ArticleNature communications2014
Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed, 49 citations in OpenAlex.
- Enhancer remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm.Developmental cell · 2025Article
- TGF-β modulates cell fate in human ES cell-derived foregut endoderm by inhibiting Wnt and BMP signaling.Stem cell reports · 2024Article
- Article
- Xenopus Ssbp2 is required for embryonic pronephros morphogenesis and terminal differentiation.Scientific reports · 2023Article
- Tissue-specific expression of carbohydrate sulfotransferases drives keratan sulfate biosynthesis in the notochord and otic vesicles ofFrontiers in cell and developmental biology · 2023Article
- Cell fate decisions, transcription factors and signaling during early retinal development.Progress in retinal and eye research · 2022Review
- Uncovering the mesendoderm gene regulatory network through multi-omic data integration.Cell reports · 2022Article
- T-Cell Factors as Transcriptional Inhibitors: Activities and Regulations in Vertebrate Head Development.Frontiers in cell and developmental biology · 2021Review
- Genomics Methods forCold Spring Harbor protocols · 2020Article
- Endodermal Maternal Transcription Factors Establish Super-Enhancers during Zygotic Genome Activation.Cell reports · 2019Article
- Morpholinos Do Not Elicit an Innate Immune Response during Early Xenopus Embryogenesis.Developmental cell · 2019Review
- Evolution of cis-regulatory modules for the head organizer geneZoological letters · 2019Article
- The Lhx1-Ldb1 complex interacts with Furry to regulate microRNA expression during pronephric kidney development.Scientific reports · 2018Article
- Innate Immune Response and Off-Target Mis-splicing Are Common Morpholino-Induced Side Effects in Xenopus.Developmental cell · 2018Article
- Tissue-Specific Gene Inactivation inGenetics · 2018Article
- A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo.Developmental biology · 2017Article
- A gene regulatory program controlling early Xenopus mesendoderm formation: Network conservation and motifs.Seminars in cell & developmental biology · 2017Review
- Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program.Developmental cell · 2017Article
- Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex.Frontiers in neuroscience · 2017Article
- Wnt target genes and where to find them.F1000Research · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 6 institutions in 2 countries.
Funding
Abstract
Head specification by the head-selector gene, orthodenticle (otx), is highly conserved among bilaterian lineages. However, the molecular mechanisms by which Otx and other transcription factors (TFs) interact with the genome to direct head formation are largely unknown. Here we employ ChIP-seq and RNA-seq approaches in Xenopus tropicalis gastrulae and find that occupancy of the corepressor, TLE/Groucho, is a better indicator of tissue-specific cis-regulatory modules (CRMs) than the coactivator p300, during early embryonic stages. On the basis of TLE binding and comprehensive CRM profiling, we define two distinct types of Otx2- and TLE-occupied CRMs. Using these devices, Otx2 and other head organizer TFs (for example, Lim1/Lhx1 (activator) or Goosecoid (repressor)) are able to upregulate or downregulate a large battery of target genes in the head organizer. An underlying principle is that Otx marks target genes for head specification to be regulated positively or negatively by partner TFs through specific types of CRMs.
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.