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Large-scale messenger RNA 3\u2032 end sequencing has revealed that cleavage sites for polyadenylation are presented with microheterogeneity. To date, the conventional determination of polyadenylation site clusters is subjective and arbitrary, leading to inaccurate annotations. Here, we present a weighted density peak clustering method, QuantifyPoly(A), to accurately quantify genome-wide polyadenylation choices. Applying QuantifyPoly(A) on published 3\u2032 end sequencing datasets from both animals and plants, their polyadenylation profiles are reshaped into myriads of novel polyadenylation site clusters. Most of these novel polyadenylation site clusters show significantly dynamic usage across different biological samples or associate with binding sites of trans-acting factors. Upstream sequences of these clusters are enriched with polyadenylation signals UGUA, UAAA and\/or AAUAAA in a species-dependent manner. Polyadenylation site clusters also exhibit species specificity, while plants ones generally show higher microheterogeneity than that of animals. QuantifyPoly(A) is broadly applicable to any types of 3\u2032 end sequencing data and species for accurate quantification and construction of the complex and dynamic polyadenylation landscape and enables us to decode alternative polyadenylation events invisible to conventional methods at a much higher resolution.<\/jats:p>","DOI":"10.1093\/bib\/bbab268","type":"journal-article","created":{"date-parts":[[2021,6,24]],"date-time":"2021-06-24T07:08:33Z","timestamp":1624518513000},"source":"Crossref","is-referenced-by-count":30,"title":["QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4803-2098","authenticated-orcid":false,"given":"Congting","family":"Ye","sequence":"first","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danhui","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenbin","family":"Ye","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University, Xiamen, Fujian 361102, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0356-7785","authenticated-orcid":false,"given":"Xiaohui","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University, Xiamen, Fujian 361102, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guoli","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Automation, Xiamen University, Xiamen, Fujian 361102, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingshun Q","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China"},{"name":"Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juncheng","family":"Lin","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China"},{"name":"FAFU-UCR Joint Center, Horticulture Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,7,13]]},"reference":[{"key":"2021110815074464000_ref1","doi-asserted-by":"crossref","first-page":"2755","DOI":"10.1101\/gad.11.21.2755","article-title":"Mechanism and regulation of mRNA polyadenylation","volume":"11","author":"Colgan","year":"1997","journal-title":"Genes Dev"},{"key":"2021110815074464000_ref2","doi-asserted-by":"crossref","first-page":"2517","DOI":"10.1101\/gad.1378105","article-title":"Eukaryotic mRNA 3\u2032 processing: a common means to different ends","volume":"19","author":"Gilmartin","year":"2005","journal-title":"Genes Dev"},{"key":"2021110815074464000_ref3","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1038\/nrm.2016.116","article-title":"Alternative polyadenylation of mRNA precursors","volume":"18","author":"Tian","year":"2017","journal-title":"Nat Rev Mol Cell 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