Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
???displayArticle.abstract???
Sea stars and sea urchins are model systems for interrogating the types of deep evolutionary changes that have restructured developmental gene regulatory networks (GRNs). Although cis-regulatory DNA evolution is likely the predominant mechanism of change, it was recently shown that Tbrain, a Tbox transcription factor protein, has evolved a changed preference for a low-affinity, secondary binding motif. The primary, high-affinity motif is conserved. To date, however, no genome-wide comparisons have been performed to provide an unbiased assessment of the evolution of GRNs between these taxa, and no study has attempted to determine the interplay between transcription factor binding motif evolution and GRN topology. The study here measures genome-wide binding of Tbrain orthologs by using ChIP-sequencing and associates these orthologs with putative target genes to assess global function. Targets of both factors are enriched for other regulatory genes, although nonoverlapping sets of functional enrichments in the two datasets suggest a much diverged function. The number of low-affinity binding motifs is significantly depressed in sea urchins compared with sea star, but both motif types are associated with genes from a range of functional categories. Only a small fraction (∼10%) of genes are predicted to be orthologous targets. Collectively, these data indicate that Tbr has evolved significantly different developmental roles in these echinoderms and that the targets and the binding motifs in associated cis-regulatory sequences are dispersed throughout the hierarchy of the GRN, rather than being biased toward terminal process or discrete functional blocks, which suggests extensive evolutionary tinkering.
Anders,
HTSeq--a Python framework to work with high-throughput sequencing data.
2015, Pubmed
Anders,
HTSeq--a Python framework to work with high-throughput sequencing data.
2015,
Pubmed Bailey,
MEME SUITE: tools for motif discovery and searching.
2009,
Pubmed Berger,
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
2006,
Pubmed Berger,
Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors.
2009,
Pubmed Bolger,
Trimmomatic: a flexible trimmer for Illumina sequence data.
2014,
Pubmed Borneman,
Divergence of transcription factor binding sites across related yeast species.
2007,
Pubmed Camacho,
BLAST+: architecture and applications.
2009,
Pubmed Cameron,
Do echinoderm genomes measure up?
2015,
Pubmed
,
Echinobase Cameron,
SpBase: the sea urchin genome database and web site.
2009,
Pubmed
,
Echinobase Cheatle Jarvela,
Evolution of transcription factor function as a mechanism for changing metazoan developmental gene regulatory networks.
2015,
Pubmed Cheatle Jarvela,
A gene regulatory network for apical organ neurogenesis and its spatial control in sea star embryos.
2016,
Pubmed
,
Echinobase Cheatle Jarvela,
Modular evolution of DNA-binding preference of a Tbrain transcription factor provides a mechanism for modifying gene regulatory networks.
2014,
Pubmed
,
Echinobase Cheatle Jarvela,
A method for microinjection of Patiria miniata zygotes.
2014,
Pubmed
,
Echinobase Conboy,
Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor.
2007,
Pubmed Croce,
ske-T, a T-box gene expressed in the skeletogenic mesenchyme lineage of the sea urchin embryo.
2001,
Pubmed
,
Echinobase Crocker,
The Soft Touch: Low-Affinity Transcription Factor Binding Sites in Development and Evolution.
2016,
Pubmed Crocker,
Low affinity binding site clusters confer hox specificity and regulatory robustness.
2015,
Pubmed Cusanovich,
The functional consequences of variation in transcription factor binding.
2014,
Pubmed Dylus,
Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks.
2016,
Pubmed
,
Echinobase Erwin,
The Cambrian conundrum: early divergence and later ecological success in the early history of animals.
2011,
Pubmed Falcon,
Using GOstats to test gene lists for GO term association.
2007,
Pubmed Garfield,
Population genetics of cis-regulatory sequences that operate during embryonic development in the sea urchin Strongylocentrotus purpuratus.
2012,
Pubmed
,
Echinobase Grant,
FIMO: scanning for occurrences of a given motif.
2011,
Pubmed Grens,
Evolutionary conservation of a cell fate specification gene: the Hydra achaete-scute homolog has proneural activity in Drosophila.
