Comparative Analysis of Human Genes Frequently and Occasionally Regulated by m⁶A Modification

Abstract

The m⁶A modification has been implicated as an important epitranscriptomic marker, which plays extensive roles in the regulation of transcript stability, splicing, translation, and localization. Nevertheless, only some genes are repeatedly modified across various conditions and the principle of m⁶A regulation remains elusive. In this study, we performed a systems-level analysis of human genes frequently regulated by m⁶A modification (m⁶Afreq genes) and those occasionally regulated by m⁶A modification (m⁶Aocca genes). Compared to the m⁶Aocca genes, the m⁶Afreq genes exhibit gene importance-related features, such as lower dN/dS ratio, higher protein–protein interaction network degree, and reduced tissue expression specificity. Signaling network analysis indicates that the m⁶Afreq genes are associated with downstream components of signaling cascades, high-linked signaling adaptors, and specific network motifs like incoherent feed forward loops. Moreover, functional enrichment analysis indicates significant overlaps between the m⁶Afreq genes and genes involved in various layers of gene expression, such as being the microRNA targets and the regulators of RNA processing. Therefore, our findings suggest the potential interplay between m⁶A epitranscriptomic regulation and other gene expression regulatory machineries.

Introduction

Various types of RNA modifications can change the chemical or structural properties of the nucleotide residues and thus constitute the core mechanism of the epitranscriptomic regulation [1], [2]. N⁶-methyladenosine (m⁶A), which is one of the most important and widespread RNA modifications [3], can be recognized as the molecular tag by its reader proteins. Accumulating evidence has shown that m⁶A is associated with several key biological processes. For example, m⁶A modification can be specifically recognized by the YTH domain family reader proteins YTHDF2 and YTHDF1 to regulate the degradation [4] and translation of RNA transcripts [5] respectively. And such regulatory processes can be facilitated by YTHDF3 [6], [7]. Besides, YTH domain containing reader protein YTHDC1 is involved in the regulation of alternative splicing [8], while YTHDC2 enhances translational efficiency [9]. Other regulatory factors like the eukaryotic translational initiation factor 3 (eIF3) could also read m⁶A modification to trigger the translation initiation [10]. As the modification could change the chemical properties of nucleotide residues, m⁶A may also perturb the local structure of RNA, and the altered structures have been shown to facilitate the binding of other proteins like heterogeneous nuclear ribonucleoprotein C (HNRNPC) to their target RNAs [11], [12]. Notably, besides the coding transcriptome, m⁶A has also been suggested to regulate the biogenesis of non-coding RNAs (ncRNAs) like microRNAs (miRNAs) [13].

Establishment of immunoprecipitation-based high-throughput sequencing techniques like MERIP-seq or m⁶A-seq greatly facilitates the transcriptome-wide identification of m⁶A modification sites [14], [15]. Data generated from such studies have been curated in the MeT-DB database [16], [17]. Moreover, the transcriptome-wide m⁶A mapping studies also benefit from the recently developed high-resolution m⁶A mapping technique, like miCLIP [18], and computational m⁶A site prediction tools, like the yeast m⁶A predictor m⁶Apred [19] and the mammalian m⁶A predictor SRAMP [20]. Currently, most of the m⁶A modification profiles have been collected in the RMBase database [21] and the MeT-DB database [16], [17]. Therefore, m⁶A sites constitute the vast majority of the RNA methylation sites in both databases. Although m⁶A profiles from various conditions have been included in these databases, the distribution of m⁶A modified genes across these conditions remains unclear. Interestingly, in our initial efforts to compile a comprehensive m⁶A dataset (see details in Table S1) from the MeT-DB V2.0 [17], we noted that only few genes (18 genes) are always modified across all 38 conditions covered in this dataset. Why are some genes regulated by m⁶A modification more extensively than others are? To address this question, we analyzed differences in the conservation, network, regulation, and functional features between gene frequently regulated by m⁶A (m⁶Afreq genes) and those occasionally regulated by m⁶A (m⁶Aocca genes).

