Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Combined Automated Annotation using Multiple IEA Methods
Lim1 related homeobox gene (HpLim1) expressed in sea urchin embryos.
-
HpLim1 is a two-LIM-domain, LIM-class homeodomain protein orthologous to Lim1 of other animals.
"HpLim1 contains two LIM domains and a LIM-class homeodomain, and amino acid sequences of these three domains are highly homologous to corresponding domains of Lim1 of other animals."
-
Transcripts accumulate from hatching, decline after mesenchyme blastula, and localise to the vegetal plate region of hatched blastulae but not to ingressed primary mesenchyme cells.
"Accumulation of HpLim1 transcripts begins at hatching, and declines after the mesenchyme blastula stage. HpLim1 mRNA was localized in the vegetal plates of hatched blastulae, but it was not detectable in primary mesenchyme cells (PMC) ingressed into the blastocele."
-
Ectopic HpLim1 mRNA suppresses gut, mesoderm and aboral ectoderm differentiation and the embryo mainly expresses an oral ectoderm marker.
"HpLim1 mRNA-injected embryos became spherical with markedly reduced gut formation, failed to express marker proteins for aboral ectoderm and mesoderm, and mainly expressed an oral ectoderm marker."
Identification and characterization of homeobox transcription factor genes in Strongylocentrotus purpuratus, and their expression in embryonic development.
-
Genome-wide survey of 96 S. purpuratus homeobox genes with QPCR time courses and whole-mount in situ hybridisation; the source of the embryonic expression catalogue that includes lim1.
"QPCR time course measurements revealed that 65% of these genes are expressed within the first 48 h of development (late gastrula)."
A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo.
-
In S. purpuratus lim1 marks a distinct ectodermal domain along the interface with the vegetal endomesoderm that spans both oral and aboral ectoderm.
"there is a separate domain along the interface with the vegetal endomesoderm that extends all across both oral and aboral ectoderm, as indicated by expression of the lim1 gene (Kawasaki et al. 1999)"
-
lim1 is expressed along the lower (vegetal) margin of both oral and aboral ectoderm and is activated independently of nodal.
"the lim1 gene, which is expressed along the lower margin of both oral and aboral ectoderm"
-
Within the aboral ectoderm the lim1 domain is the only subdivision, lying next to the endomesoderm border.
"The only subdivision within it is that mentioned above, the lim1 domain immediately adjacent to the vegetal endomesoderm border."
Ancestral regulatory circuits governing ectoderm patterning downstream of Nodal and BMP2/4 revealed by gene regulatory network analysis in an echinoderm.
-
In Paracentrotus Nodal morphants, lim1 (with onecut/hnf6, otx2 and foxA) is expressed but no longer regionalised in the presumptive ectoderm, so lim1 is not an oral-specific marker.
"we showed that the expression of onecut/hnf6, otx2, lim1, and foxA in the presumptive ectoderm region of Nodal morphants was not regionalized, consistent with the absence of any oral territory in these embryos."
Direct and indirect control of oral ectoderm regulatory gene expression by Nodal signaling in the sea urchin embryo.
-
lim1 is classed as a veg1 oral ectoderm regulatory gene and is not affected by knockdown of the Nodal-dependent repressor Not.
"no effects were seen on expression of the other veg1 oral ectoderm regulatory genes nk2.2 and lim1"
Short-range Wnt5 signaling initiates specification of sea urchin posterior ectoderm.
-
Lim1 is the earliest border ectoderm (BE) gene, expressed throughout the BE from 8 hpf and diminishing by gastrulation.
"The earliest marker expressed in the BE was Lim1. It was expressed throughout the BE beginning at 8 hpf and was diminished by gastrulation."
-
A short-range Wnt5 signal from the endoderm activates the BE subcircuit that includes the transcription factors IrxA, Nk1, Pax2/5/8 and Lim1; Nodal and BMP2/4 restrict these genes to subregions of the BE.
"This signal activates a unique subcircuit of the ectoderm gene regulatory network, including the transcription factors IrxA, Nk1, Pax2/5/8 and Lim1, which are ultimately restricted to subregions of the border ectoderm (BE)."
Encoding regulatory state boundaries in the pregastrular oral ectoderm of the sea urchin embryo.
-
Comprehensive regulatory-state maps of all spatially expressed oral ectoderm regulatory genes define the endoderm/ectoderm and ectoderm/apical-plate boundaries by region-specific repressors plus broad activators.
"Comprehensive regulatory state maps, including all spatially expressed oral ectoderm regulatory genes, were established. The circuitry at each boundary deploys specific repressors of regulatory states across the boundary, identified in this work, plus activation by broadly expressed positive regulators."