Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Combined Automated Annotation using Multiple IEA Methods
Cis-regulatory logic driving glial cells missing: self-sustaining circuitry in later embryogenesis.
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The gcm late cis-regulatory module, which sustains gcm expression from mesenchyme blastula onward, depends on two critical elements matching Gcm and Six1 consensus sites.
"Cis-perturbation analyses reveal that the two critical elements within this late module are consensus matches to Gcm and Six1 binding sites."
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Six1 depletion reduces endogenous gcm and late-module reporter output about three-fold, and Gcm depletion sharply reduces six1, so gcm and six1 form a positive intergenic feedback loop.
"These results support the conclusion gcm and six1 comprise a positive intergenic feedback loop in the mesodermal GRN."
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six1 mRNA is confined to gcm-positive pigment cell precursors from mesenchyme blastula and persists in dispersed pigment cells.
"six1 mRNA localizes to the pigment cell precursors as early as the mesenchyme blastula stage (Poustka et al., 2007) and expression is maintained in dispersed pigment cells (Figs. 7A–C)."
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Six1 knockdown does not block pigment cell formation; six1 acts after primary specification of pigment cell precursors.
"injection of 250µM six1-MO did not produce any discernable effect on embryonic development, particularly with regard to pigment cell formation or differentiation."
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The UniProt H6WNA5 sequence (JQ264781) is the corrected six1 coding sequence deposited by this study.
"An updated six1 coding sequence has been filed in GenBank [accession JQ264781]."
Diversification of oral and aboral mesodermal regulatory states in pregastrular sea urchin embryos.
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six1/2 is activated in the aboral NSM shortly after gataE and z166, together with its cofactor eya.
"The six1/2 cofactor eya is also expressed in the aboral NSM (not shown)."
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Gcm and GataE morpholinos each strongly depress six1/2 transcript levels, placing six1/2 downstream of both in the aboral NSM GRN.
"Transcript levels of six1/2 and z166 are also greatly reduced in embryos bearing GataE MASO, about equally to embryos bearing Gcm MASO, so gataE is likely to provide direct inputs into these genes of the aboral GRN"
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The six1/2-gcm feedback stabilises the aboral NSM regulatory state.
"This work demonstrated the institution of a feedback relation with six1/2, which serves to stabilize the aboral NSM regulatory state in addition to positive gcm auto-regulation."
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JQ264781 is the six1/2 sequence used in the mesoderm GRN work (gene prediction SPU_17397).
"The actual 5’ end of the six1/2 sequence differs from the gene prediction SPU_17397 (genbank accession numbers: prox1—JQ956375 , six1/2—JQ264781, z166—JQ945922)."
A comprehensive analysis of Delta signaling in pre-gastrular sea urchin embryos.
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six1/2 and eya expression in the aboral mesoderm fails in the absence of Delta/Notch signalling.
"expression of other aboral mesoderm regulatory genes, i.e., the zinc finger gene z166, the six1/2 gene, and the gene encoding its co-factor Eya, also fails in the absence of D/N signaling."
Synthetic in vivo validation of gene network circuitry.
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In the GRN summary, six1/2 lies in the subnetwork downstream of gcm and feeds back on gcm.
"A small subnetwork downstream of gcm includes the gatae gene and the six1/2 gene, which feeds back on gcm , as well as on an auto-regulatory feed from gcm onto itself"
Opposing nodal and BMP signals regulate left-right asymmetry in the sea urchin larva.
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six1/2 is a left-sided marker expressed with pax6, eya, dach and soxE in aboral veg2-derived cells of the archenteron tip and the left coelomic pouch.
"Comparable expression patterns were observed for the left-sided markers pax6, six1/2, and genes encoding Six1/2 cofactors eya"
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Left coelomic pouch six1/2 expression requires BMP signalling and is excluded from the right pouch by Nodal signalling.
"The expressions of all examined genes that were normally expressed in the aboral veg2 descendants, including soxE, pax6, six1/2, eya, and dach, were diminished in DM-treated embryos but remained in the single CP when BMP signaling was elevated (Figure 3F)."
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Nodal receptor inhibition makes six1/2 expression bilateral.
"The arrowheads indicate soxE, pax6, six1/2, eya, and dach expression in the left CP in control and in both CPs in SB-505124-treated embryos."
Deployment of a retinal determination gene network drives directed cell migration in the sea urchin embryo.
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In Lytechinus variegatus, mesoderm-targeted Six1/2 knockdown impairs homing of the small micromeres to the coelomic pouches.
"Aboral transcription factor, Six1/2, affected homing when knocked down in the mesoderm, as well (n = 17, p < 0.02) and did not affect homing when knocked down in the micromere (n = 11)."
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Six1/2 positively regulates six3, eya and itself in the coelomic pouch subcircuit.
"Six1/2 is seen to be upstream of six3, eya, and six1/2."
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The study organism is Lytechinus variegatus, not S. purpuratus.
"Adult Lytechinus variegatus were obtained from Reeftopia"
Myogenesis in the sea urchin embryo: the molecular fingerprint of the myoblast precursors.
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At late gastrula Six1/2 is expressed in the aboral-anal domain of the archenteron tip with FoxF, Gcm, MyoR, Mef2 and SoxE, not in the FoxY/FoxC myoblast precursors.
"Finally, the AbAn domain expresses FoxF, Gcm, MyoR, Mef2, Six1/2 and SoxE with some of the genes occupying smaller or larger domains of expression as described before and reported in detail in Figure 5"
Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and their expression in embryonic development.