title: Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation.
abstract: Alternative polyadenylation (APA) is a widespread mechanism for gene regulation and has been implicated in flowering, but the molecular basis governing the choice of a specific poly(A) site during the vegetative-to-reproductive growth transition remains unclear. Here we characterize HLP1, an hnRNP A/B protein as a novel regulator for pre-mRNA 3'-end processing in Arabidopsis. Genetic analysis reveals that HLP1 suppresses Flowering Locus C (FLC), a key repressor of flowering in Arabidopsis. Genome-wide mapping of HLP1-RNA interactions indicates that HLP1 binds preferentially to A-rich and U-rich elements around cleavage and polyadenylation sites, implicating its role in 3'-end formation. We show HLP1 is significantly enriched at transcripts involved in RNA metabolism and flowering. Comprehensive profiling of the poly(A) site usage reveals that HLP1 mutations cause thousands of poly(A) site shifts. A distal-to-proximal poly(A) site shift in the flowering regulator FCA, a direct target of HLP1, leads to upregulation of FLC and delayed flowering. Our results elucidate that HLP1 is a novel factor involved in 3'-end processing and controls reproductive timing via targeting APA.
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Lianfeng
authors.initials: L
authors.lastname: Gu
authors.affiliation: State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China.
authors.forename: Yifeng
authors.initials: Y
authors.lastname: Hou
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Lulu
authors.initials: L
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Xian
authors.initials: X
authors.lastname: Deng
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Runlai
authors.initials: R
authors.lastname: Hang
authors.affiliation: Center for Genome Analysis, ABLife Inc., Novonest Building, 8 Nanhu Avenue, East Lake Hi-Tech Development Zone, Wuhan, Hubei 430064, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China.
authors.forename: Xiansheng
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Center for Genome Analysis, ABLife Inc., Novonest Building, 8 Nanhu Avenue, East Lake Hi-Tech Development Zone, Wuhan, Hubei 430064, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Chunyan
authors.initials: C
authors.lastname: Liu
authors.affiliation: 1] State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China [2] Collaborative Innovation Center of Genetics and Development, Shanghai 200433, China.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Cao
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism*; D035264:Flowers / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D009154:Mutation / Q000235:genetics*; D026723:Polyadenylation / Q000235:genetics*; D012322:RNA Precursors / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism*; D039221:mRNA Cleavage and Polyadenylation Factors / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; C000608023:HLP1 protein, Arabidopsis; D012322:RNA Precursors; D016601:RNA-Binding Proteins; D039221:mRNA Cleavage and Polyadenylation Factors