Structural basis of pre-mRNA recognition by the human cleavage factor Im complex

Delineating the Structural Blueprint of the Pre-mRNA 3′-End Processing Machinery

“…Two UGUA sequences are bound to CFI25 dimers in an antiparallel fashion. The connecting loop RNA, though not included in the structure, is likely stabilized by the CFI68 RRM (125,126). On the basis of the structural data, an RNA looping mechanism directed by CFI has been proposed for poly(A) site selection in APA (126,127), perhaps explaining a correlation between CFI levels and APA observed in several studies (128,129).…”

“…3B). The presence of the RRM causes little structural change to the CFI25 dimer, nor does it affect RNA binding specificity (125,126). Two UGUA sequences are bound to CFI25 dimers in an antiparallel fashion.…”

“…6). In recent years, several complex structures have been determined, such as CFI (125,126), symplekin-Ssu72-RNAP II CTD (153,199), and Rna14-Rna15 (87,91), which substantially facilitated the molecular mapping of protein interconnections. Nevertheless, structural information about protein complexes in the 3= processing machinery is still limited and confined within subcomplexes.…”

Cleavage factor Imis a key regulator of 3′ UTR length

“…We also obtained an additional A-seq sample from a more efficient CF I m 68 knock-down compared with our none of the CF I m components cross-linked efficiently directly to UGUA. The weak crosslinking efficiency of CF I m 59 and CF I m 68 to UGUA may be explained in terms of the mode of interaction of CF I m inferred from recent structural studies, 10,11 that rather suggests that CF I m 25 specifically recognizes UGUA. The reason for the rather weak cross-linking of CF I m 25 to UGUA, however, remains unclear; a possible explanation may be that the substitution of U with 4-thio-U decreases the affinity of interaction between the UGUA sequence and CF I m 25.…”

“…9 The molecular basis of this interaction emerged from recently solved crystal structures of CF I m 25 in complex with the RNA recognition motif (RRM) of CF I m 68. 10,11 Surprisingly, it is the Nudix hydrolase domain of CF I m 25 that specifically recognizes UGUA, whereas CF I m 68 appears to increase the binding affinity of the complex. These structure models further revealed that a CF I m 25 dimer binds two UGUA sequences in an antiparallel manner forcing the looping of the RNA sequence between the UGUA motifs.…”