Dri (Spdeadringer, Spdri) is an ARID-class transcription factor of the ARID3/Dead ringer/Bright subfamily, with a central ARID DNA-binding domain and a C-terminal REKLES domain. In the sea urchin embryo it is expressed in two separate phases, each following prior territorial specification: first, from about 12 h until ingression, in the skeletogenic descendants of the large micromeres (the primary mesenchyme cell lineage), where it is activated by the skeletogenic regulators Ets1, Alx1 and Tbr; and second, from about 20 h, in the oral ectoderm, where it is released by the Gsc-controlled repressor gate and remains expressed in the oral "face" epithelium far into development. In the skeletogenic lineage Dri is a direct transcriptional activator, together with Ets1, of the terminal skeletogenic differentiation gene battery (for example cyclophilin, whose cis-regulatory module requires intact Dri target sites), and its cell-autonomous function is needed for skeletogenic gene expression before ingression and for spicule formation. In the oral ectoderm Dri is part of the central regulatory network that maintains oral ectoderm identity; when it is knocked down, oral-specific features are lost and the aboral marker spec1 spreads around the entire ectoderm, and the oral-side patterning information that the primary mesenchyme cells need to complete skeletogenesis is not presented. Knockdown also causes failure of gastrulation, through indirect, non-autonomous effects rather than a defect in endomesoderm specification.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IBA GO_REF:0000033 | MODIFY | Summary: PAINT inference for the ARID-domain family (node PTN000394188), seeded by Drosophila dead ringer, mouse Arid3a, worm cfi-1 and Arabidopsis ARID proteins. Dri is an ARID-class transcription factor and DNA binding is correct as far as it goes; the cis-regulatory evidence in S. purpuratus (Dri target sites in the Sp-cyp1 module are required for expression) supports the more informative sequence-specific, RNA polymerase II cis-regulatory-region child. Reason: The phylogenetic placement is sound and the ARID domain is a DNA-binding domain, so this is a refinement of the PAINT judgment, not a challenge to it. The S. purpuratus cis-regulatory evidence supports the RNA polymerase II cis-regulatory-region sequence-specific DNA binding child term, and the activator MF is proposed as NEW. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000394188 SUPPORTS TRANSFER ARID-domain family node seeded by Drosophila dead ringer, mouse Arid3a and worm cfi-1; DNA binding transfers correctly to Sp-Dri, but the S. purpuratus cis-regulatory evidence supports the more specific RNA polymerase II cis-regulatory region sequence-specific child. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:12941621 The Spdeadringer (Spdri) gene encodes an ARID-class transcription factor not previously known in sea urchin embryos. PMID:16574094 Ets1 and Dri target sites within the 218 bp fragment are required for normal expression. This indicates that the predicted inputs are direct. |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the ARID domain signature (IPR001606/IPR036431). Correct but uninformative for a sequence-specific transcription factor whose target sites in a skeletogenic cis-regulatory module have been mapped. Reason: Same claim as the IBA row. The S. purpuratus cis-regulatory analysis of the Sp-cyp1 module shows Dri target sites are required for expression, which supports the RNA polymerase II cis-regulatory-region sequence-specific DNA binding child term. Proposed replacements: RNA polymerase II cis-regulatory region sequence-specific DNA binding Supporting Evidence: PMID:16574094 Ets1 and Dri target sites within the 218 bp fragment are required for normal expression. This indicates that the predicted inputs are direct. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference of nuclear activity for the ARID3 family, grounded in human ARID3A/B/C, mouse and fly experimental data. Dri functions as a nuclear transcription factor whose direct inputs on cis-regulatory DNA have been mapped in S. purpuratus. Reason: Consistent with the ARID-class transcription factor function and the direct cis-regulatory inputs of Dri shown in sea urchin. Supporting Evidence: PMID:16574094 Ets1 and Dri target sites within the 218 bp fragment are required for normal expression. This indicates that the predicted inputs are direct. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: UniProt subcellular-location mapping (the Swiss-Prot entry assigns Nucleus from the ARID PROSITE rule). Correct for a transcription factor. Reason: Nuclear localisation is expected for an ARID-class transcription factor with mapped cis-regulatory inputs; duplicates the IBA row. Supporting Evidence: PMID:12941621 The Spdeadringer (Spdri) gene encodes an ARID-class transcription factor not previously known in sea urchin embryos. |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT inference from fly dead ringer, mouse Arid3a/Arid3b and worm cfi-1. Fully consistent with the sea urchin data, in which Dri is a driver of the skeletogenic differentiation gene battery and of the oral ectoderm regulatory state; the more specific positive-regulation child is proposed as NEW below. Reason: Core function. The S. purpuratus cis-regulatory and perturbation data show Dri regulates RNA polymerase II transcription of its target genes. Supporting Evidence: PMID:12941621 Spdri is shown to act in the micromere descendants in the pathways that result in the expression of batteries of terminal skeletogenic genes. PMID:16574094 elimination of either Ets1 or Dri inputs severely depresses the activity of expression constructs containing this DNA fragment |
| GO:0006357 regulation of transcription by RNA polymerase II | IEA GO_REF:0000120 | ACCEPT | Summary: ARBA/InterPro mapping from the ARID3 (ARI3A/B/C) family signature. Duplicates the IBA row and is consistent with the experimental picture. Reason: Core function; same evidence as the IBA row above. Supporting Evidence: PMID:16574094 these genes probably constitute a skeletogenic gene battery, defined by its Ets plus Dri regulatory inputs. |
