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RNA alternative polyadenylation contributes to the complexity of information transfer from genome to phenome, thus amplifying gene function. Here, we report the first X. tropicalis resource with 127,914 alternative polyadenylation (APA) sites derived from embryos and adults. Overall, APA networks play central roles in coordinating the maternal-zygotic transition (MZT) in embryos, sexual dimorphism in adults and longitudinal growth from embryos to adults. APA sites coordinate reprogramming in embryos before the MZT, but developmental events after the MZT due to zygotic genome activation. The APA transcriptomes of young adults are more variable than growing adults and male frog APA transcriptomes are more divergent than females. The APA profiles of young females were similar to embryos before the MZT. Enriched pathways in developing embryos were distinct across the MZT and noticeably segregated from adults. Briefly, our results suggest that the minimal functional units in genomes are alternative transcripts as opposed to genes.
R21 HD076845 National Institute of Child Health and Human Development, 2016-67015-24470 National Institute of Food and Agriculture, 61573296 National Natural Science Foundation of China, 61673323 National Natural Science Foundation of China, R21 HD076845 NICHD NIH HHS
Anders,
Differential expression analysis for sequence count data.
2010, Pubmed
Anders,
Differential expression analysis for sequence count data.
2010,
Pubmed Andres,
Comparative analysis of the cDNA sequences derived from the larval and the adult alpha 1-globin mRNAs of Xenopus laevis.
1984,
Pubmed
,
Xenbase Anquetil,
Polypyrimidine tract binding protein prevents activity of an intronic regulatory element that promotes usage of a composite 3'-terminal exon.
2009,
Pubmed
,
Xenbase Artieri,
Transcript length mediates developmental timing of gene expression across Drosophila.
2014,
Pubmed Banville,
Developmental changes in the pattern of larval beta-globin gene expression in Xenopus laevis. Identification of two early larval beta-globin mRNA sequences.
1985,
Pubmed
,
Xenbase Biedler,
Identification of early zygotic genes in the yellow fever mosquito Aedes aegypti and discovery of a motif involved in early zygotic genome activation.
2012,
Pubmed Derti,
A quantitative atlas of polyadenylation in five mammals.
2012,
Pubmed Fierro,
Exploring nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis.
2007,
Pubmed
,
Xenbase Guilgur,
Requirement for highly efficient pre-mRNA splicing during Drosophila early embryonic development.
2014,
Pubmed Hake,
CPEB is a specificity factor that mediates cytoplasmic polyadenylation during Xenopus oocyte maturation.
1994,
Pubmed
,
Xenbase Harland,
Xenopus research: metamorphosed by genetics and genomics.
2011,
Pubmed
,
Xenbase Hellsten,
The genome of the Western clawed frog Xenopus tropicalis.
2010,
Pubmed
,
Xenbase Jan,
Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs.
2011,
Pubmed Jiang,
Whole transcriptome analysis with sequencing: methods, challenges and potential solutions.
2015,
Pubmed Joos,
Integrin alpha 5 during early development of Xenopus laevis.
1995,
Pubmed
,
Xenbase Klein,
Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative.
2002,
Pubmed
,
Xenbase Kühl,
XB/U-cadherin mRNA contains cytoplasmic polyadenylation elements and is polyadenylated during oocyte maturation in Xenopus laevis.
1995,
Pubmed
,
Xenbase Langley,
New insights into the maternal to zygotic transition.
2014,
Pubmed
,
Xenbase Lee,
Zygotic genome activation during the maternal-to-zygotic transition.
2014,
Pubmed
,
Xenbase Ma,
Role of alternative polyadenylation in epigenetic silencing and antisilencing.
2014,
Pubmed Mason,
Polyadenylation of the Xenopus beta 1 globin mRNA at a downstream minor site in the absence of the major site and utilization of an AAUACA polyadenylation signal.
1985,
Pubmed
,
Xenbase Mason,
Mutations downstream of the polyadenylation site of a Xenopus beta-globin mRNA affect the position but not the efficiency of 3' processing.
1986,
Pubmed
,
Xenbase Matoulkova,
The role of the 3' untranslated region in post-transcriptional regulation of protein expression in mammalian cells.
2012,
Pubmed Morin,
Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling.
2006,
Pubmed
,
Xenbase Nunes,
A functional human Poly(A) site requires only a potent DSE and an A-rich upstream sequence.
2010,
Pubmed Onichtchouk,
Regulation of Zygotic Genome and Cellular Pluripotency.
2015,
Pubmed Owens,
Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development.
2016,
Pubmed
,
Xenbase Paris,
Maturation-specific polyadenylation and translational control: diversity of cytoplasmic polyadenylation elements, influence of poly(A) tail size, and formation of stable polyadenylation complexes.
1990,
Pubmed
,
Xenbase Plant,
Genes encoding isoforms of transcription elongation factor TFIIS in Xenopus and the use of multiple unusual RNA processing signals.
1996,
Pubmed
,
Xenbase Plessy,
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.
2010,
Pubmed Rabbitts,
Alternative 3' processing of Xenopus alpha-tubulin mRNAs; efficient use of a CAUAAA polyadenylation signal.
1992,
Pubmed
,
Xenbase Retelska,
Similarities and differences of polyadenylation signals in human and fly.
2006,
Pubmed Shi,
Alternative polyadenylation: new insights from global analyses.
2012,
Pubmed Tadros,
The maternal-to-zygotic transition: a play in two acts.
2009,
Pubmed Tian,
Alternative cleavage and polyadenylation: the long and short of it.
2013,
Pubmed Tian,
Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing.
2007,
Pubmed Tian,
A large-scale analysis of mRNA polyadenylation of human and mouse genes.
2005,
Pubmed Trapnell,
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
2012,
Pubmed Tripathi,
Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding.
2015,
Pubmed Ulitsky,
Extensive alternative polyadenylation during zebrafish development.
2012,
Pubmed Valen,
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.
2009,
Pubmed van Bakel,
Most "dark matter" transcripts are associated with known genes.
2010,
Pubmed Velculescu,
Serial analysis of gene expression.
1995,
Pubmed Wahle,
The biochemistry of 3'-end cleavage and polyadenylation of messenger RNA precursors.
1992,
Pubmed Yang,
The Xenopus Maternal-to-Zygotic Transition from the Perspective of the Germline.
2015,
Pubmed
,
Xenbase Yoon,
Genetics and regulatory impact of alternative polyadenylation in human B-lymphoblastoid cells.
2012,
Pubmed Zhao,
Complex alternative RNA processing generates an unexpected diversity of poly(A) polymerase isoforms.
1996,
Pubmed
,
Xenbase Zhou,
Accurate Profiling of Gene Expression and Alternative Polyadenylation with Whole Transcriptome Termini Site Sequencing (WTTS-Seq).
2016,
Pubmed
,
Xenbase