Results and discussion

m⁶Afreq genes show gene importance-related features

The overall distribution of the m⁶A modified conditions in our comprehensive m⁶A dataset is shown in Figure 1. Many genes (5854 genes) are m⁶A-modified under ≤19 condition(s) and only some genes (1551 genes) are m⁶A-modified under >35 conditions (Figure 1A). Considering not all genes are expressed under the 38 conditions covered in our dataset, we then corrected the number of m⁶A modified conditions by dividing the number of tissue/cell types in which the gene is expressed. As a result, a similar gene distribution was observed (Figure 1B). Among these genes, 4268 genes are found to be m⁶Afreq genes (modified under >3.5 corrected number of conditions), whereas 3711 genes are found to be m⁶Aocca genes (modified under ≤1.5 corrected number of conditions). To probe the biological characteristics related to such distribution, we performed comprehensive analyses to compare the features of m⁶Afreq genes and m⁶Aocca genes.

Figure 1.

The overall distribution of the number of m⁶A regulated conditions

A. The raw count of the number of m⁶A regulated conditions in our comprehensive m⁶A dataset. Intuitively, an m⁶A regulated condition is counted if there is any m⁶A peak identified in a particular gene under a specified condition. B. The corrected number of m⁶A regulated conditions in the comprehensive m⁶A dataset. The corrected number of m⁶A regulated conditions was obtained by dividing the number of m⁶A regulated conditions against that of cell types (covered by m⁶A profiles) where the gene shows baseline expression. A gene is considered to show baseline expression in a cell type, if TPM is greater than 0.5 in the corresponding cell type according to the Human Protein Atlas database. TPM, transcripts per kilobase million.

Genes expressed across many conditions and cell types tend to be essential genes. Therefore, it is interesting to check whether m⁶Afreq genes possess the essential gene-related features. Although essential genes are often defined in a context-dependent manner, several gene features, including higher conservation, higher protein–protein interaction (PPI) network degree, and broader gene expression spectrum, have been repeatedly shown to be correlated with gene importance [22], [23]. Compared to the m⁶Aocca genes, the m⁶Afreq genes are more conserved as indicated by the significantly lower sequence divergence rate (i.e., lower dN/dS ratio; 0.116 ± 0.00182 vs. 0.157 ± 0.00275, Wilcoxon’s test P = 7.63E−36), although there are fewer orthologous genes across various species for m⁶Afreq genes (102 ± 2.80 vs. 127 ± 4.36, Wilcoxon’s test P = 0.0389). Moreover, the m⁶Afreq genes have higher PPI network degree (44.1 ± 1.23 vs. 28.0 ± 0.921, Wilcoxon’s test P = 8.12E−64), indicating that they tend to interact with more genes and show higher importance in the PPI network. Genes that are constantly expressed across various tissues, i.e., housekeeping genes, likely play essential roles. Compared to the m⁶Aocca genes, the m⁶Afreq genes show significantly lower tissue expression specificity (0.250 ± 0.00156 vs. 0.297 ± 0.00236, Wilcoxon’s test P = 1.95E−68), indicating that m⁶Afreq genes tend to be more widely expressed across different tissues.

The classification of m⁶Afreq genes and m⁶Aocca genes depends on the threshold used. To avoid bias induced by the arbitrary threshold, we then calculated the Spearman’s correlation coefficients between the corrected number of m⁶A regulated conditions and the aforementioned gene importance-related features. As shown in Figure 2, our results are in line with the m⁶Afreq genes vs. m⁶Aocca genes comparisons shown above for most features, with the exception that no significant correlation is observed for the number of orthologous genes. The corrected number of m⁶A regulated conditions shows positive correlations with PPI network degree, but negative correlations with dN/dS ratio and the tissue expression specificity. Given the corrected number of m⁶A regulated conditions is in accordance with most of the aforementioned gene importance-related features (except the number of orthologous genes), genes frequently regulated by m⁶A modification are more likely to be important to the cell.

Figure 2.

