title: The time-resolved transcriptome of C. elegans.
abstract: We generated detailed RNA-seq data for the nematode Caenorhabditis elegans with high temporal resolution in the embryo as well as representative samples from post-embryonic stages across the life cycle. The data reveal that early and late embryogenesis is accompanied by large numbers of genes changing expression, whereas fewer genes are changing in mid-embryogenesis. This lull in genes changing expression correlates with a period during which histone mRNAs produce almost 40% of the RNA-seq reads. We find evidence for many more splice junctions than are annotated in WormBase, with many of these suggesting alternative splice forms, often with differential usage over the life cycle. We annotated internal promoter usage in operons using SL1 and SL2 data. We also uncovered correlated transcriptional programs that span >80 kb. These data provide detailed annotation of the C. elegans transcriptome.
authors.affiliation: Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA; Department of Biology, Regis University, Denver, Colorado 80221, USA.
authors.forename: Max E
authors.initials: ME
authors.lastname: Boeck
authors.affiliation: Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Chau
authors.initials: C
authors.lastname: Huynh
authors.affiliation: Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Lou
authors.initials: L
authors.lastname: Gevirtzman
authors.affiliation: Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Owen A
authors.initials: OA
authors.lastname: Thompson
authors.affiliation: Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Guilin
authors.initials: G
authors.lastname: Wang
authors.affiliation: Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Dionna M
authors.initials: DM
authors.lastname: Kasper
authors.affiliation: Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut 06520, USA.
authors.forename: Valerie
authors.initials: V
authors.lastname: Reinke
authors.affiliation: Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA.
authors.forename: LaDeana W
authors.initials: LW
authors.lastname: Hillier
authors.affiliation: Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Robert H
authors.initials: RH
authors.lastname: Waterston
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000254:growth & development; D018507:Gene Expression Regulation, Developmental; D058977:Molecular Sequence Annotation; D059467:Transcriptome