Mutation in cpsf6/CFIm68 (Cleavage and Polyadenylation Specificity Factor Subunit 6) causes short 3'UTRs and disturbs gene expression in developing embryos, as revealed by an analysis of primordial germ cell migration using the medaka mutant naruto

Abstract

Our previous studies analyzing medaka mutants defective in primordial germ cell (PGC) migration identified cxcr4b and cxcr7, which are both receptors of the chemokine sdf1/cxcl12, as key regulators of PGC migration. Among PGC migration mutants, naruto (nar) is unique in that the mutant phenotype includes gross morphological abnormalities of embryos, suggesting that the mutation affects a broader range of processes. A fine genetic linkage mapping and genome sequencing showed the nar gene encodes Cleavage and Polyadenylation Specificity Factor subunit 6 (CPSF6/CFIm68). CPSF6 is a component of the Cleavage Factor Im complex (CFIm) which plays a key role in pre-mRNA 3'-cleavage and polyadenylation. 3'RACE of sdf1a/b and cxcr7 transcripts in the mutant embryos indicated shorter 3’UTRs with poly A additions occurring at more upstream positions than wild-type embryos, suggesting CPSF6 functions to prevent premature 3’UTR cleavage. In addition, expression of the coding region sequences of sdf1a/b in nar mutants was more anteriorly extended in somites than wild-type embryos, accounting for the abnormally extended distribution of PGCs in nar mutants. An expected consequence of shortening 3'UTR is the escape from the degradation mechanism mediated by microRNAs interacting with distal 3’UTR sequence. The abnormal expression pattern of sdf1a coding sequence may be at least partially accounted for by this mechanism. Given the pleiotropic effects of nar mutation, further analysis using the nar mutant will reveal processes in which CPSF6 plays essential regulatory roles in poly A site selection and involvement of 3'UTRs in posttranscriptional gene regulation in various genes in vivo.

Reconstitution of 3’-processing of mammalian pre-mRNA reveals a central role of RBBP6

“…Both observations suggest that CF I selectively participates in the processing of some RNAs but not others. This is consistent with the prominent role of the protein in alternative polyadenylation (Gruber and Zavolan, 2019): Reduced expression of CF I had a much stronger effect on alternative polyadenylation than the depletion of any other individual 3’ processing factor and consistently caused pronounced shifts to the use of proximal (upstream) polyadenylation sites in many genes (Alcott et al, 2020; Kim et al, 2010; Kubo et al, 2006; Li et al, 2015; Martin et al, 2012; Masamha et al, 2014; Sasado et al, 2017; Zhu et al, 2018). The CF I binding motif, UGUA, was enriched in distal sites neglected and depleted in proximal sites favored upon knock-down, consistent with preferred cross-linking of CF I to distal sites (Li et al, 2015; Martin et al, 2012; Zhu et al, 2018).…”

Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development

“…Interestingly, knockdown of Cpsf6 induces widespread use of proximal PAS, resulting in 3’ UTR shortening [ 70 , 71 ]. Moreover, a mutation in the Medaka Cpsf6 gene causes 3’ UTR shortening in developing embryos and a defect in primordial germ cell migration [ 72 ].…”

The 8p11 myeloproliferative syndrome: Genotypic and phenotypic classification and targeted therapy

“…Cleavage and polyadenylation specificity factor 6, also called CPSF6, is a member of the CFIm (Cleavage Factor Im complex), which plays a key role in the 3’cleavage and polyadenylation of pre-mRNA ( 36 , 37 ). It is also involved in the selection of poly-A sites for multiple genes and in the regulation of the 3’UTR ( 36 , 37 ). The CPSF6-FGFR1 fusion consists of exon 8 of CPSF6 fused to exon 9 of FGFR1 in-frame, and its breakpoint is in intron 8 of CPSF6 ( 35 ).…”