The correlation between the corrected number of m⁶A regulated conditions and various gene features

The correlation curves between the corrected number of m⁶A regulated conditions and various gene features are plotted by using the LOESS smoothing technique. The line indicates the local average estimated by LOESS smoothing and the shade indicates the confidence interval. Outlier genes (0.5%) with extremely high corrected number of m⁶A regulated conditions are omitted due to their high variation in gene feature values, which could result in badly skewed regression lines. A. Correlation of corrected number of m⁶A regulated conditions with dN/dS ratio. B. Correlation of corrected number of m⁶A regulated conditions with number of orthologous genes. C. Correlation of corrected number of m⁶A regulated conditions with PPI network degree. D. Correlation of corrected number of m⁶A regulated conditions with tissue expression specificity. E. Correlation of corrected number of m⁶A regulated conditions with number of targeting microRNAs. F. The summary of Spearman’s correlation coefficient and P values for panels A–E. PPI, protein–protein interaction.

Signaling network properties of the m⁶Afreq genes

As shown in the previous section, the m⁶Afreq genes have higher PPI network degree. However, the in vivo relationships between genes are more complicated than what is described by the binary PPI network. We thus performed the comprehensive signaling network analysis for the detailed network topology properties of m⁶Afreq genes. Besides PPIs, directed activating (positive) interactions and repressing (negative) interactions between genes are also included in the signaling network.

As a result, 1530 m⁶Afreq genes and 1194 m⁶Aocca genes were mapped onto the signaling network, respectively. No significant difference was observed in the network degree with respect to the directed edges when comparing the m⁶Afreq genes and m⁶Aocca genes (Wilcoxon’s test P = 0.611). We tried to classify edges into activating and repressing edges, and compare the degree by considering activating edges or repressing edges alone. We found that compared to m⁶Aocca genes, m⁶Afreq genes have higher network degree when considering repressing edges alone (Wilcoxon’s test P = 3.28E−4). More specifically, m⁶Afreq genes have higher negative out-degree (i.e., the number of signal receivers repressed by this gene) than m⁶Aocca genes (1.63 ± 0.116 vs. 0.965 ± 0.0729, Wilcoxon’s test P = 1.05E−7), indicating that m⁶Afreq genes tend to repress other genes in the signaling network. We also tested other node centrality properties, including betweenness centrality, closeness centrality, eigenvector centrality, and transitivity centrality. Most of these properties do not significantly differ between m⁶Afreq genes and m⁶Aocca genes (Wilcoxon’s test P > 0.05), except that the m⁶Afreq genes show marginally higher betweenness centrality (2.52E−4 ± 3.18E − 5 vs. 1.78E−4 ± 2.22E−5, Wilcoxon’s test P = 0.0203) and closeness centrality (5.64E−3 ± 2.17E−5 vs. 5.62E−3 ± 2.41E−5, Wilcoxon’s test P = 0.0285) than m⁶Aocca genes. These results suggest that m⁶Afreq genes and m⁶Aocca genes are of largely comparable importance to the signaling network.

The difference in betweenness centrality and closeness centrality between m⁶Afreq genes and m⁶Aocca genes also implies that the localization of m⁶Afreq genes and m⁶Aocca genes in the signaling network would differ. To test this hypothesis, for each node, we calculated its shortest distance to the upstream receptors and that to the downstream effectors, and deduced its relative level in the signaling network by comparing these two distances. The relative level of a gene ranges from 0 to 1 with larger values indicative the downstream location (i.e., closer to the downstream effectors than to the upstream receptors) of the gene. While the upstream receptors could be clearly defined by the Gene Ontology (GO) term ‘receptor activity’, the identification of downstream effectors was not straightforward. We adopted two alternative definitions of downstream effectors. First, the downstream effectors could be identified as the nodes with zero out-degree after removing feedback loops. Since no signal would be sent from such kind of nodes, these nodes are intuitively downstream effectors at the bottom ends of signaling cascades. Second, the topology-based definition of downstream effectors could be misled by the incomplete signaling network topology, when the edges in the signaling network are limited. Therefore, we also assigned all transcription factors, which are often the outputting nodes in signaling pathways, as the downstream effectors. When applying topology-based definition of downstream effectors, no difference in signaling network could be observed between m⁶Afreq genes and m⁶Aocca genes (Wilcoxon’s test P = 0.289). A more prominent difference was noticed between m⁶Afreq genes and m⁶Aocca genes when we assigned the transcription factors as the downstream effectors (Figure 3A; 0.660 ± 0.00943 vs. 0.553 ± 0.0110; Wilcoxon’s test P = 2.19E−23). This result indicates that the m⁶Afreq genes, especially transcription factors, tend to act as the downstream effectors along the signaling cascades.

