In silico mining of EST databases for novel pre-implantation embryo-specific zinc finger protein genes

Kong Bung Choo, Huang Hui Chen, Winston T K Cheng, Hung Shue Chang, Manni Wang

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Progress in the understanding of early mammalian embryo development has been severely hampered by scarcity of study materials. To circumvent such a constraint, we have developed a strategy that involves a combination of in silico mining of new genes from expressed sequence tags (EST) databases and rapid determination of expression profiles of the dbEST-derived genes using a PCR-based assay and a panel of cDNA libraries derived from different developmental stages and somatic tissues. We demonstrate that in a random sample of 49 independent dbEST-derived zinc finger protein genes mined from a mouse embryonic 2-cell cDNA library, more than three-quarters of these genes are novel. Examination of characteristics of the human orthologues derived from these mouse genes reveals that many of them are associated with human malignancies. Expression studies have further led to the identification of three novel genes that are exclusively expressed in mouse embryos before or up to the 8-cell stage. Two of the genes, designated 2czf45 and 2czf48 (2czf for 2-cell zinc finger), are zinc finger protein genes coding for a RBCC protein with a RFP domain and a protein with three C2H2 fingers, respectively. The third gene, designated 2cpoz56, codes for a protein with a POZ domain that is often associated with zinc finger proteins. These three genes are candidate genes for regulatory or other functions in early embryogenesis. The strategy described in this report should generally be applicable to rapid and large-scale mining of other classes of rare genes involved in other biological and pathological processes.

Original languageEnglish
Pages (from-to)249-255
Number of pages7
JournalMolecular Reproduction and Development
Volume59
Issue number3
DOIs
Publication statusPublished - 2001
Externally publishedYes

Fingerprint

Expressed Sequence Tags
Zinc Fingers
Computer Simulation
Databases
Genes
Proteins
Gene Library
Embryonic Development
Mammalian Embryo
Biological Phenomena
Pathologic Processes
Regulator Genes
Fingers
Embryonic Structures
Polymerase Chain Reaction

Keywords

  • Expression profiling
  • In silico cloning
  • Pre-implantation embryos
  • Zinc finger protein genes

ASJC Scopus subject areas

  • Genetics
  • Developmental Biology
  • Cell Biology

Cite this

In silico mining of EST databases for novel pre-implantation embryo-specific zinc finger protein genes. / Choo, Kong Bung; Chen, Huang Hui; Cheng, Winston T K; Chang, Hung Shue; Wang, Manni.

In: Molecular Reproduction and Development, Vol. 59, No. 3, 2001, p. 249-255.

Research output: Contribution to journalArticle

Choo, Kong Bung ; Chen, Huang Hui ; Cheng, Winston T K ; Chang, Hung Shue ; Wang, Manni. / In silico mining of EST databases for novel pre-implantation embryo-specific zinc finger protein genes. In: Molecular Reproduction and Development. 2001 ; Vol. 59, No. 3. pp. 249-255.
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