Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1

Abstract

Human hnRNP A2/B1 is an RNA-binding protein that plays important roles in many biological processes, including maturation, transport, and metabolism of mRNA, and gene regulation of long noncoding RNAs. hnRNP A2/B1 was reported to control the microRNAs sorting to exosomes and promote primary microRNA processing as a potential m6A “reader.” hnRNP A2/B1 contains two RNA recognition motifs that provide sequence-specific recognition of RNA substrates. Here, we determine crystal structures of tandem RRM domains of hnRNP A2/B1 in complex with various RNA substrates, elucidating specific recognitions of AGG and UAG motifs by RRM1 and RRM2 domains, respectively. Further structural and biochemical results demonstrate multivariant binding modes for sequence-diversified RNA substrates, supporting a RNA matchmaker mechanism in hnRNP A2/B1 function. Moreover, our studies in combination with bioinformatic analysis suggest that hnRNP A2/B1 may mediate effects of m6A through a “m6A switch” mechanism, instead of acting as a direct “reader” of m6A modification.

The Emerging Roles of RNA Modifications in Glioblastoma

“…During nuclear RNA processing period, hnRNPC and hnRNPA2B1 are other types of m 6 A readers that can bind to unfolded RNA through an m 6 A structural switch mechanism, since the m 6 A marked RNA cannot efficiently form secondary structures because the base pairing of m 6 A-U is weaker of than that of A-U [105,106]. A study on the SOX2 protein-protein interactome reveals that hnRNPC and hnRNPA2B1 can interact with SOX2 in GBM [107], suggesting that they may play key roles in maintaining the stemness of GSCs.…”

m6A-binding proteins: the emerging crucial performers in epigenetics

“…Besides, there are members of HNRNP family who have the potential to identify the m 6 A modification of mRNAs, including heterogeneous nuclear ribonucleoproteins A2/B1 (HNRNPA2B1), heterogeneous nuclear ribonucleoproteins C (HNRNPC) and heterogeneous nuclear ribonucleoproteins G (HNRNPG). The binding of HNRNP proteins to m 6 A sites can be enhanced via the mRNAs structural alteration induced by m 6 A methylation [31,38,39], which is called as "m 6 A-switch". HNRNPA2B1 is a nuclear m 6 A-binding protein that accelerates the processing of primary miRNAs (pri-miRNAs) through interacting with DGCR8 protein in an m 6 A-dependent manner [27,28].…”

Cross-talk between m6A and m1A regulators, YTHDF2 and ALKBH3 fine-tunes mRNA expression

“…The two potential m1A sites in human and CHO ALKBH3 mRNA are conserved in sequence and location. M1A sites in the 5'UTR have been found to be positively correlated with protein production (16,17) while those in the coding region were not (23,24). We demonstrated that the ALKBH3 mRNA is precipitated by an anti-m1A antibody though is yet to be determined which sites are targets for m1A methylation and their exact roles.…”

“…The m6A readers bind m6A RNA targets to mediate their fate. At present, more than twenty m6A have been identified (1,6,(15)(16)(17), of which, the 5-member YT521-B Homology (YTH) domain-containing protein reader family (YTHDF1-3, YTHDC1, and YTHDC2), which directly bind m6A through the YTH domain, are the most studied (18). Notably, the three cytoplasmic YTHDF members (YHTDF1-3 or DF1-3 for short) have been shown to act in an integrated and coordinated manner in affecting the fate of their shared m6A RNA targets and ultimately protein expression.…”