Malloch EL et al. (2009), Gene expression profiles of lens regeneration a...

XB-ART-40141

Dev Dyn 2009 Sep 01;2389:2340-56. doi: 10.1002/dvdy.21998.

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Gene expression profiles of lens regeneration and development in Xenopus laevis.

Malloch EL , Perry KJ , Fukui L , Johnson VR , Wever J , Beck CW , King MW , Henry JJ .

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Seven hundred and thirty-four unique genes were recovered from a cDNA library enriched for genes up-regulated during the process of lens regeneration in the frog Xenopus laevis. The sequences represent transcription factors, proteins involved in RNA synthesis/processing, components of prominent cell signaling pathways, genes involved in protein processing, transport, and degradation (e.g., the ubiquitin/proteasome pathway), matrix metalloproteases (MMPs), as well as many other proteins. The findings implicate specific signal transduction pathways in the process of lens regeneration, including the FGF, TGF-beta, MAPK, Retinoic acid, Wnt, and hedgehog signaling pathways, which are known to play important roles in eye/lens development and regeneration in various systems. In situ hybridization revealed that the majority of genes recovered are expressed during embryogenesis, including in eye tissues. Several novel genes specifically expressed in lenses were identified. The suite of genes was compared to those up-regulated in other regenerating tissues/organisms, and a small degree of overlap was detected.

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Species referenced: Xenopus laevis
Genes referenced: anos1 ckb cmtm5 cryba1 crygdl.30 crygdl.43 crygn gpr84 ids ino80d lmo4 lmo4.2 mapk1 mmp1 pax7 paxbp1 pheta2 prpf39 prps1 pym1 shh smpd3 taf9b tgfb1
GO keywords: lens development in camera-type eye [+]

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References [+] :

Altschul, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997, Pubmed

	Figure 3. Representative in situ hybridization patterns showing mRNA localization for selected genes, as labeled (clone IDs). The NCBI accession numbers and putative identities corresponding to each clone ID are listed in Table 1 (bold entries). For additional images, including other stages of development, see www.life.illinois.edu/henry. In addition, refer to Supplemental Figure S1 for information summarizing specific and general patterns of expression in certain tissues/regions. Stages shown are as indicated (all Xenopus developmental stages follow those of Nieuwkoop and Faber,[1956]). All embryos are show as lateral views with the anterior end directed to the right. Black arrowheads point to the lens or the lens-forming region in some examples where there was highly elevated or specific expression in that tissue. Scale bar = 300 mu m.
	pheta2 (PH domain containing endocytic trafficking adaptor 2) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior right, dorsal up.
	Figure 1 Open in figure viewerPowerPoint Pie charts showing the general representation of particular classes of genes in the sequenced data set. A: Fraction of genes with and without significant similarity to other known genes or ESTs represented in various databases, as described in the text. B: Fraction of genes that exhibited some versus no embryonic expression in various tissues. See Supplemental Figure S1, and Figure S2, and www.life.illinois.edu/henry for more specific details.
	Figure 2 Open in figure viewerPowerPoint Distribution of Gene Ontology (GO) annotations assigned for each main category, including (A) molecular functions, (B) biological processes, and (C) cellular components. The 17 most frequent classifications (annotation terms) are shown for each category, along with the number of genes associated with those particular assignments. The data is based on that included in Supplemental Figure S2. A total of 392 of the 734 unique Xenopus genes recovered exhibited significant similarity to human and other genes and could be related to equivalent Human UniProt IDs (376 of those genes possessed specific GO annotations).
	prpf39.1 (pre-mRNA processing factor 39) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 32, lateral view, anterior left, dorsal up.
	pym1 (PYM homolog 1, exon junction complex associated factor ) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 26, lateral view, anterior right, dorsal up.

	novel Zinc finger protein ( possinly zfp 568 ) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.


	cmtm5 (CKLF-like MARVEL transmembrane domain containing 5) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 19, lateral view, anterior left, dorsal up.

	cryga (crystallin gamma A) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 32, lateral view, anterior right, dorsal up.
	crybb1l (crystallin beta B1 like) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 32, lateral view, anterior left, dorsal up.


	paxbp1 (PAX3 and PAX7 binding protein 1) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 31, lateral view, anterior right, dorsal up.