Twinkle twinkle brittle star: the draft genome of Ophioderma brevispinum (Echinodermata: Ophiuroidea) as a resource for regeneration research

Mashanov, Vladimir; Machado, Denis Jacob; Reid, Robert; Brouwer, Cory; Kofsky, Janice; Janies, Daniel A.

doi:10.1186/s12864-022-08750-y

Table 5 Select components of the Notch signaling pathway identified in the draft genome of O. brevispinum using reference sequences from UniProt and Echinobase. For each gene, we list its name, the known function in the pathway, and whether or not the gene was recovered from the draft genome with independent BLAST and exonerate alignments. In addition, we also indicate if we could identify conserved protein domains in the predicted protein sequences

From: Twinkle twinkle brittle star: the draft genome of Ophioderma brevispinum (Echinodermata: Ophiuroidea) as a resource for regeneration research

Name	Role in the Pathway	BLAST	Exonerate	Conserved domains	References
Delta/Serrate (Jagged)	Ligand of the Notch receptor	Yes	Yes	Yes	[21, 35]
Notch	Receptor	Yes	Yes	No	[21, 107]
RBP-J	Transcription factor activated by Notch	Yes	Yes	No	[21, 35]
Mastermind	Co-activator of RBP-J	Yes	Yes	No	[21, 35, 107]
p300	Co-activator of RBP-J	Yes	Yes	No	[108, 109]
NACK	Co-activator of RBP-J	Yes	No	No	[108, 110]
CIR1	Co-repressor of RBP-J	Yes	Yes	No	[21, 35]
NCoR	Co-repressor of RBP-J	Yes	Yes	Yes	[111]
HDAC1	Co-repressor of RBP-J	Yes	Yes	Yes	[112]
MINT	Co-repressor of RBP-J	Yes	Yes	Yes	[111]
Fringe	Post-translational maturation of Notch	Yes	Yes	No	[21, 35]
POFUT1	Post-translational maturation of Notch	Yes	Yes	Yes	[113]
Poglut	Post-translational maturation of Notch	Yes	Yes	Yes	[114]
Furin	Receptor proteolysis	Yes	Yes	Yes	[115]
Neuralized	Ubiquitination of Jagged	Yes	Yes	Yes	[3, 116]
Mindbomb	Ubiuitination of Delta	Yes	Yes	Yes	[117]
Nicastrin	Receptor proteolysis	Yes	Yes	Yes	[21, 118]
Presenilin 1	Receptor proteolysis	Yes	No	No	[21, 118]
ADAM 10/17	Metalloprotease	Yes	Yes	No	[21]
HES	Canonical target gene	Yes	Yes	Yes	[118–120]
HEY1	Canonical target gene	Yes	Yes	Yes	[118–120]
Numb	Negative regulator of the Notch pathway	Yes	Yes	No	[118]
LNX2	Negative regulator of Numb	Yes	Yes	Yes	[121]
ACBD3	Activator of Numb	Yes	Yes	Yes	[118, 122]
NAK	Positive regulator of the Notch pathway	Yes	Yes	No	[118]
Mesp2	Activates Fringe, induces degradation of Mastermind	Yes	No	Yes	[107]
Nedd4	Targets Notch and Deltex for degradation	Yes	Yes	Yes	[123]
Notchless	Context-dependent positive or negative regulator	Yes	Yes	Yes	[36]
Deltex	Context-dependent positive or negative regulator. Antagonizes Nedd4	Yes	Yes	Yes	[112, 123]

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ISSN: 1471-2164

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