Functional genomics analysis and annotation of large-scale expressed sequence tags (ESTs) from porcine embryos during early development
Date Issued
2007
Date
2007
Author(s)
Wu, Ruei-Syuan
DOI
zh-TW
Abstract
Preimplantation development of mammalian embryo is marked by many critical and unique events, such as starting of zygotic transcription, the first blastomere compaction and initiation of cell differentiation. Sequential gene expression influences the physiological processes through specific stages of embryogenesis for normal functionality of mammalian early development. The objective of this study was to annotate the gene identity of large-scale expressed sequence tags (ESTs) expressed in the preimplantation period of pig by using bioinformatics tools of functional genomic
analysis.
This study has adopted the cDNA sequences of the EST libraries cloned from porcine embryos during various stages of early development including 4-cell, 8-cell, morula and early blastocyst. The cDNA sequences were filtered using several quality control criteria and resulted in 24,605 high quality EST sequences. Thereafter, these sequences were clustered into groups according to sequence similarity to produce 1,327 clusters and 1,736 singletons. Tentative consensus sequences (contigs) assembled in different clusters along with singletons were searched by blastn against the non-redundant nucleotide sequence (nt) database of National Center for Biotechnology Information (NCBI) for gene identification; then, these sequences were searched against UniGene database (species: mouse and pig) to confirm the specific tissues in which they were expressed. Those contigs and singletons without known identity were translated to amino acid sequences using Open Reading Frame Finder (ORF Finder) to provide more information on protein level. In order to classify the functionality of sequences with known identity, the list of gene identity was analyzed for functional annotation using Gene Ontology (GO) database.
Results showed that expression of ribosomal protein (RP) genes were increased at morula stage, and abundantly activated at early blastocyst stage with the functional annotations related to metabolic and biosynthetic processes. It suggests that RP genes might play a fundamental role for supporting the development of porcine early stage embryo. The non-RP genes expressed at the 4-cell stage were mainly annotated to nucleic acid binding which might be responsible for activation of zygotic genome transcription during this stage. The major functions of those non-RP genes activated at the 8-cell stage were protein binding and structure constituent of ribosome demonstrating that they might work for degradation of maternal protein and initiation of embryonic-derived protein translation. Those genes expressed at the morula stage were numerously mapped to cell communication and cell proliferation indicating that cell-cell interaction was activated at this stage for compaction to prepare the blastocyst formation. There were 412 contigs and singletons without known identity could be translated to amino acid sequence with greater than 50 amino acid residues, which might be helpful in further annotation of such type of EST sequences.
Annotation of these cDNA libraries using bioinformatics tools is essential for identifying the expressed genes of early embryogenesis with their functionality. Therefore, such strategy of study would facilitate laboratory to select interesting genes which involve in early embryogenesis for further studies.
Subjects
表現序列標籤
cDNA基因庫
功能性基因體
早期胚
豬
expressed sequence tag
cDNA library
functional genomics
early embryo
pigs
Type
thesis
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