibody. The data is presented as the fold change in the α-CP29A relative to α-His RIP samples. Error bars, ± SD. *, **, and *** indicate p value < 0.05, < 0.001, and < 1×10⁻¹⁰, respectively, Fisher’s t test. See also Figure S7 and Table S4.