Zebrafish Encyclopedia of DNA Elements (ZENCODE)

Genomics research in recent years, especially the human ENCODE project, have made great strides in understanding the genomic and epigenomic structure and organization of humans. These advances promise a new era of precision medicine, through a better understanding of the genomic correlates of human physiology and promise to offer precise and personalized preventive and therapeutic options. The translation of genome-scale maps of genomic and epigenomic markers to clinically relevant information and further to medical practice await functional validation of the genomic features identified through these large-scale efforts. Such studies must essentially be done in model systems where it is possible to model physiological and pathological processes and enquire how they could be modulated by genomic elements and epigenomic signatures. The availability of large number of personal genomes and maps of genomic variations at population scale has created an acute necessity for model systems to model phenotypic and molecular effects of variations, especially in regulatory regions. Efforts to create orthologous maps have been underway in other model systems including Caenorhabditis elegans and Drosophila through the modENCODE programe and in Mus musculus through the mouse ENCODE. We propose that the enormous wealth of disease models and excellent tools to engineer genomes in zebrafish could be effectively capitalized towards making it an effective and widely used model system for precision medicine. This would be possible only through a concerted and systematic effort to create orthologous genomic and epigenomic maps for zebrafish.We discuss how the present understanding and genome-scale methodologies available in this model organism could be effectively used towards realizing this goal.

ZENCODE Data Track Hub and Genome Browser

A number of tracks from publicly available data-sets are compiled and made available as part of the curation efforts. Access the ZENCODE Data Track Hub and Genome Browser

Haque S, Kaushik K, Leonard VE, Kapoor S, Sivadas A, Joshi A, Scaria V*, Sivasubbu S*
Short stories on zebrafish long noncoding RNAs
Zebrafish (2014) Accepted

Kaushik K, Leonard VE, Shamsudheen KV, Lalwani MK, Jalali S, Patowary A, Joshi A, Scaria V, Sivasubbu S.
PLoS One. 2013 Dec 31;8(12):e83616. doi: 10.1371/journal.pone.0083616.

Sivasubbu S, Sachidanandan C, Scaria V.
Time for the zebrafish ENCODE.
J Genet. 2013 Dec;92(3):695-701.