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dc.contributor.authorNepal, Chirageng
dc.contributor.authorHadzhiev, Yavoreng
dc.contributor.authorPreviti, A. Christophereng
dc.contributor.authorHaberle, Vanjaeng
dc.contributor.authorLi, Naneng
dc.contributor.authorTakahashi, Hazukieng
dc.contributor.authorSuzuki, Ana Mariaeng
dc.contributor.authorSheng, Yingeng
dc.contributor.authorAbdelhamid, Rehabeng
dc.contributor.authorAnand, Santosheng
dc.contributor.authorGehrig, Jocheneng
dc.contributor.authorAkalin, Altunaeng
dc.contributor.authorKockx, Christel E.M.eng
dc.contributor.authorvan der Sloot, Antoine A.J.eng
dc.contributor.authorvan Ijcken, Wilfred F.J.eng
dc.contributor.authorArmant, Oliviereng
dc.contributor.authorRastegar, Sepandeng
dc.contributor.authorWatson, Craigeng
dc.contributor.authorSträhle, Uweeng
dc.contributor.authorStupka, Eliaeng
dc.contributor.authorCarninci, Pieroeng
dc.contributor.authorLenhard, Boriseng
dc.contributor.authorMüller, Ferenceng
dc.description.abstractSpatiotemporal 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.en_US
dc.publisherCold Spring Harbor Laboratory Pressen_US
dc.relation.ispartof<a href="" target="_blank">Overlapping transcription initiation codes and promoter interpretation in vertebrate development and differentiation</a>en_US
dc.rightsAttribution-NonCommercial CC BY-NCeng
dc.titleDynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesisen_US
dc.typePeer reviewed
dc.typeJournal article
dc.rights.holderCopyright 2013 Nepal et alen_US
dc.source.journalGenome Research

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Except where otherwise noted, this item's license is described as Attribution-NonCommercial CC BY-NC