Web supplement to
"Multiparameter functional diversity of human C2H2 zinc finger proteins"

C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2 arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. In addition, little is known about whether or how these proteins regulate transcription. Most of the ~700 human C2H2-ZF proteins also contain at least one KRAB, SCAN, BTB, or SET domain, suggesting that they may have common interacting partners and/or effector functions. Here, we report a multifaceted functional analysis of 131 human C2H2-ZF proteins, encompassing DNA binding sites, interacting proteins, and transcriptional response to genetic perturbation. Surprisingly, the diversity in protein-protein interactions is nearly as high as diversity in DNA binding motifs: most C2H2-ZF proteins interact with a unique spectrum of co-activators and co-repressors. Thus, multiparameter diversification likely underlies the evolutionary success of this large class of human proteins.

• Overview: Gene IDs, construct IDs, DNA sequences and information about experiments performed for all constructs used in this study. Overview.xlsx
• Vector Information: DNA sequence and map of the pDEST pcDNA5/FRT/TO-eGFP vector used for the ChIP-seq, AP-MS and RNA-seq experiments in this study. Vector_map_V4873.pdf, Vector_sequence_V4873.fa

• MACS 1.4.1 output: For each ChIP-seq experiment, a separate text file is provided, containing the coordinates of peaks and summits based on hg19 genome assembly, as well as associated scores. All the peaks above MACS score of 30 are included. Proteins are identified by their UniProt IDs. macs.per_replicate.hg19.tar.gz
• Combined peak summits: For each protein, peak summits from replicates are merged to obtain a unified set of peaks. A separate BED file for each protein is provided. Proteins are identified by their UniProt IDs. combined_summits.per_protein.hg19.tar.gz
• Filtered motif-containing peaks: For each proteins, a BED file is provided, containing only peaks that pass both the optimized MACS score threshold and the optimized PWM score threshold. Proteins are identified by their UniProt IDs. combined_summits.motif_hits.per_protein.hg19.tar.gz
• Motifs: For each protein, a single Position Frequency Matrix (PFM) is provided. Proteins are identified by their UniProt IDs, and the program that was used to generate each motif (RCADE or MEME) is shown in the motif label. For the RCADE motifs, the numbers in the motif label (after the UniProt IDs) represent the zinc fingers that were used for initial seed motif prediction. motifs.pfm.txt
• Missing: Hughes_SI0534_ZNF594_AGTCAA_L007_R1_001.fastq.gz Hughes_SI0534_ZNF594_AGTCAA_L008_R1_001.fastq.gz

• SAINT Scores: The first page shows a table indicating the fold change spectral count and SAINT confidence score (AvgP) for each interaction with a prey that has at least one interaction with AvgP=1. A total of 118 C2H2 baits, 388 preys and 11582 interactions are listed. 'Filtering' column denotes whether the interaction is retained and presented in Figure 5, or whether the prey was removed due to prey assignment as a non nuclear or promiscuous protein ('frequent_flier'). C2H2 bait effector domains are also listed. The second page shows the fold change spectral count in matrix layout for all 118 baits (rows) by all 388 preys (columns). The third page shows the SAINT confidence score in the same layout. PPI_Summary_Table.xlsx
• ROC Table:Receiver operating characteristic for SAINT AvgP cutoff with tables showing internal positive and negative control protein-protein interactions with citations. ROC Table, internal positive and negative controls with citations.xls
• Raw SAINT output: Raw output from SAINT + CRAPome analysis and list of negative control CRAPome datasets incorporated. A total of 67639 interactions with 118 C2H2 baits are listed. Data for both experimental replicates is provided in the column "Spec". Raw SAINT Output.xlsx
• PANTHER overrepresentation analysis: Output of the PANTHER GO-Slim analysis showing categories overrepresented at p<0.05 for all 388 prey proteins with at least one SAINT AvgP equal to 1, before nuclear filtering and promiscuous protein filtering. PANTHER overrepresentation analysis.xlsx

• Figure 1: Jaccard similarity matrix underlying the heatmap in Figure 1. ChIP_Jaccard.per_protein.txt
• Figure 4: Matrix of C2H2-ZF protein binding sites in EREs underlying the heatmap in Figure 4. Figure4_heatmap_matrix.txt
• Figure 5 & Figure S2: Matrices of numerical data for fold change spectral count and AvgP for 118 baits x 227 nuclear preys used to produce Figure 5. Heatmap matrices: 5A_SPC; 5A_AvgP.xlsx
• Figure 7: Sequence and multi-parameter similarity of paralogous C2H2-ZFs: Pairs of paralogous proteins were identified based on inferred homology of C2H2-ZFs as well as BLAST E-value. Similarity of paralogous pairs in terms of different parameters are indicated in columns 7-13. Paralogs.xlsx
• Figure S1A: AUROC values used for Figure S1A. AUROC.20151213.xlsx
• Figure S3: All data underlying Figure S3. Raw TRIM28 spectral counts for each replicate for each bait, raw spectral counts of each for each bait's own purification, and the total number of significant (AvgP=1) interactions for each bait. Fig S3.xlsx
• Figure S5: The normalized matrix of gene expression after over-expression of different C2H2-ZF proteins. Values represent log2 fold-change in expression relative to batch median. Genes are identified by their Ensembl IDs . OE.vsd_normalized.log2.txt.gz