Identification of DNA motifs that regulate DNA methylation

Mengchi Wang¹, Kai Zhang¹, Vu Ngo¹, Chengyu Liu², Shicai Fan^2,4, John W Whitaker⁵, Yue Chen^2,6, Rizi Ai², Zhao Chen², Jun Wang², Lina Zheng¹, Wei Wang^1,2,3*.
1. Bioinformatics and Systems Biology Graduate Program, 2. Department of Chemistry and Biochemistry, 3. Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA.
4. School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu, China.
5. Department of Genomics, Denovo Biopharma, 10240 Science Center Dr., San Diego, California, USA.
6. School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.

* Correspondence: wei-wang@ucsd.edu

We present here the results for motifs that correlates with methylation modifications.

We have analyzed 34 diverse whole-genome bisulfite sequencing datasets in human (from ROADMAP) and identified 313 motifs tightly associated with locus-specific DNA methylation, among which 92 and 221 are associated with methylation (methylation motifs, or MMs) and unmethylation (Unmethylation motifs or UMs)

Here we show results of 313 motifs compared to both known transcription factors (from HOCOMOCO v11), DNA motifs that regulate histone modification in human (from Ngo. et al 2019), and reported methylation motifs by Lin. et al 2019.

Additional Information:

313 motifs in MEME format: link

313 motifs occurrence sites defined by FIMO: dir

Motifs used in the study "DNA motifs regulating histone modifications in human and mouse" (Ngo. at el 2019): link

Motif-TF occupancy reported in the paper: rawCounts clustering