PolyASite
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Alternative cleavage and polyadenylation (APA) of RNAs gives rise to isoforms with different terminal exons, which in turn determine the fate of the RNA and the encoded protein. APA has thus been implicated in the regulation of cell proliferation, differentiation and disease development. PolyASite is a portal to the curated set of poly(A) sites inferred from publicly available 3’ end sequencing datasets. It allows efficient finding, exploration and export of poly(A) sites in several organisms. In constructing our poly(A) site atlas, we applied uniform quality measures, including the flagging of putative internal priming sites, to input datasets originating from different 3’ end sequencing techniques, cell types or tissues. Through integrated processing of all data, we identified and clustered sites that are closely spaced and share polyadenylation signals, as these are likely the result of stochastic variations in processing. For each cluster, we identified the representative - most frequently processed - site and estimated the relative use in the transcriptome across all samples. While other existing alternative polyadenylation databases rely on a single experimental method, or on poly(A) site estimation from RNA-seq data, PolyASite is built on data from several 3’ end sequencing techniques. This allows a broader coverage of cell types and poly(A) sites to support further genomics studies.
可变切割与多聚腺苷酸化（Alternative cleavage and polyadenylation, APA）可产生携带不同末端外显子的转录本异构体，进而决定RNA分子及其编码蛋白的命运。APA已被证实参与调控细胞增殖、分化及疾病发生发展过程。 PolyASite是一个数据平台，集成了从公开可用的3'端测序数据集推导得到的经人工整理的多聚腺苷酸化位点（poly(A) sites）集合。该平台支持在多个物种中高效检索、探索并导出多聚(A)位点。 在构建本研究的多聚(A)位点图谱时，我们对源自不同3'端测序技术、细胞类型或组织的输入数据集采用了统一的质量控制标准，其中包括对潜在内部引发位点（internal priming sites）的标记。 通过对所有数据的整合处理，我们对间距紧密且共享多聚腺苷酸化信号的位点进行了识别与聚类——这类位点大概率是转录加工过程中随机变异的产物。针对每个聚类，我们确定了其代表性位点（即加工频率最高的位点），并估算了该位点在所有样本转录组中的相对使用占比。 现有其他可变多聚腺苷酸化数据库要么仅依赖单一实验方法，要么仅基于RNA-seq数据进行多聚(A)位点估算，而PolyASite则整合了多种3'端测序技术产生的数据集。 这使得该平台能够覆盖更广泛的细胞类型与多聚(A)位点，从而为后续基因组学研究提供强有力的支撑。
