ADAR1 is required for differentiation and neural induction by regulating microRNA processing in a catalytically independent manner

Abstract

Adenosine deaminases acting on RNA (ADARs) are involved in adenosine-to-inosine RNA editing and are implicated in development and diseases. Here we observed that ADAR1 deficiency in human embryonic stem cells (hESCs) significantly affected hESC differentiation and neural induction with widespread changes in mRNA and miRNA expression, including upregulation of self-renewal-related miRNAs, such as miR302s. Global editing analyses revealed that ADAR1 editing activity contributes little to the altered miRNA/mRNA expression in ADAR1-deficient hESCs upon neural induction. Genome-wide iCLIP studies identified that ADAR1 binds directly to pri-miRNAs to interfere with miRNA processing by acting as an RNA-binding protein. Importantly, aberrant expression of miRNAs and phenotypes observed in ADAR1-depleted hESCs upon neural differentiation could be reversed by an enzymatically inactive ADAR1 mutant, but not by the RNA-binding-null ADAR1 mutant. These findings reveal that ADAR1, but not its editing activity, is critical for hESC differentiation and neural induction by regulating miRNA biogenesis via direct RNA interaction.

A-to-I editing of coding and non-coding RNAs by ADARs

“…Expression of miRNAs is indeed altered in Adar2 -null mouse embryos, most probably through an editing-independent mechanism 120 . ADAR1 also suppresses the expression of many miRNAs, including the stem cell self-renewal-promoting miR-302 family of miRNAs, in an RNA editing-independent manner, which is essential for neural differentiation of human ES cells 121 . Editing-independent suppression of miR-222 expression by ADAR1 and the consequent upregulation of ICAM1, and the relevance of this to melanoma immune resistance, have also been reported 122 .…”

MicroRNAs in neural development: from master regulators to fine-tuners

“…(2) Regulation of pri-miRNA processing and stability. Examples include amyloid precursor protein (APP), which inhibits miR-547 expression in the developing cerebral cortex by inducing pri-miR-547 degradation ; ADAR1, which blocks pri-miR-302 processing (Chen et al, 2015); and MeCP2, which interferes with the processing of several neuronal miRNAs (e.g. miR-134, miR-383) by sequestering the microprocessor co-factor Dgcr8 (Cheng et al, 2014).…”

Regulation of circRNA biogenesis

“…Whereas, with the reduced level of A-to-I editing after ADAR1 knockdown, RNA pairing across flanking introns is more stable and favors backsplicing for circRNA production. 23 Notably, ADAR1 was recently shown to act as a dsRNA binding protein to interfere with microRNA processing, 36 thus it is also possible that ADAR1 may regulate circRNA formation directly through its dsRNA binding activity, independent of RNA editing. As there are hundreds (and maybe thousands) of RNA binding proteins, 37 it will be of interest to identify additional trans-factors involved in circRNA formation.…”