1995,
Pubmed He,
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species.
2011,
Pubmed Hinman,
Expression and function of a starfish Otx ortholog, AmOtx: a conserved role for Otx proteins in endoderm development that predates divergence of the eleutherozoa.
2003,
Pubmed
,
Echinobase Hinman,
Evolutionary plasticity of developmental gene regulatory network architecture.
2007,
Pubmed
,
Echinobase Hinman,
Developmental gene regulatory network architecture across 500 million years of echinoderm evolution.
2003,
Pubmed
,
Echinobase Hinman,
Caught in the evolutionary act: precise cis-regulatory basis of difference in the organization of gene networks of sea stars and sea urchins.
2007,
Pubmed
,
Echinobase Kim,
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
2013,
Pubmed Koga,
Experimental Approach Reveals the Role of alx1 in the Evolution of the Echinoderm Larval Skeleton.
2016,
Pubmed
,
Echinobase Kunarso,
Transposable elements have rewired the core regulatory network of human embryonic stem cells.
2010,
Pubmed Langmead,
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
2009,
Pubmed Li,
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding.
2011,
Pubmed Lund,
Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates.
2012,
Pubmed Lynch,
Resurrecting the role of transcription factor change in developmental evolution.
2008,
Pubmed McCauley,
A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos.
2010,
Pubmed
,
Echinobase McCauley,
Dose-dependent nuclear β-catenin response segregates endomesoderm along the sea star primary axis.
2015,
Pubmed
,
Echinobase McGinnis,
Human Hox-4.2 and Drosophila deformed encode similar regulatory specificities in Drosophila embryos and larvae.
1990,
Pubmed Meader,
Massive turnover of functional sequence in human and other mammalian genomes.
2010,
Pubmed Mortazavi,
Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.
2006,
Pubmed Nam,
Functional cis-regulatory genomics for systems biology.
2010,
Pubmed
,
Echinobase Odom,
Tissue-specific transcriptional regulation has diverged significantly between human and mouse.
2007,
Pubmed Oliveri,
Global regulatory logic for specification of an embryonic cell lineage.
2008,
Pubmed
,
Echinobase Ouimette,
Divergent transcriptional activities determine limb identity.
2010,
Pubmed Quinlan,
BEDTools: a flexible suite of utilities for comparing genomic features.
2010,
Pubmed Rafiq,
The genomic regulatory control of skeletal morphogenesis in the sea urchin.
2012,
Pubmed
,
Echinobase Ramos,
Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution.
2013,
Pubmed Revilla-i-Domingo,
R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres.
2004,
Pubmed
,
Echinobase Robinson,
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
2010,
Pubmed Röttinger,
A Raf/MEK/ERK signaling pathway is required for development of the sea urchin embryo micromere lineage through phosphorylation of the transcription factor Ets.
2004,
Pubmed
,
Echinobase Rowan,
Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity.
2010,
Pubmed Sakabe,
Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function.
2012,
Pubmed Saunders,
Sub-circuits of a gene regulatory network control a developmental epithelial-mesenchymal transition.
2014,
Pubmed
,
Echinobase Schmidt,
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding.
2010,
Pubmed Smith,
Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata).
2006,
Pubmed
,
Echinobase Smith,
The oldest echinoderm faunas from Gondwana show that echinoderm body plan diversification was rapid.
2013,
Pubmed
,
Echinobase Sun,
Signal-dependent regulation of the sea urchin skeletogenic gene regulatory network.
2014,
Pubmed
,
Echinobase Tong,
A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation.
2016,
Pubmed Wray,
The evolutionary significance of cis-regulatory mutations.
2007,
Pubmed Yamazaki,
Larval mesenchyme cell specification in the primitive echinoid occurs independently of the double-negative gate.
2014,
Pubmed
,
Echinobase Yankura,
Gene regulatory network for neurogenesis in a sea star embryo connects broad neural specification and localized patterning.
2013,
Pubmed
,
Echinobase Zhang,
Model-based analysis of ChIP-Seq (MACS).
2008,
Pubmed
