Sayanti Guha Majumdar

Demand for livestock products is constantly increasing with the continuous population growth. To meet such demand it is essential to understand molecular mechanisms of livestock species. With the advent of new technologies, it has become possible to understand the underlying mechanisms present in the growth and development of important traits of livestock species. Epigenetics is an emerging field which deals with the study of mitotic and meiotic (or both) heritable changes in gene function that cannot be explained by changes in DNA sequence. Broadly, three epigenetic mechanisms occur in nature and they are (i) DNA methylation (ii) Histone modification and (iii) RNA interference (RNAi). However, the information related to the said epigenetic mechanisms in livestock species is not available at one place. Moreover, analysis of epigenetic information is required for improvement in production traits and controlling diseases in livestock. Keeping this in view, the present study is taken up with the objectives (i) to parse and analyze data of different epigenetic mechanisms in livestock species, (ii) to populate a database on epigenetic mechanism and make it available through web interface. Initially, the gene and protein sequence information related to epigenetic mechanisms of livestock species has been downloaded from NCBI, UCSC and CABin. Besides, the microRNA information of cattle and sheep has been retrieved from miRBase. Subsequently, a tool known as “Sequence Manipulation Suit: CpG Islands” is used to obtain the probable methylation sites present in the 1k upstream region of 10,990 genes in cattle. The results reveal that the CpG islands are found in 8033 genes. In addition, the three dimensional structures of histone proteins of cow, sheep, goat, camel have been predicted, validated, refined and stabilized. Also, the probable genomic regions of histone proteins in buffalo were identified by using tBLASTn tool. The BLAST results were then parsed and kept in a suitable format to populate a database. In case of RNAi, the secondary and tertiary structures of microRNAs of cattle and sheep were predicted by RNAfold and RNAcomposer respectively. Since the miRNA information in buffalo species is not available, the genomic regions of the same were mapped by considering miRNAs of cattle as query sequences in BLASTn. For ready use of the parsed data by users, a web-based “Livestock Epigenetic Information System” has been developed with MySQL database as bottom layer, PHP as server side application-middle layer and HTML, CSS and JavaScript at top layer. The developed information system can be accessed at http://bioinformatics.iasri.res.in/edil/.