Figure 3.

The network feature of the m⁶Afreq genes

A. Boxplot comparing the distributions of relative level in the signaling network, between the m⁶Afreq genes and m⁶Aocca genes. The relative level in the signaling network shown here was calculated as the shortest distance to any upstream receptor divided by the sum of the shortest distance to any upstream receptor and the shortest distance to any downstream transcriptional factors. B. Cumulative distribution plot comparing the PPI-only degree distribution of the m⁶Afreq genes and that of m⁶Aocca genes. The PPI-only degree only considers PPI edges in the signaling network but omits the activating and repressing edges. C. Cumulative distribution plot comparing the PPI-only degree distribution of the interacting partners of m⁶Afreq genes and that of the interacting partners of m⁶Aocca genes. D. The overrepresented network motifs of m⁶Afreq genes. In a network motif, if there are more m⁶Afreq genes than 9500 out of 10,000 sets of randomly picked genes (corresponding to an empirical P value < 0.05), this motif is considered as an overrepresented motif. The respective motifs are explicitly depicted by the schemas on top. The activating and repressing edges are indicated using lines with arrowhead and circle, respectively. The name of the motif is composed of the motif type and the code describing the edge topology in the motif. For example, IFF3a1i2abbc indicates an incoherent feedforward loop with three nodes (a, b, and c) that form one activating edge and two repressing edges. Among the three edges, the major class of the edges (in this motif, the major class is repressing edge) comprises the edge between a and b, and the edge between b and c. IFF, incoherent feedforward loop; CFF, coherent feedforward loop; NFB, negative feedback loop; PFB, positive feedback loop.

Besides the activating/repressing edges, there are considerable numbers of PPI edges present in the signaling network. Nodes with many PPI partners in the signaling network often act as the adaptors, which can recruit other signaling components for efficient signaling [24]. We checked the PPI-only degree (the degree after ignoring the activating and repressing edges) of m⁶Afreq genes and m⁶Aocca genes. As a result, we found that m⁶Afreq genes have higher PPI-only degree than m⁶Aocca genes (Figure 3B; 2.64 ± 0.161 vs. 2.38 ± 0.177, Wilcoxon’s test P = 7.27E−5). In addition, the interacting partners of m⁶Afreq genes also exhibited higher PPI-only degree than the partners of m⁶Aocca genes (Figure 3C; 10.2 ± 0.441 vs. 8.16 ± 0.443, Wilcoxon’s test P = 3.99E−5). Therefore, the m⁶Afreq genes are inclined to be the recruited partners of high-linked signaling adaptors, or they themselves can act as high-linked signaling adaptors.

Signaling cascades are not always linear, and the signaling network motifs like feedback loops and feedforward loops are prevalent to achieve the fine-tuned cellular signaling [25], [26], [27]. We thus tested whether the m⁶Afreq genes were overrepresented in some specific network motifs in comparison with random expectation (see Materials and methods section for details). All overrepresented network motifs are shown in Figure 3D and we found that the m⁶Afreq genes are most overrepresented in various types of incoherent feedforward loops. Unlike the negative feedback loops and coherent feedforward loops, which often work for cellular homeostasis, adaptation, and de-sensitivity, the incoherent feedforward loops are often associated with ultra-sensitivity and non-monotonic response [25], [26], [27], [28]. The m⁶Afreq genes are also overrepresented in specific types of coherent feedforward loops that are unlikely to achieve adaptation [26]. Taken together, these results indicate that the m⁶Afreq genes are more likely to be involved in regulating the signal sensitivity than cellular homeostasis.

