Landscape of m6A readouts across multiple cell types [RNA-seq]

ABSTRACT: RNA modification-driven epitranscriptome regulations play important roles on gene expression at the post-transcriptional level. N6-methyladenosine (m6A) modification is one of the most prevalent RNA modification types. As one of the core component of human epitranscriptome, the functional consequences of m6A modification, also known as m6A readouts, have been suggested to cover various aspects including but not limited to the alterations of the stability, alternative splicing or translation efficiency of the modified RNA transcripts. Of note, previous studies have shown the m6A readouts could be diverged between different transcripts and depend on the binding of various RNA-binding protein (RBP) regulators. Our analysis of the public data further suggested the readouts are also cell type-dependent, with the contribution of RBP regulators also varied between different cell type. Therefore, for a comprehensive understanding of the regulatory mechanism of m6A readouts, a multiple cell type profiling of m6A readouts have been performed here. More specifically, the three major aspects of m6A readouts, i.e. alterations of the stability, alterations of alternative splicing and alterations of translation efficiency, were evaluated by the time-series RNA-Seq, ultra-deep RNA-Seq and Ribo-Seq comparing m6A modification enzyme METTL3 knockdown (siMETTL3) with the siControl group, respectively. With those high-throughput sequencing data, the cell type-dependent responses to m6A perturbation were described. Further integrative analysis with the public transcriptome-wide m6A modification site profiles and RBP binding site profiles revealed the potentially important RBP regulators in different context. In all, our analysis provide an informative resource to decipher the landscape of m6A readouts and the underlying complicated post-transcriptional regulatory network.

ORGANISM(S): Homo sapiens

PROVIDER: GSE179870 | GEO | 2026/02/09

REPOSITORIES: GEO