title: Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis.
abstract: Spatiotemporal control of gene expression is central to animal development. Core promoters represent a previously unanticipated regulatory level by interacting with cis-regulatory elements and transcription initiation in different physiological and developmental contexts. Here, we provide a first and comprehensive description of the core promoter repertoire and its dynamic use during the development of a vertebrate embryo. By using cap analysis of gene expression (CAGE), we mapped transcription initiation events at single nucleotide resolution across 12 stages of zebrafish development. These CAGE-based transcriptome maps reveal genome-wide rules of core promoter usage, structure, and dynamics, key to understanding the control of gene regulation during vertebrate ontogeny. They revealed the existence of multiple classes of pervasive intra- and intergenic post-transcriptionally processed RNA products and their developmental dynamics. Among these RNAs, we report splice donor site-associated intronic RNA (sRNA) to be specific to genes of the splicing machinery. For the identification of conserved features, we compared the zebrafish data sets to the first CAGE promoter map of Tetraodon and the existing human CAGE data. We show that a number of features, such as promoter type, newly discovered promoter properties such as a specialized purine-rich initiator motif, as well as sRNAs and the genes in which they are detected, are conserved in mammalian and Tetraodon CAGE-defined promoter maps. The zebrafish developmental promoterome represents a powerful resource for studying developmental gene regulation and revealing promoter features shared across vertebrates.
authors.affiliation: Department of Biology, University of Bergen, Bergen N-5008, Norway;
authors.forename: Chirag
authors.initials: C
authors.lastname: Nepal
authors.forename: Yavor
authors.initials: Y
authors.lastname: Hadzhiev
authors.forename: Christopher
authors.initials: C
authors.lastname: Previti
authors.forename: Vanja
authors.initials: V
authors.lastname: Haberle
authors.forename: Nan
authors.initials: N
authors.lastname: Li
authors.forename: Hazuki
authors.initials: H
authors.lastname: Takahashi
authors.forename: Ana Maria M
authors.initials: AM
authors.lastname: Suzuki
authors.forename: Ying
authors.initials: Y
authors.lastname: Sheng
authors.forename: Rehab F
authors.initials: RF
authors.lastname: Abdelhamid
authors.forename: Santosh
authors.initials: S
authors.lastname: Anand
authors.forename: Jochen
authors.initials: J
authors.lastname: Gehrig
authors.forename: Altuna
authors.initials: A
authors.lastname: Akalin
authors.forename: Christel E M
authors.initials: CE
authors.lastname: Kockx
authors.forename: Antoine A J
authors.initials: AA
authors.lastname: van der Sloot
authors.forename: Wilfred F J
authors.initials: WF
authors.lastname: van Ijcken
authors.forename: Olivier
authors.initials: O
authors.lastname: Armant
authors.forename: Sepand
authors.initials: S
authors.lastname: Rastegar
authors.forename: Craig
authors.initials: C
authors.lastname: Watson
authors.forename: Uwe
authors.initials: U
authors.lastname: Strähle
authors.forename: Elia
authors.initials: E
authors.lastname: Stupka
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Boris
authors.initials: B
authors.lastname: Lenhard
authors.forename: Ferenc
authors.initials: F
authors.lastname: Müller
mesh_terms: D000818:Animals; D047108:Embryonic Development / Q000235:genetics*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D005796:Genes; D016678:Genome; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D011687:Purines / Q000378:metabolism*; D012313:RNA / Q000235:genetics / Q000378:metabolism; D012315:RNA Caps / Q000235:genetics; D012326:RNA Splicing; D024363:Transcription Initiation Site; D059467:Transcriptome; D014714:Vertebrates / Q000235:genetics; D015027:Zebrafish / Q000196:embryology* / Q000235:genetics*
chemical_list: D011687:Purines; D012315:RNA Caps; D012313:RNA; C030985:purine