m⁶Afreq genes overlap with microRNA targets and development-related genes

Interestingly, a previous study shows that miRNA targets tend to be the downstream components in the signaling networks, interact with high-linked adaptors, and participate in the positively-linked network motifs [27]. Considering that m⁶Afreq genes show similar network properties, it is interesting to see whether genes extensively regulated by the m⁶A modification are also intensively targeted by miRNAs. We calculated the number of targeting miRNAs on each gene and found that the m⁶Afreq genes are more intensively regulated by miRNAs than the m⁶Aocca genes (number of targeting miRNAs 2.40 ± 0.113 vs. 1.18 ± 0.0858; Wilcoxon’s test P = 1.23E−20). Moreover, we also observed a positive correlation between the corrected number of m⁶A regulated conditions and the number of targeting miRNAs (Spearman’s correlation = 0.085, P = 3.47E−22; Figure 2E). The similar positive correlation persists when the positively co-expressed miRNA–target pairs (which were derived from mirCox database [29], see also Materials and Methods) (Figure S1A; Spearman’s correlation = 0.0562, P = 1.43E−10) or the negatively co-expressed miRNA–target pairs were considered alone (Figure S1B; Spearman’s correlation = 0.0514, P = 4.42E−9). Together, these results indicate potential crosstalk between m⁶A regulation and miRNA regulation. Recently Molinie et al. have reported that transcript isoforms heavily modified by m⁶A tend to have shorter 3′-UTR and therefore fewer miRNA binding sites [30]. Nevertheless, the conclusions of two studies are not necessarily conflicting: while Molinie et al. focused on the intensively modified RNAs and performed the comparison between transcripts isoforms (i.e., modified isoforms vs. non-modified isoforms), in this study we focused on the extensively modified RNAs and performed comparison between different genes (i.e., genes widely modified across various conditions vs. genes occasionally modified). It is possible that some genes are surveilled by multiple miRNAs and frequent m⁶A methylation. When heavily methylated, the isoforms lacking miRNA binding sites of such genes could be expressed to escape the regulation of miRNAs; conversely, the isoforms with multiple miRNA binding sites could be expressed when the m⁶A regulation is not present. How the miRNAs and m⁶A cooperate to regulate the gene expression in a sophisticated way deserves further experimental investigation.

miRNAs have been shown to be associated with cell proliferation and apoptosis [31]. We speculate that the m⁶Afreq genes could have similar enriched functions. We thus performed the GO functional enrichment analysis for m⁶Afreq genes. As a result, we found that the m⁶Afreq genes are significantly enriched for the terms like “embryo development”, “mitotic cell cycle”, “growth”, and “apoptotic signaling pathway” (Table S2). It is of note that these terms are not significantly enriched in m⁶Aocca genes (Table S3). This result again indicates potential functional crosstalk between m⁶A modification and miRNA targeting. In addition, m⁶A modification has also been implicated in the regulation of transcript translation, localization, stability, and splicing [4], [5], [8]. Interestingly, m⁶Afreq genes are also significantly associated with the functional terms like “negative regulation of transcription from RNA polymerase II promoter” and “RNA processing” (Table S2), which are not significantly enriched in m⁶Aocca genes (Table S3). Therefore, in addition to directly participating in the RNA metabolism process, it is plausible that m⁶A could also regulate RNA metabolism indirectly via extensively targeting the RNA metabolism-related genes, ultimately achieving more sophisticated regulation of the gene expression.

