ArticleGenome research2013
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
68 citing papers in PubMed, 144 citations in OpenAlex.
- Article
- Important role in transcription start site selection for the RNA polymerase II-TFIIE-TFIIH interface in Saccharomyces cerevisiae.Genetics · 2026Article
- RNA polymerase II-TFIIE-TFIIH interface functions in transcription start site selection inbioRxiv : the preprint server for biology · 2025Article
- The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis.Developmental cell · 2025Article
- The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus.Nature reviews. Genetics · 2025Review
- SINEUP RNA rescues molecular phenotypes associated with CHD8 suppression in autism spectrum disorder model systems.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1.PLoS biology · 2024Article
- miR-430 regulates zygotic mRNA during zebrafish embryogenesis.Genome biology · 2024Article
- Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels.Nature structural & molecular biology · 2024Article
- Intra-promoter switch of transcription initiation sites in proliferation signaling-dependent RNA metabolism.Nature structural & molecular biology · 2023Article
- The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis.bioRxiv : the preprint server for biology · 2023Article
- Identifying promoter sequence architectures via a chunking-based algorithm using non-negative matrix factorisation.PLoS computational biology · 2023Article
- Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin.Science (New York, N.Y.) · 2023Article
- Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes.Nature communications · 2023Article
- The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation.Developmental cell · 2023Article
- mRNA 5' terminal sequences drive 200-fold differences in expression through effects on synthesis, translation and decay.PLoS genetics · 2022Article
- Simple and accurate transcriptional start site identification using Smar2C2 and examination of conserved promoter features.The Plant journal : for cell and molecular biology · 2022Article
- Dynamic Transcriptional Landscape of Grass Carp (International journal of molecular sciences · 2022Article
- Alternative transcription start sites contribute to acute-stress-induced transcriptome response in human skeletal muscle.Human genomics · 2022Article
- Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.Nature genetics · 2022Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
23 authors at 9 institutions in 6 countries.
Funding
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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.