The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation

Abstract

The CCHC-type zinc finger nucleic acid-binding protein (CNBP/ZNF9) is conserved in eukaryotes and is essential for embryonic development in mammals. It has been implicated in transcriptional, as well as post-transcriptional, gene regulation; however, its nucleic acid ligands and molecular function remain elusive. Here, we use multiple systems-wide approaches to identify CNBP targets and function. We used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) to identify 8,420 CNBP binding sites on 4,178 mRNAs. CNBP preferentially bound G-rich elements in the target mRNA coding sequences, most of which were previously found to form G-quadruplex and other stable structures in vitro. Functional analyses, including RNA sequencing, ribosome profiling, and quantitative mass spectrometry, revealed that CNBP binding did not influence target mRNA abundance but rather increased their translational efficiency. Considering that CNBP binding prevented G-quadruplex structure formation in vitro, we hypothesize that CNBP is supporting translation by resolving stable structures on mRNAs.

Keywords: CLIP-seq; PAR-CLIP; RNA binding protein; posttranscriptional gene regulation; ribosome profiling; translational regulation; zinc-finger.

Figure 1. Overview of CNBP protein

(A) ClustalW multiple sequence alignment of CNBP isoform 1 from various eukaryotes. CCHC domains are indicated by light grey boxes, the RGG domain by a dark grey box. Signature C and H amino acid positions are highlighted (red). (B) Clone count distribution across the six CNBP isoforms from 22 sequenced full length clones from HEK293 cDNA. (C) Comparison and protein length (amino acids, Aa) of the six different CNBP isoforms. (D) Analysis of the nucleocytoplasmic distribution of wild-type CNBP and FH-CNBP isoforms 1–6 HEK293 cell lines, as indicated. Cytoplasmic and nuclear fractions were probed with anti-CNBP, anti-FLAG (FH-CNBP), anti-Histone H3 (nuclear marker), anti-GAPDH (cytoplasmic marker), and anti-Calnexin (endoplasmic reticulum marker) antibodies.

Figure 2. CNBP PAR-CLIP

(A) Autoradiograph showing in vivo crosslinked CNBP-RNA RNPs from stably expressing FLAG-HA tagged CNBP isoform1–6 cell lines (arrow indicates crosslinked CNBP-RNPs). Cells not irradiated with UV served as control (lane 1). Western blot analysis of immunoprecipitated CNBP isoform1–6 probed with anti-FLAG antibody is shown in the lower panel. (B) Analysis of target transcript preferences for CNBP. The number of exonic binding sites annotated as derived from the 5′ UTR, CDS, or 3′ UTR of a target transcript is shown (orange bars). Grey bars show the expected location distribution of clusters if CNBP bound without regional preference to the set of target transcripts. (C) Density of CNBP binding sites (red line) downstream of the mRNA start codon, compared to 1,000 mismatched randomized controls (grey lines). (D) Weblogo of representative RREs from CNBP PAR-CLIP binding sites generated by HOMER (Heinz et al. 2010). Percentage of CNBP binding sites containing the respective RRE is indicated. (E) Alignment of top 19 PAR-CLIP clusters with G-rich RREs indicated in red. The number of total (Total) and crosslinked (XL) reads for each cluster is shown. Crosslinking sites determined by the diagnostic T-to-C mutation are underlined.

Figure 3. CNBP interacts with G-rich sequence elements in vitro

(A) Binding curves and dissociation constants (Kd) obtained from filter binding assay using recombinant CNBP with synthetic RNA targets containing no GGAG (black), one GGAG (red), and two GGAG (blue) sequence elements. Sequences are given below. (B) Sequences of CNBP-binding sites used for filter binding assays. Nucleotides highlighted in red correspond to the predicted CNBP RREs. Mutations of the putative RRE are underlined. (C) Binding curves and dissociation constants (K_d) obtained from filter binding assays using recombinant CNBP and sequences from (B).

Figure 4. CNBP increases the ribosome density on its targets

(A) Cumulative distribution analysis of change in average mRNA expression comparing CNBP KO cell lines (n=3) with parental HEK293 cells (n=3). Target mRNAs are binned based on the number of crosslinked reads. Significance was determined using a two-sided Kolmogorov-Smirnov (KS) test. Bin size is indicated. (B) Sucrose gradient separation profile of HEK293 cells extract. The western blot below shows co-sedimentation of CNBP with free ribosomal subunits (fractions 5–8), monoribosomes (fractions 9–12), and polysomes (fractions 13–19). RPS6 from the 40S ribosomal subunit served as a control protein. (C) Cumulative distribution analysis of change in ribosome protected fragments (RPF) upon CNBP knockout as determined by ribosome profiling. Target mRNAs are binned based on the number of crosslinked reads. Significance was determined using a two-sided KS test. Bin size is indicated. (D) Same as in (C), except the cumulative distribution of the translation efficiency (TE, calculated as log₂[RPF/RNA abundance]) ratio is plotted. (E) Distribution of RPF around CNBP binding sites in control (blue) and CNBP KO (red) cells. Curves were fitted using LOESS regression and the envelope indicates a 95% confidence interval.

Figure 5. CNBP promotes translation of mRNA targets

(A) Absolute protein abundance per cell in control (WT) and CNBP KO (KO) cells. (B) Effect of CNBP knockdown on luciferase reporter gene expression. Firefly luciferase expression is normalized to Renilla luciferase expression and set to 1 for the control knockdown. Results of paired t-test are indicated (****, p <0.0001; ***, p <0.0006). (C) Cumulative distribution analysis of protein level changes upon CNBP knock down as determined by pSILAC. Significance was determined using a two-sided KS test. Bin size is indicated. (D) Same as in (C), except the cumulative distribution of a protein (derived by pSILAC) per mRNA (derived by RNA-seq) metric (log₂[protein abundance/RNA abundance]) ratio is plotted. (E) CD measurement of a G4 structure without CNBP and with increasing concentrations of CNBP. (F) Number of CNBP binding sites overlapping RT-stop reads (from (Guo and Bartel 2016) compared to a set of background sequence clusters. Background sequences for each CNBP binding site were randomly selected from the same mRNA and the same annotation category (CDS, UTR). (G) Distribution of RT stop reads 100 nt up- and down-stream of CNBP PAR-CLIP sites (red line, anchored at cluster start coordinate). Distribution of RT-stop reads relative to the background sequence set from (F) (black line).