The APT complex is involved in non-coding RNA transcription and is distinct from CPF [ChIP-seq]

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 the CPF including two protein phosphatases are also found in a related complex, the ‘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 has functions separable from those of CPF. Syc1 plays a role in sn/snoRNA production whereas CPF processes the 3ʹ-ends of protein-coding pre-mRNAs. These results define distinct protein machineries for synthesis of mature eukaryotic protein-coding and non-coding RNAs.真核生物前体mRNA（eukaryotic pre-mRNAs）的3'端在细胞核内由大型多蛋白复合物——剪切与多聚腺苷酸化因子（cleavage and polyadenylation factor, CPF）介导加工。CPF可对RNA进行剪切、添加多聚腺苷酸尾（poly(A) tail），并介导转录终止（transcription termination）信号。该复合物具备上述过程必需的四种酶活性（enzymatic activities），但目前对这些活性的协同调控机制仍不甚明晰。 CPF的多个亚基（subunits）（包含两种蛋白磷酸酶（protein phosphatases））同样存在于另一相关复合物——“与Pta1相关”复合物（associated with Pta1, APT）中，但CPF与APT之间的相互关系仍不明确。 本研究证实，APT复合物在物理层面独立于CPF。分子量为21 kDa的Syc1蛋白仅与APT结合，而不与CPF发生相互作用，因此它是APT复合物的特征性亚基。 通过染色质免疫沉淀测序（ChIP-seq）、光活性核糖核苷交联免疫沉淀（PAR-CLIP）与RNA测序（RNA-seq）实验，我们证实Syc1的功能与CPF相互独立。Syc1参与核小RNA/核仁小RNA（sn/snoRNA）的生成过程，而CPF则负责加工编码蛋白质的前体mRNA（protein-coding pre-mRNAs）的3'端。 上述结果明确了两套截然不同的蛋白质机器，分别参与成熟真核编码蛋白RNA与非编码RNA的合成过程。