Nucleolin-Mediated Stabilization of Human β-Globin mRNA.
Authors: Russell J. Eric , Xu Xiang-Sheng , Jiang Yong 
Published: April 2020

The normal expression of human β globin is critically dependent upon the high stability of its encoding mRNA. The mechanism that protects β-globin mRNA from premature degradation--including the positions of cis-acting stability determinants, the identities of relevant trans-acting factors, and the processes through which they interact--are poorly understood. We have designed and executed a series of experiments that detail the critical importance of the 3′UTR to the high constitutive stability of β-globin mRNA. To identify mRNA-stability determinants in this region, we constructed a wild-type β-globin gene (βWT), as well as 17 derivative genes containing site-specific 3′UTR hexanucleotide substitutions (βMUT1-βMUT17), each under the transcriptional control of a tetracycline-response element (TRE). In cultured cells that express a corresponding transcriptional transactivator, the expression of TRE-linked βWT and βMUT genes can be rapidly silenced by adding tetracycline to the culture medium, permitting the stabilities of the cognate mRNAs to be established using a transcriptional chase approach. Two of the 17 mRNAs, carrying adjacent hexanucleotide substitutions (βMUT12 and βMUT13), were destabilized in intact HeLa cells, identifying a sequence that is critical to β-globin mRNA stability. Three potentially important trans-acting factors that bind to this region were subsequently isolated using an in vitro affinity-enrichment method. One of the proteins was unequivocally identified by mass spec analysis to be nucleolin, a ubiquitous nuclear-cytoplasmic factor that exhibits RNA helicase activity and is reported to stabilize several non-erythroid mRNAs. A link between this factor and β-globin mRNA stability was provided by in vitro studies demonstrating that purified nucleolin binds tightly to the βWT 3′UTR but poorly to both βMUT12 and βMUT13 3′UTRs. This result was validated by RNA-immunoprecipitation (RIP) analyses confirming a strong interaction between nucleolin and βWT mRNA in intact cells that is fully ablated by MUT12 or MUT13 hexanucleotide substitutions. The critical importance of nucleolin binding to the stability of β-globin mRNA may relate to a stem-and-loop motif within its 3′UTR that is predicted by mRNA-folding algorithms. This structure contains the nucleolin-binding site on its right half-stem, opposite a putative binding site for αCP, a 34 kDa factor that stabilizes α-globin mRNA, on the left half-stem. Surprisingly, recombinant αCP displays a low affinity for the full-length β-globin 3′UTR, while binding avidly to the isolated left half-stem as well as to full-length β-globin 3′UTRs that contain stem-disrupting mutations. These results indicate that high-order structures within the β-globin 3′UTR, if permitted to form, may interfere with αCP function in vivo. Based upon our studies, we suggest that nucleolin binding is required to relax a highly stable stem-and-loop motif within the β-globin 3′UTR, exposing a functional binding site for the mRNA-stabilizing factor αCP. Thus, we identify a cis-element and a specific trans-acting factor that participate in stabilizing β-globin mRNA, and suggest a mechanism through which they are likely to act in vivo. The full elucidation of this process will clearly benefit the design of therapeutic transgenes for individuals with β-globin gene defects, and may additionally facilitate the conception of novel therapies intended to differentially regulate the stabilities of βS- and γ-globin mRNAs in individuals with sickle cell disease.