Alternative Polyadenylation Allows Differential Negative Feedback of Human miRNA miR-579 on Its Host Gene ZFR

Abstract

About half of the known miRNA genes are located within protein-coding host genes, and are thus subject to co-transcription. Accumulating data indicate that this coupling may be an intrinsic mechanism to directly regulate the host gene’s expression, constituting a negative feedback loop. Inevitably, the cell requires a yet largely unknown repertoire of methods to regulate this control mechanism. We propose APA as one possible mechanism by which negative feedback of intronic miRNA on their host genes might be regulated. Using in-silico analyses, we found that host genes that contain seed matching sites for their intronic miRNAs yield longer 32UTRs with more polyadenylation sites. Additionally, the distribution of polyadenylation signals differed significantly between these host genes and host genes of miRNAs that do not contain potential miRNA binding sites. We then transferred these in-silico results to a biological example and investigated the relationship between ZFR and its intronic miRNA miR-579 in a U87 cell line model. We found that ZFR is targeted by its intronic miRNA miR-579 and that alternative polyadenylation allows differential targeting. We additionally used bioinformatics analyses and RNA-Seq to evaluate a potential cross-talk between intronic miRNAs and alternative polyadenylation. CPSF2, a gene previously associated with alternative polyadenylation signal recognition, might be linked to intronic miRNA negative feedback by altering polyadenylation signal utilization.

Cleavage and polyadenylation: Ending the message expands gene regulation

“…miR-579 also regulates CPSF2 , creating a negative feedback loop wherein transcription of ZFR results in the production of miR-579, which targets CPSF2, favoring usage of the proximal pA site, which is resistant to regulation by miR-579. 252 Transcription of ZFR to produce miR-579 also regulates CPSF2 in a negative feedback loop. The longer CPSF2 isoform is targeted by miR-579, favoring the usage of the proximal pA site, which is resistant to regulation by miR-579.…”

miR-579-3p controls melanoma progression and resistance to target therapy

“…Recent data strongly correlated loss of MITF expression with drug resistance (46)(47)(48). miR-579-3p is an intronic miR located in intron 11 of the human gene ZFR (Zink-finger recombinase), and it is probably coexpressed with its host gene (49). Interestingly, the ZFR gene is a putative target of MITF because its promoter has MITF consensus binding sites.…”

MiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes

“…Nowadays, in the era of large scale data generation in genomics and transcriptomics, it is essential to have powerful and user-friendly tools to mine the right information, to propose and to test hypotheses regarding the studied model. The special genomic colocalization of most vertebrate miRNAs intragenically is of great relevance and current studies have been revealing that the functional implications of this coupling extend beyond simple feedback regulatory mechanisms but seems to support miRNA evolution ( 2 , 5 , 14 ). This revelation expands the focus of research requiring tools to study intragenic miRNAs and genes in an evolutionary context.…”

“…Recent research suggests evolutionary implications of intragenic miRNA development ( 14 , 15 ), yielding that novel miRNAs seem to benefit from intragenic colocalization by utilizing existing regulatory circuitries of their host genes ( 14 ). Furthermore, increasing evidence highlights the importance of the role of alternative polyadenylation (APA) to characterize the relationship between intragenic miRNAs and their host genes ( 5 , 6 ). These novel discoveries prompted us to develop a major update of the miRIAD database and interface to account for these new aspects of intragenic miRNA–host gene relationship.…”