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | IDA PMID:16574094 cis-Regulatory control of cyclophilin, a member of the ETS-D... | NEW | Summary: Dri is a direct transcriptional activator in S. purpuratus. In the 218-bp Sp-cyp1 cis-regulatory module, Dri target sites are required for reporter expression and elimination of the Dri input severely depresses it; Ets1 plus Dri inputs define the skeletogenic differentiation gene battery. The spdri reporter also responds to Dri itself, consistent with positive autoregulation. Reason: Reporter/cis-regulatory evidence in S. purpuratus shows a direct, positive input, so the activator child of GO:0000981 is warranted; the sign is known. Supporting Evidence: PMID:16574094 elimination of either Ets1 or Dri inputs severely depresses the activity of expression constructs containing this DNA fragment; and that Ets1 and Dri target sites within the 218 bp fragment are required for normal expression. This indicates that the predicted inputs are direct. PMID:18718463 the reporter responded to known spdri's transcriptional regulators (Ets1, Alx1, Gsc and Dri). |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IMP PMID:12941621 Spdeadringer, a sea urchin embryo gene required separately i... | NEW | Summary: Morpholino knockdown of Spdri reduces expression of the terminal skeletogenic gene batteries in the micromere descendants and of oral ectoderm genes (QPCR of 17 mesodermal and 8 oral ectoderm genes), and the direct cis-regulatory input on Sp-cyp1 is positive. Dri therefore positively regulates transcription of its target genes. Reason: Knockdown (IMP) plus direct cis-regulatory (IDA) evidence in S. purpuratus for positive transcriptional regulation performed by Dri itself. Supporting Evidence: PMID:12941621 Spdri is shown to act in the micromere descendants in the pathways that result in the expression of batteries of terminal skeletogenic genes. PMID:16574094 elimination of either Ets1 or Dri inputs severely depresses the activity of expression constructs containing this DNA fragment |
| GO:0070169 positive regulation of biomineral tissue development | IMP PMID:12941621 Spdeadringer, a sea urchin embryo gene required separately i... | NEW | Summary: Dri is required cell-autonomously in the skeletogenic lineage for expression of the skeletogenic (biomineralization) gene batteries before ingression, and its knockdown causes failure of spiculogenesis; it is a direct driver, with Ets1, of skeletogenic effector genes such as Sp-cyp1. This is the same term used in this project for the upstream skeletogenic regulators Alx1 and Ets1. Reason: Dri performs the regulatory step (transcriptional activation of the skeletogenic differentiation battery) that drives spicule formation; the chimera experiments show the requirement is autonomous to the micromere lineage, so this is not a pleiotropic non-autonomous effect. Supporting Evidence: PMID:12941621 while Spdri expression is required autonomously for expression of skeletogenic genes prior to ingression, complete skeletogenesis also requires the expression of oral ectoderm patterning information. PMID:12941621 morphological consequences of alphaSpdri MASO treatment include failure of spiculogenesis and of correct primary mesenchyme cell (pmc) patterning in the postgastrular embryo PMID:18413610 these differentiation genes require as drivers products of all of the now familiar components of the skeletogenic regulatory state ( alx1 , ets1 , tbr , tel , erg , hex , foxb , dri ) |
| GO:0001715 ectodermal cell fate specification | IMP PMID:12941621 Spdeadringer, a sea urchin embryo gene required separately i... | NEW | Summary: In its second expression phase Dri is one of the definitive oral ectoderm regulatory genes (released by the Gsc-controlled repressor gate) and participates in the central GRN controlling oral ectoderm identity. Knockdown abolishes oral-specific features and the aboral marker spec1 spreads over the entire ectoderm, i.e. the oral ectodermal regulatory state is not maintained and the ectoderm adopts aboral character. Reason: Dri is a transcription factor within the oral ectoderm GRN, so it performs part of the regulatory work of specifying and maintaining oral (versus aboral) ectodermal cell fate; this follows the convention used in this project for other sea urchin regulators of sub-ectodermal fates (Otx, Eve, SoxB1). The role is restricted to the oral ectoderm sub-territory, not ectoderm generally. Supporting Evidence: PMID:12941621 But, in the oral ectoderm, the same gene participates in the central GRN controlling oral ectoderm identity. PMID:12941621 If its expression is blocked by treatment with alphaSpdri MASO, oral-specific features disappear and expression of the aboral ectoderm marker spec1 encompasses the whole of the ectoderm. PMID:19268450 treatments which interfere with the operation of the GRN, such as knock-down of dri (Amore et al., 2003), of hnf6 (Otim et al., 2004), or of gsc (Angerer et al., 2001), all cause expression of spec1 to spread around the whole ectoderm. |
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Download this section (compressed HTML)Q: Should the oral ectoderm role be captured with GO:0060834 oral/aboral axis specification (which currently carries no annotations in QuickGO) rather than, or in addition to, ectodermal cell fate specification?
Q: Does Dri act as a repressor of aboral ectoderm genes (spec1 and its regulators) in the oral ectoderm, or only as an activator of oral regulatory genes, with aboral repression being indirect?
Q: Is the response of the spdri reporter to Dri a direct positive autoregulatory loop, and does it operate in both expression phases?
Experiment: Dri ChIP-seq (or ChIP-qPCR on candidate modules such as Sp-cyp1 and oral ectoderm regulatory genes) in S. purpuratus at 18-24 h to identify direct targets in the PMC and oral ectoderm phases and to establish the sign of Dri input in the oral ectoderm.
Experiment: Electrophoretic mobility shift assays with purified Dri ARID domain on the mapped Sp-cyp1 218-bp module to confirm sequence-specific binding of the sites required for reporter expression.
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