Antagonistic actions of two human Pan3 isoforms on global mRNA turnover

Abstract

Deadenylation is a fundamental process that regulates eukaryotic gene expression. Mammalian deadenylation exhibits biphasic kinetics, with the Pan2-Pan3 and Ccr4-Caf1 deadenylase complexes mediating the first and second phase, respectively; however, the significance of the biphasic nature of deadenylation in mRNA turnover remains unclear. In this study, we discovered that two distinct isoforms of human Pan3 display opposing properties necessary for coordinating the two phases of deadenylation. The shorter isoform (Pan3S) interacts more strongly with PABP than the longer isoform (Pan3L) does. Pan2 deadenylase activity is enhanced by Pan3S but suppressed by Pan3L. Knocking down individual Pan3 isoforms has opposing effects on the global poly(A) tail length profile, P-body formation, and different mRNA decay pathways. Transcriptome-wide analysis of Pan3 knockdown effects on mRNA turnover shows that depleting either Pan3 isoform causes profound and extensive changes in mRNA stability globally. These results reveal a new fundamental step governing mammalian mRNA metabolism. We propose that the first phase of deadenylation, coordinated through the interplay among the two Pan3 isoforms, Pan2, and PABP, represents a cytoplasmic mRNA maturation step important for proper mRNA turnover.

Single molecule poly(A) tail-seq shows LARP4 opposes deadenylation throughout mRNA lifespan with most impact on short tails

“…The Caf1 subunit of CNOT can deadenylate unprotected poly(A) but the Ccr4 subunit is required to dislodge or peel off PABP ( Webster et al, 2018 ; Yi et al, 2018 ). These and other findings help explain some aspects of irregular deadenylation noted during mRNA decay ( Chen et al, 2017 ; Webster et al, 2018 ; Yamashita et al, 2005 ; Yi et al, 2018 ).…”

“…PABP promotes PAT shortening by recruiting the PAM2-containing proteins, PAN3, Tob1, Tob2, GW182 and their associated deadenylases (reviewed in Xie et al, 2014 ). The PAN2–PAN3 and CCR4–NOT (CNOT) complexes employ multiple deadenylases that can act during different phases of PAT shortening and are activated or blocked by PABP in ways that yield complex mRNA decay patterns reflective of varying deadenylation rates ( Chen et al, 2017 ; Webster et al, 2018 ; Yamashita et al, 2005 ; Yi et al, 2018 ). In addition, deadenylases can be actively recruited in response to different cues, for example, involving AU-rich element binding proteins or miRNA-mediated mRNA decay factors ( Fabian et al, 2009 ; Huntzinger et al, 2013 ).…”

Handshakes and Fights: The Regulatory Interplay of RNA-Binding Proteins

“…Two PAN3 isoforms, PAN3S and PAN3L, compete for PABPC1 to regulate deadenylation with opposite effects. Their interaction sees PAN3S enhancing deadenylation and PAN3L repressing it (Chen et al, 2017 ).…”

PABP Cooperates with the CCR4-NOT Complex to Promote mRNA Deadenylation and Block Precocious Decay

“…Our current knowledge on deadenylation was primarily inferred from studies using artificial reporter systems, a few representative genes, or bulk poly(A) measurements. Genome-wide analyses defining deadenylase targets relied upon indirect RNA quantification by RNA sequencing (RNA-seq) or microarray (Aslam et al, 2009;Chen et al, 2017;Eulalio et al, 2009;Lee et al, 2012;Mittal et al, 2011). Direct measurement of poly(A) tail length has been technically challenging and has not previously been applied to deadenylation studies; thus, many critical questions remain unanswered despite the central importance of deadenylation in gene regulation.…”