Preliminary validation on the quantitative m⁶A dataset and non-methylated genes

In the aforementioned analyses, we focused on the genes that are m⁶A regulated across various conditions. Given these analyses were based only on the binary methylation profiles (i.e., m⁶A modified or not), the m⁶A methylation level was not taken into consideration. Therefore, we also took advantage of the quantitative m⁶A methylation profiles in the MeT-DB V2.0 database [17] for preliminary validation of the main results shown above. These m⁶A methylation profiles were collected using the standardized pipeline, and a quantitative enrichment score was provided for each m⁶A site peak. For each gene, a normalized m⁶A regulation breadth score was calculated in a way similar to the calculation of tissue expression specificity [32], [33] (see also Materials and methods section). The normalized m⁶A regulation breadth ranges from 0 to 1, with higher score indicative genes frequently regulated by m⁶A.

We checked the correlations between the normalized m⁶A regulation breadth and several gene features that have been shown to be associated with m⁶Afreq genes in the analyses above. In line with the results from binary methylation profiles, the normalized m⁶A regulation breadth shows positive correlation with the PPI network degree, the relative level in signaling network, and the number of targeting miRNAs, while a negative correlation of the normalized m⁶A regulation breadth with dN/dS ratio and tissue expression specificity was observed (Figure S2). These results further support our findings from the binary methylation profile analyses.

Another issue of our analyses is that we did not take into consideration the genes that are not methylated. Due to the limited coverage of currently available m⁶A profiles, it is hard to identify bona fide non-regulated genes (i.e., m⁶Anone genes) without significant bias. To perform a preliminary test, we defined genes that have baseline expression in at least one cell type covered by the m⁶A profiles but have no known m⁶A sites as the m⁶Anone genes. Consequently, we identified 2779 m⁶Anone genes for comparison of the gene features that have been shown to be associated with m⁶Afreq genes. Generally, the gene features of m⁶Anone genes are much more similar to those of m⁶Aocca genes than to those of m⁶Afreq genes (Figure S3). For example, m⁶Afreq genes have the highest PPI network degree, followed by m⁶Aocca genes, and then m⁶Anone genes. These results are in line with intuitive expectation. We anticipate that with the accumulation of m⁶A profiles in public databases, a less biased comparison between m⁶Afreq genes, m⁶Aocca genes, and m⁶Anone genes will be performed in the future.

Although our analyses suggest largely consistent results about the difference between m⁶Afreq genes and m⁶Aocca genes, substantial limitation exists in this study. First, the current human m⁶A methylation profiles were largely derived from cell lines especially cancer cell lines like HeLa and A549 [16], [17], [21]. Therefore, these profiles could not fully recapitulate the in vivo m⁶A methylation patterns in normal human tissues. We hope that more tissue-derived m⁶A profiles can be generated in the future so that a dataset more representative of human biology would be compiled. Second, although we are able to compile a quantitative m⁶A dataset according to the enrichment score of m⁶A methylation peaks, the actual stoichiometry of m⁶A methylation is still hard to be measured using current MeRIP-seq technologies [30], [34]. A novel m⁶A methylation quantification method is crucial to generate less biased methylation profiles for more reliable comparative analyses. Third, it is known that the topology of m⁶A sites along the genes could convey biological functions [14], [15]. However, we did not perform analysis at m⁶A site level in the current study. The recent progress in single-nucleotide m⁶A site mapping technique and m⁶A site prediction methods [18], [20] could enable a comprehensive comparison of m⁶A methylation sites across different conditions. Finally, to study the (functional) conservation of m⁶A modifications, it would also be interesting to evaluate our findings in other species.

In summary, our results indicate that the m⁶A modification tends to regulate important genes. Besides, the miRNA targets and regulators of gene expression like transcriptional factors and RNA processing factors are also suggested to be preferred targets of m⁶A modification. Therefore, extensive functional crosstalk between m⁶A epitranscriptomic regulation and other regulatory machineries of gene expression is implied.

