ArticleBMC genomics2011
Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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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.
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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.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2015Pooled it
- Identification of ancestral gnathostome Gli3 enhancers with activity in mammals.Development, growth & differentiation · 2024Article
- Evolution of the expression and regulation of the nuclear hormone receptor ERR gene family in the chordate lineage.Developmental biology · 2023Article
- Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers.Developmental dynamics : an official publication of the American Association of Anatomists · 2021Article
- PBX1 is a valuable prognostic biomarker for patients with breast cancer.Experimental and therapeutic medicine · 2020Article
- An atlas of anterior hox gene expression in the embryonic sea lamprey head: Hox-code evolution in vertebrates.Developmental biology · 2019Article
- A conserved regulatory program initiates lateral plate mesoderm emergence across chordates.Nature communications · 2019Article
- I-SceI Meganuclease-mediated transgenesis in the acorn worm, Saccoglossus kowalevskii.Developmental biology · 2019Article
- TALE factors use two distinct functional modes to control an essential zebrafish gene expression program.eLife · 2018Article
- Conserved non-coding elements: developmental gene regulation meets genome organization.Nucleic acids research · 2017Review
- Lampreys, the jawless vertebrates, contain only two ParaHox gene clusters.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- A unique stylopod patterning mechanism by Shox2-controlled osteogenesis.Development (Cambridge, England) · 2016Article
- A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes.PloS one · 2015Article
- A Hox regulatory network of hindbrain segmentation is conserved to the base of vertebrates.Nature · 2014Article
- A reporter assay in lamprey embryos reveals both functional conservation and elaboration of vertebrate enhancers.PloS one · 2014Article
- Purifying selection in deeply conserved human enhancers is more consistent than in coding sequences.PloS one · 2014Article
- Parallel evolution of chordate cis-regulatory code for development.PLoS genetics · 2013Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
backgroundGene regulation through cis-regulatory elements plays a crucial role in development and disease. A major aim of the post-genomic era is to be able to read the function of cis-regulatory elements through scrutiny of their DNA sequence. Whilst comparative genomics approaches have identified thousands of putative regulatory elements, our knowledge of their mechanism of action is poor and very little progress has been made in systematically de-coding them.
resultsHere, we identify ancient functional signatures within vertebrate conserved non-coding elements (CNEs) through a combination of phylogenetic footprinting and functional assay, using genomic sequence from the sea lamprey as a reference. We uncover a striking enrichment within vertebrate CNEs for conserved binding-site motifs of the Pbx-Hox hetero-dimer. We further show that these predict reporter gene expression in a segment specific manner in the hindbrain and pharyngeal arches during zebrafish development.
conclusionsThese findings evoke an evolutionary scenario in which many CNEs evolved early in the vertebrate lineage to co-ordinate Hox-dependent gene-regulatory interactions that pattern the vertebrate head. In a broader context, our evolutionary analyses reveal that CNEs are composed of tightly linked transcription-factor binding-sites (TFBSs), which can be systematically identified through phylogenetic footprinting approaches. By placing a large number of ancient vertebrate CNEs into a developmental context, our findings promise to have a significant impact on efforts toward de-coding gene-regulatory elements that underlie vertebrate development, and will facilitate building general models of regulatory element evolution.
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