Integrated analyses of zebrafish miRNA and mRNA expression profiles identify miR-29b and miR-223 as potential regulators of optic nerve regeneration

Table 4 Putative miR-29b and miR-223 targets downregulated after optic nerve crush

Ensembl ID	Gene	mRNA change^a	miRNA	Context + score^b	No. binding sites
ENSDART00000087565	eva1a	0.61	miR-29b	−0.46	1 (8mer)
ENSDART00000087565	eva-1 homolog a	0.61	(miR-223) ^c	(−0.09)	1 (7mer-1A)
ENSDART00000050945	layna	0.45	miR-29b	−0.50	1 (8mer)
ENSDART00000050945	Layilin a	0.45	(miR-223) ^c	(−0.16; −0.17)	2 (7mer-1A)
ENSDART00000064163	nefmb	0.28	miR-29b	−0.41	1 (8mer)
ENSDART00000064163	Neurofilament, medium polypeptide, b	0.28	miR-29b	−0.41	1 (8mer)
ENSDART00000018351	ina (zgc:65851)	0.50	miR-29b	−0.41; −0.05	2 (8mer; 7mer-1A)
ENSDART00000018351	Internexin neuronal intermediate filament alpha	0.50	(miR-223) ^c	(−0.02; >0.03; >0.01)	3 (8mer; 7mer-m8; 7mer-1A)
ENSDART00000021556	si:ch211-51a6.2	0.57	miR-29b	−0.33	1 (7mer-m8)
ENSDART00000021556	Homolog of prss12	0.57	miR-223	−0.32; −0.07	2 (7mer-m8; 7mer-1A)
ENSDART00000126365	smoc1	0.41	miR-223	−0.39; > − 0.02	2 (8mer; 7mer-m8)
ENSDART00000126365	SPARC related modular calcium binding 1	0.41	miR-223	−0.39; > − 0.02	2 (8mer; 7mer-m8)
ENSDART00000124670	lrrn3	0.65	miR-223	−0.32	1 (8mer)
ENSDART00000124670	Leucine rich repeat neuronal protein 3-like	0.65	miR-223	−0.32	1 (8mer)
ENSDART00000081039	^d sb:cb252	52.9	miR-223	−0.31	1 (7mer-m8)
ENSDART00000081039	Homolog of es1-like	52.9	miR-223	−0.31	1 (7mer-m8)

^aFold change represents microarray expression. All genes had an adjusted p-value ≤0.05
^bSee Methods for summary of Targetscan Fish context + score
^cPredicted binding sites of miR-223 in genes with a context scores less stringent then our cut-off (i.e., ≤ − 0.30)
^dMicroarray results revealed sb:cb252 was the most upregulated gene on microarray, yet it was also one of the top predicted miR-223 target genes by Targetscan Fish; we chose to included it in subsequent experiments to determine if it was a valid miR-223 target

ISSN: 1471-2164