MethMotif.Org 2024: a database integrating context-specific transcription factor-binding motifs with DNA methylation patterns

Abstract

MethMotif (https://methmotif.org) is a publicly available database that provides a comprehensive repository of transcription factor (TF)-binding profiles, enriched with DNA methylation patterns. In this release, we have enhanced the platform, expanding our initial collection to over 700 position weight matrices (PWM), all of which include DNA methylation profiles. One of the key advancements in this release is the segregation of TF-binding motifs based on their cofactors and DNA methylation status. We have previously demonstrated that gene ontology (GO) enriched terms associated with TF target genes may differ based on their association with alternative cofactors and DNA methylation status. MethMotif provides precomputed GO annotations for each human TF of interest, as well as for TF-co-TF complexes, enabling a comprehensive analysis of TF functions in the context of their co-factors. Additionally, MethMotif has been updated to encompass data for two new species, Mus musculus and Arabidopsis thaliana, widening its applicability to a broader community. MethMotif stands out as the first and only TF-binding motifs database to incorporate context-specific PWM coupled with epigenetic information, thereby enlightening context-specific TF functions. This enhancement allows the community to explore and gain deeper insights into the regulatory mechanisms governing transcriptional processes.

Graphical Abstract

Figure 1.

Updated MethMotif card. The MethMotif card consists of distinct panels that provide a comprehensive overview of TF-binding motifs, offering various insights into TF-binding motif characteristics to cater to diverse research needs. The novel panels introduced in MethMotif 2024 are emphasized with a red-dashed box. (A) The main MethMotif logo panel displays the TF cell-specific motif with the corresponding DNA methylation profile (MethMotif). (B) The cell line information panel offers exhaustive details about the cell, including species, sex, life stage, age, cell line, health and references. (C) The TF panel presents TF classifications, general attributes, expression levels and external database links. (D) The motif Information panel provides information about the origin of the ChIP-seq dataset, download date, peak counts, sequence counts used for motif generation, motif locations, and options for visualizing, opening, and downloading motif matrices in MEME and TRANSFAC formats, as well as a beta score matrix for DNA methylation profiles. (E) The pioneer factor information panel is dedicated to pioneer TF features and classifications and includes links to references about the pioneer features of the selected TF. (F) The co-factors information Panel offers an interactive heatmap of encompassing the main TF co-factors, with a color gradient proportional to the percentage of TF-co-TF co-binding (right). Clicking on a co-TF of interest displays the TF-co-TF co-binding MethMotif logo (an example of FOSL2 as a co-factor is shown on the left). A report of the TF-co-TF list can be downloaded from this panel.

Figure 2.

Example of context-specific TFBS query with MethMotif 2024, focusing on EGR2 and its co-factors in HEK293 cell line. (A) The heatmap shows the percentage of highly methylated (≥90%), moderately methylated (>10% and <90%), and not methylated (≤10%) CG sites in the TF-cofactor motif and surrounding area. Each row illustrates a TF-cofactor pair, each column displays a methylation status range, and color intensity represents a CG percentage within a given location and partner pair. Boxplots display ChIP-seq read enrichment scores in the co-binding peaks for EGR2 and its partners. The co-binding percentage is further displayed as a heatmap and the corresponding paired TF-cofactor motif logo is provided. (B) EGR2 MethMotif logos build on all ChIP-seq peaks (left) and in the presence of SP2 ChIP-seq peaks (right). Stacked bars above the motif logo describe CG sites methylation status. The blue, green and orange colors correspond to low, moderate and high methylation level, respectively. (C) Pie charts categorize the genomic locations of EGR2 (left) and EGR2-SP2 (right) ChIP-seq peaks, following an order starting from promoter/transcription start sites (TSS), transcription termination sites (TTS), 5′ untranslated region (UTR) exons, 3′ UTR exons, introns and intergenic regions. (D) Listing of the main enriched GO terms associated with the genes targeted by EGR2 (left) and EGR2-SP2 (right).

Figure 3.

A/symmetric MethMotif logo designed for plants’ TFs. (A) CG-context symmetric MethMotif logo displaying MAF1-binding motif and the corresponding CG methylation status in a strand-specific manner. (B) MethMotif logos for MAF1 symmetric CHG- and asymmetric CHH-contexts. CHG and CHH distribution scores are represented by strand-specific boxplots.