Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition

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Abstract
At least half of all human pre-mRNAs are subject to alternative 3′ processing that may modulate both the coding capacity of the message and the array of post-transcriptional regulatory elements embedded within the 3′ UTR. Vertebrate poly(A) site selection appears to rely primarily on the binding of CPSF to an A(A/U)UAAA hexamer upstream of the cleavage site and CstF to a downstream GU-rich element. At least one-quarter of all human poly(A) sites, however, lack the A(A/U)UAAA motif. We report that sequence-specific RNA binding of the human 3′ processing factor CFIm can function as a primary determinant of poly(A) site recognition in the absence of the A(A/U)UAAA motif. CFIm is sufficient to direct sequence-specific, A(A/U)UAAA-independent poly(A) addition in vitro through the recruitment of the CPSF subunit hFip1 and poly(A) polymerase to the RNA substrate. ChIP analysis indicates that CFIm is recruited to the transcription unit, along with CPSF and CstF, during the initial stages of transcription, supporting a direct role for CFIm in poly(A) site recognition. The recognition of three distinct sequence elements by CFIm, CPSF, and CstF suggests that vertebrate poly(A) site definition is mechanistically more similar to that of yeast and plants than anticipated.