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Sayyab, Shumaila, 2010. Bioinformatics analysis of ZBED6, a novel transcription factor in mammals. Second cycle, A2E. Uppsala: SLU, Dept. of Animal Breeding and Genetics (until 231231)



The identification of a regulatory mutation in the intron 3 of Insulin like growth factor 2, was a major finding. This single nucleotide mutation in the non coding region abrogates the interaction of nuclear factor ZBED6, resulting in the 3-4% increase in the muscle mass of domesticated pigs. The mutation was observed in the evolutionary conserved CpG island that is hypomethylated in skeletal muscle. ZBED6 has been derived from a domesticated DNA transposon exclusively present in the placental mammals. Chromatin immuno precipitation (ChIP) sequencing in mouse C2C12 myoblasts using anti-ZBED6 antibody identified 2499 ZBED6 binding fragments. The de novo search on the binding fragments of ZBED6 showed the consensus sequence of 5´-GCTCG-3´. ZBED6 binding fragments contain more than 1200 genes with annotated functions in biological processes, transcriptional regulation, neurogenesis, cell signaling and muscle development. In present study we have done bioinformatics analysis on the ZBED6 using TRANSFAC database professional version 2010.1 in order to identify the other transcription factors co-regulating the expression of ZBED6 target genes. The ChIP data (ZBED6 target genes) and microarray expression data (siRNA silenced ZBED6) in mouse C2C12 cells were used in this study for finding the binding sites for transcription factors in the promoter regions. The genes associated with ZBED6 showed significant overrepresentation of binding sites of transcription factors SP1, ZF5, E2F1, ZBED6, AP2alpha and KROX in their promoter regions. Majority of factors found have GC rich binding sites and belongs to zinc finger families. The obtained factors show role in tumor suppression. The microarray expression data analysis showed that MEF2 and SRF transcription factors binding sites are significantly present in the promoters of co-pressed genes. The ZBED6 binding sites that were at a distance of 500 kb away from known transcription start site TSS, showed OCT1 and IRF1 binding sites. There is a possibility that these factors are the enhancer elements for many ZBED6 target genes. Few long non-coding RNAs were also identified in the vicinity of ZBED6 binding sites present at a distance of 500 kb away from known TSS.

Main title:Bioinformatics analysis of ZBED6, a novel transcription factor in mammals
Authors:Sayyab, Shumaila
Supervisor:Andersson, Göran and Bongcam-Rudloff, Erik
Examiner:Lindgren, Gabriella
Series:Examensarbete / SLU, Institutionen för husdjursgenetik
Volume/Sequential designation:331
Year of Publication:2010
Level and depth descriptor:Second cycle, A2E
Student's programme affiliation:Other
Supervising department:(VH) > Dept. of Animal Breeding and Genetics (until 231231)
Keywords:Chromatin Immuno precipitation ChIP sequencing, non-coding RNA, transcription factor, overrepresentation, enhancer elements, co regulation, repressor
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Subject. Use of subject categories until 2023-04-30.:Animal genetics and breeding
Deposited On:09 Oct 2012 14:02
Metadata Last Modified:16 Jul 2013 23:15

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