Student information

Biju did his thesis on a bioinformatic gene analysis

Biju Sivan from India finished his EMABG thesis in summer 2009 at the University of Agriculture Sciences (SLU) in Uppsala, Sweden.

Thesis title

Bioinformatic Analysis of Zinc finger domain in IGF2 gene


The quantitative trait locus (QTL) responsible for the lean meat and low fat deposition in pigs was located near the IGF2 locus on chromosome number 2. The quantitative trait nucleotide (QTN), single nucleotide mutation IGF2-intron3-G3072-A, underlying the QTL was identified and located on the regulatory region of IGF2 gene. The QTN will lead to the increase in transcript originating from P2, P3 and P4 promoters located downstream of mutation thus increasing the muscle mass. A repressor protein, ZBED6 was identified that binds effectively to the QTN and enhance the activity of IGF2 in postnatal muscle mass development. ZBED6 is added as a new member to the ZBED family, they all have BED domain while only some members have hATC dimerization domain at C terminal. The present study involves the Bioinformatic and phylogenetic analysis of BED domain from all the members of ZBED family in different species. The genomic sequence of ZBED family members, in different species was searched against the Genbank database using BLAST program and these sequences were used for comparative sequence analysis in MEGA using the ClustalW program. Finally, Phylogenetic analysis was done with Neighbor Joining method using nucleotide and amino acid sequences.

The specialized domain database search showed that all the ZBED proteins have BED domains while some of the members have an additional hATC domain. The comparative sequence analysis of BED domains from all the ZBED proteins (ZBED1-6) revealed that BED domain from each protein is well conserved in widely divergent species. However, the BED domain from different ZBED proteins did not show significant sequence similarity. The phylogenetic analysis based on DNA and protein sequences also gave us the result in concordance with comparative sequence analysis. The genomic organization of ZBED genes can be viewed under UCSC genome browser and found that ZBED1, 2, 5 and 6 are located in the intron of another gene thereby acting as nested genes and sharing the common regulatory elements. But ZBED3, unlike other members form a bidirectional gene pair with another gene with a common bidirectional promoter between them. ZBED4 stands independently and has no genes in the vicinity denoting that they have their own regulatory elements.