The APT complex is involved in non-coding RNA transcription and is distinct from CPF.

Michael Lidschreiber,Sofia Battaglia,Manuel Carminati,Juan B Rodríguez-Molina,Pawel Grzechnik,Lori A Passmore,Ashley D Easter,Carlo Baejen,Kerstin C Maier,Patrick Cramer,Ana Casañal

doi:10.1093/nar/gky845

Abstract

The 3′-ends of eukaryotic pre-mRNAs are processed in the nucleus by a large multiprotein complex, the cleavage and polyadenylation factor (CPF). CPF cleaves RNA, adds a poly(A) tail and signals transcription termination. CPF harbors four enzymatic activities essential for these processes, but how these are coordinated remains poorly understood. Several subunits of CPF, including two protein phosphatases, are also found in the related ‘associated with Pta1′ (APT) complex, but the relationship between CPF and APT is unclear. Here, we show that the APT complex is physically distinct from CPF. The 21 kDa Syc1 protein is associated only with APT, and not with CPF, and is therefore the defining subunit of APT. Using ChIP-seq, PAR-CLIP and RNA-seq, we show that Syc1/APT has distinct, but possibly overlapping, functions from those of CPF. Syc1/APT plays a more important role in sn/snoRNA production whereas CPF processes the 3′-ends of protein-coding pre-mRNAs. These results define distinct protein machineries for synthesis of mature eukaryotic protein-coding and non-coding RNAs.

Highlights

RNA polymerase II (Pol II) synthesizes protein-coding mRNAs as well as a number of non-coding RNAs including snoRNAs, snRNAs, lncRNAs and miRNAs
The intact associated with Pta1’ (APT) complex migrated as a peak on a gel filtration column with a second trailing peak consisting of a subcomplex of Pta1, Pti1, Ssu72 and Syc1
We show that yeast contains distinct cleavage and polyadenylation factor (CPF) and APT complexes

Summary

Introduction

RNA polymerase II (Pol II) synthesizes protein-coding mRNAs as well as a number of non-coding RNAs including snoRNAs, snRNAs, lncRNAs and miRNAs. Pol II requires additional proteins for transcription including initiation, elongation and termination factors, as well as proteins involved in processing of the nascent RNA transcript. Pol II requires additional proteins for transcription including initiation, elongation and termination factors, as well as proteins involved in processing of the nascent RNA transcript One of these is the Cleavage and Polyadenylation Factor (CPF in yeast, or CPSF in higher eukaryotes), which carries out 3 -end processing of mRNAs [1,2]. The enzymatic activities of CPF––endonuclease, polymerase and phosphatase––must be tightly coupled to transcription and to each other to ensure that the pre-mRNA is cleaved only once, the poly(A) tail is synthesized to an appropriate length before mRNA is exported from the nucleus, and transcription termination occurs in a timely manner

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Conclusion