Materials and methods

Definition of gene groups based on the number of m⁶A modification conditions

The human m⁶A modification profiles, which cover 38 different m⁶A modification conditions (Table S1), were downloaded from the recently-updated 2.0 version of the MeT-DB database (http://compgenomics.utsa.edu/MeTDB/ and http://www.xjtlu.edu.cn/metdb2) [16]. We first discarded the m⁶A profiles, where the expression of any m⁶A methylation core components (including METTL3, METTL14, WTAP, ALKBH5, and FTO) was perturbed (knockout, knockdown or, over-expression), and combined the modification sites from the biological replicates. Then, the modification sites were mapped to Entrez genes and the number of conditions when the gene was modified on at least one m⁶A site was counted. To reduce bias, we corrected the number of m⁶A regulated conditions by dividing the number of cell types with baseline expression. For each gene, the number of cell types or tissues covered by m⁶A studies and showing baseline expression (i.e., transcripts per million, TPM >0.5) of this gene was derived from the Human Protein Atlas database (https://www.proteinatlas.org/) [35]. The genes with corrected number of m⁶A regulated conditions >3.5 (roughly corresponding to the top 25% in the distribution of corrected number of m⁶A regulated conditions) were defined as the m⁶Afreq genes, while those with corrected number of m⁶A regulated conditions ≤1.5 (roughly corresponding to the bottom 25% in the distribution) were defined as the m⁶Aocca genes.

We also complied a quantitative m⁶A dataset (m⁶A-quantitative dataset) based on the quantitative methylation profiles from MeT-DB V2.0. Then, the m⁶A peaks were mapped onto the Entrez genes, and the total enrichment score along each transcript was calculated. For the gene with multiple transcripts, only the maximum of the total enrichment scores was retained. The total enrichment score of the genes between different technical replicates were averaged and log₁₀-transformed to reduce the bias from the extremely high enrichment scores. Consequently, for each gene in the m⁶A-quantitative dataset, 38 total enrichment scores, which are in correspondence to 38 different conditions, were obtained. Based on these 38 total enrichment scores, a specificity score τ is calculated in the same way as the calculation of tissue expression specificity [32], [33]. Finally, the normalized m⁶A regulation breadth was defined as 1 − τ. By definition, the normalized m⁶A regulation breadth ranges from 0 to 1, where higher score indicates more frequently regulated genes.

Statistical analysis of the gene importance-related gene features

The human-to-mouse dN/dS ratios were downloaded from the Ensembl database (http://www.ensembl.org/) [36]. The numbers of orthologous genes were retrieved from the orthologous matrix (OMA) database (http://omabrowser.org/oma/) [37]. The PPI data were obtained from the BioGRID database (http://thebiogrid.org/) [38]. After removing genetic interactions and protein–RNA interactions, the degree of each protein was calculated by counting the total number of its interacting partners [39]. As for the tissue expression specificity, we first obtained the gene expression atlas across 79 human tissues measured by Su et al. [40] (GEO accession number: GDS590). For each gene, the tissue expression specificity was measured according to the state-of-the-art τ method which was described in the previous studies [32], [33]. The conversion of gene symbols and RefSeq IDs to Entrez gene ID was performed according to the ID mapping file retrieved from the Ensembl database. All statistical analysis was performed in R (https://www.r-project.org/).

Signaling network analysis

The most recent human signaling network was downloaded from the Wang lab database (http://www.cancer-systemsbiology.org/) [27]. The node centrality analysis was performed using the igraph package in R. The relative level in the signaling network was calculated as the shortest distance to any upstream receptor divided by the sum of the shortest distance to any upstream receptor and the shortest distance to any downstream effector (e.g., transcriptional factors). Therefore, higher relative level indicates that the gene is located at the downstream of signaling network. The shortest distance between two genes was also calculated using igraph package with the edge direction constraint. The common network motifs in the signaling network were defined in previous work [26]. The total occurrence of one gene in a specific network motif was summarized using an in-house Perl script. We also randomly re-sampled equal number of genes in the signaling network to that of the m⁶Afreq genes or m⁶Aocca genes. This random re-sampling procedure was repeated for 10,000 times, which enables us to evaluate whether the enrichment of m⁶Afreq or m⁶Aocca genes for a specific motif can be also observed in randomly picked genes (thus randomly expected) or not. If the observed real occurrence is higher than the random occurrence for more than 9500 out of 10,000 re-sampling trials, the observed over-representation is considered as non-random (i.e., re-sampling test P < 0.05).

