Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2021 Jun 22;49(16):e92. doi: 10.1093/nar/gkab485

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

PMC Copyright notice

Figure 5. — m6Aboost predicts 36,556 m⁶A sites from HEK293T miCLIP2 data. (A) Predicted m⁶A sites are located around the stop codon. Visualization as in Figure 2F. (B) Selected m⁶A sites were validated by SELECT with HEK293T cells treated with METTL3 inhibitor (STM2457) or DMSO control. Visualization as in Figure 2H. Neighboring unmodified A nucleotides as control are given in Supplementary Figure S5C. *** P value < 0.001, ** P < 0.01, two-sided Student's t-test, n = 3. (C) Predicted m⁶A sites overlap with YTHDF1 binding sites. Genome browser view of the gene CCDC85B shows crosslink events from published YTHDF1 iCLIP data for HEK293T together with miCLIP2 signal (merge of four replicates) and m6Aboost-predicted m⁶A site (green arrowhead) from our HEK293T miCLIP2 data. (D) YTHDF1 precisely binds at the predicted m⁶A sites. Percentage of m⁶A sites (position 0) with YTHDF1 binding sites (y-axis) in a 21-nt window are given for predicted m⁶A sites at DRACH (yellow) and non-DRACH (green), as well as predicted unmodified sites (grey). (E) Predicted m⁶A sites from HEK293T miCLIP2 overlap with published m⁶A data. Venn diagram shows single-nucleotide overlap with miCLIP and m6ACE-seq data (m⁶A antibody by Synaptic Systems and Abcam, respectively). Note that m⁶A sites in Boulias et al., 2019 had been filtered for DRACH motifs. (F, G) Analysis of m⁶A sites that are unique to one of the three datasets compared in (E). (F) Unique m⁶A sites accumulate around stop codons. Visualization as in Figure 2F. (G) Unique m⁶A sites are enriched in YTHDF1 binding sites. Visualization as in (D). (H) Most m⁶A sites are shared between two different human cell lines. Venn diagram shows overlap of predicted m⁶A sites in expressed genes (TPM ≥ 20, n = 3,298) from HEK293T and C643 cells. A Venn diagram without expression filter is shown in Supplementary Figure S5E. (I) More m⁶A sites are shared between two human cell lines in higher expressed genes. TPM threshold representing the gene expression (x-axis) against the Jaccard index (y-axis). Numbers of overlapping m⁶A sites are shown as comparison (blue).