Comparison of microRNA targets and functional association

The experimentally-identified miRNA–target interactions were obtained from the miRTarBase (http://mirtarbase.mbc.nctu.edu.tw/) [41]. To reduce false positive results, only miRNA–target interactions supported by at least one piece of strong evidence record or by at least three pieces of weak evidence records were retained. We also examined the co-expressed miRNA–target database according to the mirCoX database [29]. For each miRNA–gene pair, the mirCoX database calculates the percentiles of correlation coefficients on either miRNA side or gene side. Therefore, the geometric mean of these two percentiles, also known as mutual rank [42], could serve as a reasonable measurement of miRNA–gene co-expression to filter the miRTarBase miRNA–target pairs. We assigned miRNA–target pair that has positive correlation coefficient and mutual rank <0.5 to be the positively co-expressed pairs, and those having negative correlation coefficient and mutual rank >0.5 to be the negatively co-expressed pairs.

The functional enrichment (GO biological process) analysis was performed using gProfileR online tool (http://biit.cs.ut.ee/gprofiler) with default parameters and threshold except the unspecific terms that are associated with more than 1000 genes were excluded before analysis [43]. To reduce the redundant terms, we applied “best per parent group” filtration provided by the gProfileR tool to the significantly-enriched terms.

Authors’ contributions

YZ and QC conceived and designed the analysis. QC supervised the study. YZ performed the analysis. YZ wrote the manuscript and QC edited the manuscript. Both authors read and approved the final manuscript.

Competing interests

The authors have declared no competing interests.

Handled by Yi Xing

Supplementary material

Supplementary Figure S1

The correlation between the corrected number of m⁶A regulated conditions and the number of co-expressed targeting microRNAsThe correlation curves between the corrected number of m⁶A regulated conditions and the number of co-expressed targeting microRNAs are plotted using the LOESS smoothing technique. The line indicates the local average estimated by LOESS smoothing and the shade indicates the confidence interval. Outlier genes (0.5%) with extremely high corrected number of m⁶A regulated conditions are omitted due to their high variation in gene feature values, which could result in badly skewed regression lines. A. Correlation with the number of positively co-expressed targeting microRNAs. B. Correlation with the number of negatively co-expressed targeting microRNAs.

Supplementary Figure S2

The correlation between the normalized m⁶A regulation breadth and various gene features in the quantitative m⁶A datasetThe correlation curve is plotted by using the LOESS smoothing techniques. The line indicates the local average estimated by LOESS and the shade indicates the confidence interval. A. Correlation of normalized m⁶A regulation breadth score with dN/dS ratio. The normalized m⁶A regulation breadth score of one gene summarizes the m⁶A peak scores of the gene across 38 conditions, calculated similarly as for the tissue expression specificity (see Materials & Methods for details). B. Correlation of normalized m⁶A regulation breadth score with tissue expression specificity. C. Correlation of normalized m⁶A regulation breadth score with PPI network degree. D. Correlation of normalized m⁶A regulation breadth score with relative level in signaling network. E. Correlation of normalized m⁶A regulation breadth score with number of targeting microRNAs. F. The summary of Spearman’s correlation coefficient and P values corresponding to the panels A−E. PPI, protein–protein interaction.

Supplementary Figure S3

Boxplots for the comparison of various gene features between m⁶Anone genes, m⁶Aocca genes, and m⁶Afreq genesA. Comparison of dN/dS ratio. B. Comparison of tissue expression specificity. C. Comparison of PPI network degree. Eight proteins with extremely high degree (>800) are considered as outliners and thus not shown in the plot. D. Comparison of number of targeting microRNAs. E. Comparison of the relative level in the signaling network. F. The summary of Wilcoxon’s test P values corresponding to the panels A−E.

Supplementary Table S1

Information about the 38 conditions covered by the comprehensive m⁶A dataset.

Supplementary Table S2

Top 20 enriched functional terms for m⁶Afreq genes.

Supplementary Table S3

Top 20 enriched functional terms for m⁶Aocca genes.